data_3SKR # _entry.id 3SKR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3SKR pdb_00003skr 10.2210/pdb3skr/pdb NDB NA1180 ? ? RCSB RCSB066323 ? ? WWPDB D_1000066323 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-08-17 2 'Structure model' 1 1 2011-10-26 3 'Structure model' 1 2 2024-02-28 4 'Structure model' 1 3 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Source and taxonomy' 6 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_site 6 4 'Structure model' entity 7 4 'Structure model' pdbx_entity_src_syn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' 7 4 'Structure model' '_entity.details' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3SKR _pdbx_database_status.recvd_initial_deposition_date 2011-06-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3SKL . unspecified PDB 3SKT . unspecified PDB 3SKW . unspecified PDB 3SKZ . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pikovskaya, O.' 1 'Polonskaia, A.' 2 'Patel, D.J.' 3 'Serganov, A.' 4 # _citation.id primary _citation.title ;Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch. ; _citation.journal_abbrev Nat.Chem.Biol. _citation.journal_volume 7 _citation.page_first 748 _citation.page_last 755 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1552-4450 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21841796 _citation.pdbx_database_id_DOI 10.1038/nchembio.631 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pikovskaya, O.' 1 ? primary 'Polonskaia, A.' 2 ? primary 'Patel, D.J.' 3 ? primary 'Serganov, A.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'RNA (66-MER)' 21368.484 2 ? ? ? 'dG riboswitch' 2 non-polymer syn "2'-DEOXY-GUANOSINE" 267.241 2 ? ? ? 'In vitro transcription' 3 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 9 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 4 ? ? ? ? 5 water nat water 18.015 18 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(GTP)GCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGU(CCC)' _entity_poly.pdbx_seq_one_letter_code_can GGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "2'-DEOXY-GUANOSINE" GNG 3 'COBALT HEXAMMINE(III)' NCO 4 'MAGNESIUM ION' MG 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GTP n 1 2 G n 1 3 C n 1 4 U n 1 5 U n 1 6 A n 1 7 U n 1 8 A n 1 9 C n 1 10 A n 1 11 G n 1 12 G n 1 13 G n 1 14 U n 1 15 A n 1 16 G n 1 17 C n 1 18 A n 1 19 U n 1 20 A n 1 21 A n 1 22 U n 1 23 G n 1 24 G n 1 25 G n 1 26 C n 1 27 U n 1 28 A n 1 29 C n 1 30 U n 1 31 G n 1 32 A n 1 33 C n 1 34 C n 1 35 C n 1 36 C n 1 37 G n 1 38 C n 1 39 C n 1 40 U n 1 41 U n 1 42 C n 1 43 A n 1 44 A n 1 45 A n 1 46 C n 1 47 C n 1 48 U n 1 49 A n 1 50 U n 1 51 U n 1 52 U n 1 53 G n 1 54 G n 1 55 A n 1 56 G n 1 57 A n 1 58 C n 1 59 U n 1 60 A n 1 61 U n 1 62 A n 1 63 A n 1 64 G n 1 65 U n 1 66 CCC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'In vitro transcription' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CCC 'RNA linking' n ;CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE ; ? 'C9 H13 N3 O10 P2' 385.161 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GNG non-polymer n "2'-DEOXY-GUANOSINE" ? 'C10 H13 N5 O4' 267.241 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GTP 1 23 23 GTP GTP A . n A 1 2 G 2 24 24 G G A . n A 1 3 C 3 25 25 C C A . n A 1 4 U 4 26 26 U U A . n A 1 5 U 5 27 27 U U A . n A 1 6 A 6 28 28 A A A . n A 1 7 U 7 29 29 U U A . n A 1 8 A 8 30 30 A A A . n A 1 9 C 9 31 31 C C A . n A 1 10 A 10 32 32 A A A . n A 1 11 G 11 33 33 G G A . n A 1 12 G 12 34 34 G G A . n A 1 13 G 13 35 35 G G A . n A 1 14 U 14 36 36 U U A . n A 1 15 A 15 37 37 A A A . n A 1 16 G 16 38 38 G G A . n A 1 17 C 17 39 39 C C A . n A 1 18 A 18 40 40 A A A . n A 1 19 U 19 41 41 U U A . n A 1 20 A 20 42 42 A A A . n A 1 21 A 21 43 43 A A A . n A 1 22 U 22 44 44 U U A . n A 1 23 G 23 45 45 G G A . n A 1 24 G 24 46 46 G G A . n A 1 25 G 25 47 47 G G A . n A 1 26 C 26 48 48 C C A . n A 1 27 U 27 49 49 U U A . n A 1 28 A 28 50 50 A A A . n A 1 29 C 29 51 51 C C A . n A 1 30 U 30 52 52 U U A . n A 1 31 G 31 53 53 G G A . n A 1 32 A 32 54 54 A A A . n A 1 33 C 33 55 55 C C A . n A 1 34 C 34 56 56 C C A . n A 1 35 C 35 57 57 C C A . n A 1 36 C 36 58 58 C C A . n A 1 37 G 37 59 59 G G A . n A 1 38 C 38 60 60 C C A . n A 1 39 C 39 61 61 C C A . n A 1 40 U 40 62 62 U U A . n A 1 41 U 41 63 63 U U A . n A 1 42 C 42 64 64 C C A . n A 1 43 A 43 65 65 A A A . n A 1 44 A 44 66 66 A A A . n A 1 45 A 45 67 67 A A A . n A 1 46 C 46 68 68 C C A . n A 1 47 C 47 69 69 C C A . n A 1 48 U 48 70 70 U U A . n A 1 49 A 49 71 71 A A A . n A 1 50 U 50 72 72 U U A . n A 1 51 U 51 73 73 U U A . n A 1 52 U 52 74 74 U U A . n A 1 53 G 53 75 75 G G A . n A 1 54 G 54 76 76 G G A . n A 1 55 A 55 77 77 A A A . n A 1 56 G 56 78 78 G G A . n A 1 57 A 57 79 79 A A A . n A 1 58 C 58 80 80 C C A . n A 1 59 U 59 81 81 U U A . n A 1 60 A 60 82 82 A A A . n A 1 61 U 61 83 83 U U A . n A 1 62 A 62 84 84 A A A . n A 1 63 A 63 85 85 A A A . n A 1 64 G 64 86 86 G G A . n A 1 65 U 65 87 87 U U A . n A 1 66 CCC 66 88 88 CCC CCC A . n B 1 1 GTP 1 23 23 GTP GTP B . n B 1 2 G 2 24 24 G G B . n B 1 3 C 3 25 25 C C B . n B 1 4 U 4 26 26 U U B . n B 1 5 U 5 27 27 U U B . n B 1 6 A 6 28 28 A A B . n B 1 7 U 7 29 29 U U B . n B 1 8 A 8 30 30 A A B . n B 1 9 C 9 31 31 C C B . n B 1 10 A 10 32 32 A A B . n B 1 11 G 11 33 33 G G B . n B 1 12 G 12 34 34 G G B . n B 1 13 G 13 35 35 G G B . n B 1 14 U 14 36 36 U U B . n B 1 15 A 15 37 37 A A B . n B 1 16 G 16 38 38 G G B . n B 1 17 C 17 39 39 C C B . n B 1 18 A 18 40 40 A A B . n B 1 19 U 19 41 41 U U B . n B 1 20 A 20 42 42 A A B . n B 1 21 A 21 43 43 A A B . n B 1 22 U 22 44 44 U U B . n B 1 23 G 23 45 45 G G B . n B 1 24 G 24 46 46 G G B . n B 1 25 G 25 47 47 G G B . n B 1 26 C 26 48 48 C C B . n B 1 27 U 27 49 49 U U B . n B 1 28 A 28 50 50 A A B . n B 1 29 C 29 51 51 C C B . n B 1 30 U 30 52 52 U U B . n B 1 31 G 31 53 53 G G B . n B 1 32 A 32 54 54 A A B . n B 1 33 C 33 55 55 C C B . n B 1 34 C 34 56 56 C C B . n B 1 35 C 35 57 57 C C B . n B 1 36 C 36 58 58 C C B . n B 1 37 G 37 59 59 G G B . n B 1 38 C 38 60 60 C C B . n B 1 39 C 39 61 61 C C B . n B 1 40 U 40 62 62 U U B . n B 1 41 U 41 63 63 U U B . n B 1 42 C 42 64 64 C C B . n B 1 43 A 43 65 65 A A B . n B 1 44 A 44 66 66 A A B . n B 1 45 A 45 67 67 A A B . n B 1 46 C 46 68 68 C C B . n B 1 47 C 47 69 69 C C B . n B 1 48 U 48 70 70 U U B . n B 1 49 A 49 71 71 A A B . n B 1 50 U 50 72 72 U U B . n B 1 51 U 51 73 73 U U B . n B 1 52 U 52 74 74 U U B . n B 1 53 G 53 75 75 G G B . n B 1 54 G 54 76 76 G G B . n B 1 55 A 55 77 77 A A B . n B 1 56 G 56 78 78 G G B . n B 1 57 A 57 79 79 A A B . n B 1 58 C 58 80 80 C C B . n B 1 59 U 59 81 81 U U B . n B 1 60 A 60 82 82 A A B . n B 1 61 U 61 83 83 U U B . n B 1 62 A 62 84 84 A A B . n B 1 63 A 63 85 85 A A B . n B 1 64 G 64 86 86 G G B . n B 1 65 U 65 87 87 U U B . n B 1 66 CCC 66 88 88 CCC CCC B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 GNG 1 120 120 GNG GNG A . D 3 NCO 1 401 401 NCO NCO A . E 3 NCO 1 402 402 NCO NCO A . F 3 NCO 1 403 403 NCO NCO A . G 3 NCO 1 405 405 NCO NCO A . H 3 NCO 1 406 406 NCO NCO A . I 4 MG 1 201 201 MG MG A . J 4 MG 1 202 202 MG MG A . K 4 MG 1 204 204 MG MG A . L 2 GNG 1 120 120 GNG GNG B . M 3 NCO 1 404 404 NCO NCO B . N 3 NCO 1 407 407 NCO NCO B . O 3 NCO 1 408 408 NCO NCO B . P 3 NCO 1 409 409 NCO NCO B . Q 4 MG 1 203 203 MG MG B . R 5 HOH 1 301 301 HOH HOH A . R 5 HOH 2 302 302 HOH HOH A . R 5 HOH 3 303 303 HOH HOH A . R 5 HOH 4 304 304 HOH HOH A . R 5 HOH 5 305 305 HOH HOH A . R 5 HOH 6 306 306 HOH HOH A . R 5 HOH 7 307 307 HOH HOH A . R 5 HOH 8 308 308 HOH HOH A . R 5 HOH 9 318 318 HOH HOH A . S 5 HOH 1 309 309 HOH HOH B . S 5 HOH 2 310 310 HOH HOH B . S 5 HOH 3 311 311 HOH HOH B . S 5 HOH 4 312 312 HOH HOH B . S 5 HOH 5 313 313 HOH HOH B . S 5 HOH 6 314 314 HOH HOH B . S 5 HOH 7 315 315 HOH HOH B . S 5 HOH 8 316 316 HOH HOH B . S 5 HOH 9 317 317 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A GTP 23 ? PG ? A GTP 1 PG 2 1 Y 1 A GTP 23 ? O1G ? A GTP 1 O1G 3 1 Y 1 A GTP 23 ? O2G ? A GTP 1 O2G 4 1 Y 1 A GTP 23 ? O3G ? A GTP 1 O3G 5 1 Y 1 A GTP 23 ? O3B ? A GTP 1 O3B 6 1 Y 1 A GTP 23 ? PB ? A GTP 1 PB 7 1 Y 1 A GTP 23 ? O1B ? A GTP 1 O1B 8 1 Y 1 A GTP 23 ? O2B ? A GTP 1 O2B 9 1 Y 1 B GTP 23 ? PG ? B GTP 1 PG 10 1 Y 1 B GTP 23 ? O1G ? B GTP 1 O1G 11 1 Y 1 B GTP 23 ? O2G ? B GTP 1 O2G 12 1 Y 1 B GTP 23 ? O3G ? B GTP 1 O3G 13 1 Y 1 B GTP 23 ? O3B ? B GTP 1 O3B 14 1 Y 1 B GTP 23 ? PB ? B GTP 1 PB 15 1 Y 1 B GTP 23 ? O1B ? B GTP 1 O1B 16 1 Y 1 B GTP 23 ? O2B ? B GTP 1 O2B # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 3SKR _cell.length_a 98.530 _cell.length_b 35.018 _cell.length_c 110.761 _cell.angle_alpha 90.00 _cell.angle_beta 92.18 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3SKR _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3SKR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.23 _exptl_crystal.density_percent_sol 44.94 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details ;0.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M KCl and 2.0 mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2010-04-27 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.45 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X29A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X29A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.45 # _reflns.entry_id 3SKR _reflns.observed_criterion_sigma_I 3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 3.1 _reflns.number_obs 7041 _reflns.number_all 7273 _reflns.percent_possible_obs 96.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 3.1 _reflns_shell.d_res_low 3.21 _reflns_shell.percent_possible_all 98.2 _reflns_shell.Rmerge_I_obs 0.497 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.9 _reflns_shell.pdbx_redundancy 4.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 701 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3SKR _refine.ls_number_reflns_obs 6209 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 3.10 _refine.ls_percent_reflns_obs 96.58 _refine.ls_R_factor_obs 0.24157 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23557 _refine.ls_R_factor_R_free 0.29872 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.6 _refine.ls_number_reflns_R_free 663 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.931 _refine.correlation_coeff_Fo_to_Fc_free 0.894 _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.00 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct Phaser _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.666 _refine.overall_SU_ML 0.626 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 2810 _refine_hist.pdbx_number_atoms_ligand 105 _refine_hist.number_atoms_solvent 18 _refine_hist.number_atoms_total 2933 _refine_hist.d_res_high 3.10 _refine_hist.d_res_low 20.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.006 0.021 ? 3244 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.145 3.000 ? 5081 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.003 0.020 ? 1382 ? 'X-RAY DIFFRACTION' r_nbd_refined 0.186 0.200 ? 1388 ? 'X-RAY DIFFRACTION' r_nbtor_refined 0.284 0.200 ? 1918 ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined 0.178 0.200 ? 101 ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined 0.179 0.200 ? 30 ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined 0.157 0.200 ? 8 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.100 _refine_ls_shell.d_res_low 3.179 _refine_ls_shell.number_reflns_R_work 437 _refine_ls_shell.R_factor_R_work 0.322 _refine_ls_shell.percent_reflns_obs 98.01 _refine_ls_shell.R_factor_R_free 0.398 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 55 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3SKR _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 3SKR _struct.title ;Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cobalt Hexammine soak ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3SKR _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'three-way junction, riboswitch, deoxyguanosine, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 4 ? J N N 4 ? K N N 4 ? L N N 2 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 3 ? Q N N 4 ? R N N 5 ? S N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3SKR _struct_ref.pdbx_db_accession 3SKR _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUC _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3SKR A 1 ? 66 ? 3SKR 23 ? 88 ? 23 88 2 1 3SKR B 1 ? 66 ? 3SKR 23 ? 88 ? 23 88 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 author_defined_assembly ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,D,E,F,G,H,I,J,K,R 2 1 B,L,M,N,O,P,Q,S # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GTP 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A GTP 23 A G 24 1_555 ? ? ? ? ? ? ? 1.585 ? ? covale2 covale both ? A U 65 "O3'" ? ? ? 1_555 A CCC 66 P ? ? A U 87 A CCC 88 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale3 covale both ? B GTP 1 "O3'" ? ? ? 1_555 B G 2 P ? ? B GTP 23 B G 24 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale4 covale both ? B U 65 "O3'" ? ? ? 1_555 B CCC 66 P ? ? B U 87 B CCC 88 1_555 ? ? ? ? ? ? ? 1.602 ? ? hydrog1 hydrog ? ? A GTP 1 N1 ? ? ? 1_555 A CCC 66 N3 ? ? A GTP 23 A CCC 88 1_555 ? ? ? ? ? ? 'GTP-CCC PAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 65 O2 ? ? A G 24 A U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 65 N3 ? ? A G 24 A U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog4 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 64 O6 ? ? A C 25 A G 86 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog5 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 63 N1 ? ? A U 26 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 63 N6 ? ? A U 26 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 62 N1 ? ? A U 27 A A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 62 N6 ? ? A U 27 A A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 61 N3 ? ? A A 28 A U 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 61 O4 ? ? A A 28 A U 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 60 N1 ? ? A U 29 A A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 60 N6 ? ? A U 29 A A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 59 N3 ? ? A A 30 A U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 59 O4 ? ? A A 30 A U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 37 N1 ? ? A C 31 A G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 37 O6 ? ? A C 31 A G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 37 N2 ? ? A C 31 A G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 11 N2 ? ? ? 1_555 A G 12 O6 ? ? A G 33 A G 34 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog19 hydrog ? ? A G 11 N2 ? ? ? 1_555 A U 30 O4 ? ? A G 33 A U 52 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog20 hydrog ? ? A G 12 N1 ? ? ? 1_555 A U 30 O2 ? ? A G 34 A U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 12 O6 ? ? ? 1_555 A U 30 N3 ? ? A G 34 A U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 35 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 35 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 35 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 36 A A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 36 A A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 15 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 37 A U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 15 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 37 A U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 16 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 38 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 16 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 38 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 16 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 38 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 17 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 39 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 17 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 39 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 17 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 39 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 20 N1 ? ? ? 1_555 A G 23 N2 ? ? A A 42 A G 45 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog36 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 47 N3 ? ? A G 45 A C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 47 O2 ? ? A G 45 A C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 47 N4 ? ? A G 45 A C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 24 N1 ? ? ? 1_555 A C 46 N3 ? ? A G 46 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 24 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 46 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 24 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 46 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 53 A C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 53 A C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 53 A C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 39 N3 ? ? ? 1_555 A G 56 N1 ? ? A C 61 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 39 N4 ? ? ? 1_555 A G 56 O6 ? ? A C 61 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 39 O2 ? ? ? 1_555 A G 56 N2 ? ? A C 61 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A U 40 N3 ? ? ? 1_555 A A 55 N1 ? ? A U 62 A A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A U 40 O4 ? ? ? 1_555 A A 55 N6 ? ? A U 62 A A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A U 41 N3 ? ? ? 1_555 A G 54 O6 ? ? A U 63 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog51 hydrog ? ? A U 41 O2 ? ? ? 1_555 A G 54 N1 ? ? A U 63 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog52 hydrog ? ? A C 42 N3 ? ? ? 1_555 A G 53 N1 ? ? A C 64 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 42 N4 ? ? ? 1_555 A G 53 O6 ? ? A C 64 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 42 O2 ? ? ? 1_555 A G 53 N2 ? ? A C 64 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A A 43 N1 ? ? ? 1_555 A U 52 N3 ? ? A A 65 A U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A A 43 N6 ? ? ? 1_555 A U 52 O4 ? ? A A 65 A U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A A 44 N1 ? ? ? 1_555 A U 51 N3 ? ? A A 66 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A A 44 N6 ? ? ? 1_555 A U 51 O4 ? ? A A 66 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A A 45 N1 ? ? ? 1_555 A U 50 N3 ? ? A A 67 A U 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A A 45 N6 ? ? ? 1_555 A U 50 O4 ? ? A A 67 A U 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B GTP 1 N2 ? ? ? 1_555 B CCC 66 N3 ? ? B GTP 23 B CCC 88 1_555 ? ? ? ? ? ? 'GTP-CCC PAIR' ? ? ? hydrog62 hydrog ? ? B G 2 N1 ? ? ? 1_555 B U 65 O2 ? ? B G 24 B U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog63 hydrog ? ? B G 2 O6 ? ? ? 1_555 B U 65 N3 ? ? B G 24 B U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog64 hydrog ? ? B C 3 N3 ? ? ? 1_555 B G 64 N1 ? ? B C 25 B G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B C 3 N4 ? ? ? 1_555 B G 64 O6 ? ? B C 25 B G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B C 3 O2 ? ? ? 1_555 B G 64 N2 ? ? B C 25 B G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? B U 4 N3 ? ? ? 1_555 B A 63 N1 ? ? B U 26 B A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? B U 4 O4 ? ? ? 1_555 B A 63 N6 ? ? B U 26 B A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? B U 5 N3 ? ? ? 1_555 B A 62 N1 ? ? B U 27 B A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? B U 5 O4 ? ? ? 1_555 B A 62 N6 ? ? B U 27 B A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? B A 6 N1 ? ? ? 1_555 B U 61 N3 ? ? B A 28 B U 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? B A 6 N6 ? ? ? 1_555 B U 61 O4 ? ? B A 28 B U 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? B U 7 N3 ? ? ? 1_555 B A 60 N1 ? ? B U 29 B A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? B U 7 O4 ? ? ? 1_555 B A 60 N6 ? ? B U 29 B A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? B A 8 N1 ? ? ? 1_555 B U 59 N3 ? ? B A 30 B U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? B A 8 N6 ? ? ? 1_555 B U 59 O4 ? ? B A 30 B U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? B C 9 N3 ? ? ? 1_555 B G 37 N1 ? ? B C 31 B G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 37 O6 ? ? B C 31 B G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? B C 9 O2 ? ? ? 1_555 B G 37 N2 ? ? B C 31 B G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? B G 11 N2 ? ? ? 1_555 B G 12 O6 ? ? B G 33 B G 34 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog81 hydrog ? ? B G 11 N2 ? ? ? 1_555 B U 30 O4 ? ? B G 33 B U 52 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog82 hydrog ? ? B G 12 N1 ? ? ? 1_555 B U 30 O2 ? ? B G 34 B U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog83 hydrog ? ? B G 12 O6 ? ? ? 1_555 B U 30 N3 ? ? B G 34 B U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog84 hydrog ? ? B G 13 N1 ? ? ? 1_555 B C 29 N3 ? ? B G 35 B C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? B G 13 N2 ? ? ? 1_555 B C 29 O2 ? ? B G 35 B C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? B G 13 O6 ? ? ? 1_555 B C 29 N4 ? ? B G 35 B C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? B U 14 N3 ? ? ? 1_555 B A 28 N1 ? ? B U 36 B A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? B U 14 O4 ? ? ? 1_555 B A 28 N6 ? ? B U 36 B A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? B A 15 N1 ? ? ? 1_555 B U 27 N3 ? ? B A 37 B U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? B A 15 N6 ? ? ? 1_555 B U 27 O4 ? ? B A 37 B U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? B G 16 N1 ? ? ? 1_555 B C 26 N3 ? ? B G 38 B C 48 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog92 hydrog ? ? B C 17 O2 ? ? ? 1_555 B G 25 N2 ? ? B C 39 B G 47 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog93 hydrog ? ? B A 20 N1 ? ? ? 1_555 B G 23 N2 ? ? B A 42 B G 45 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog94 hydrog ? ? B G 23 N1 ? ? ? 1_555 B C 47 N3 ? ? B G 45 B C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? B G 23 N2 ? ? ? 1_555 B C 47 O2 ? ? B G 45 B C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog96 hydrog ? ? B G 23 O6 ? ? ? 1_555 B C 47 N4 ? ? B G 45 B C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog97 hydrog ? ? B G 24 N1 ? ? ? 1_555 B C 46 N3 ? ? B G 46 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog98 hydrog ? ? B G 24 N2 ? ? ? 1_555 B C 46 O2 ? ? B G 46 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog99 hydrog ? ? B G 24 O6 ? ? ? 1_555 B C 46 N4 ? ? B G 46 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog100 hydrog ? ? B G 31 N1 ? ? ? 1_555 B C 38 N3 ? ? B G 53 B C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog101 hydrog ? ? B G 31 N2 ? ? ? 1_555 B C 38 O2 ? ? B G 53 B C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog102 hydrog ? ? B G 31 O6 ? ? ? 1_555 B C 38 N4 ? ? B G 53 B C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog103 hydrog ? ? B C 35 N4 ? ? ? 1_555 B U 59 O2 ? ? B C 57 B U 81 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog104 hydrog ? ? B C 39 N3 ? ? ? 1_555 B G 56 N1 ? ? B C 61 B G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog105 hydrog ? ? B C 39 N4 ? ? ? 1_555 B G 56 O6 ? ? B C 61 B G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog106 hydrog ? ? B C 39 O2 ? ? ? 1_555 B G 56 N2 ? ? B C 61 B G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog107 hydrog ? ? B U 40 N3 ? ? ? 1_555 B A 55 N1 ? ? B U 62 B A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog108 hydrog ? ? B U 40 O4 ? ? ? 1_555 B A 55 N6 ? ? B U 62 B A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog109 hydrog ? ? B U 41 N3 ? ? ? 1_555 B G 54 O6 ? ? B U 63 B G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog110 hydrog ? ? B U 41 O2 ? ? ? 1_555 B G 54 N1 ? ? B U 63 B G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog111 hydrog ? ? B C 42 N3 ? ? ? 1_555 B G 53 N1 ? ? B C 64 B G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog112 hydrog ? ? B C 42 N4 ? ? ? 1_555 B G 53 O6 ? ? B C 64 B G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog113 hydrog ? ? B C 42 O2 ? ? ? 1_555 B G 53 N2 ? ? B C 64 B G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog114 hydrog ? ? B A 43 N1 ? ? ? 1_555 B U 52 N3 ? ? B A 65 B U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog115 hydrog ? ? B A 43 N6 ? ? ? 1_555 B U 52 O4 ? ? B A 65 B U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog116 hydrog ? ? B A 44 N1 ? ? ? 1_555 B U 51 N3 ? ? B A 66 B U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog117 hydrog ? ? B A 44 N6 ? ? ? 1_555 B U 51 O4 ? ? B A 66 B U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog118 hydrog ? ? B A 45 N1 ? ? ? 1_555 B U 50 N3 ? ? B A 67 B U 72 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GNG 120 ? 6 'BINDING SITE FOR RESIDUE GNG A 120' AC2 Software B GNG 120 ? 8 'BINDING SITE FOR RESIDUE GNG B 120' AC3 Software A NCO 401 ? 3 'BINDING SITE FOR RESIDUE NCO A 401' AC4 Software A NCO 402 ? 4 'BINDING SITE FOR RESIDUE NCO A 402' AC5 Software A NCO 403 ? 2 'BINDING SITE FOR RESIDUE NCO A 403' AC6 Software B NCO 404 ? 5 'BINDING SITE FOR RESIDUE NCO B 404' AC7 Software A NCO 405 ? 5 'BINDING SITE FOR RESIDUE NCO A 405' AC8 Software A NCO 406 ? 6 'BINDING SITE FOR RESIDUE NCO A 406' AC9 Software B NCO 407 ? 5 'BINDING SITE FOR RESIDUE NCO B 407' BC1 Software B NCO 408 ? 2 'BINDING SITE FOR RESIDUE NCO B 408' BC2 Software B NCO 409 ? 5 'BINDING SITE FOR RESIDUE NCO B 409' BC3 Software A MG 201 ? 3 'BINDING SITE FOR RESIDUE MG A 201' BC4 Software B MG 203 ? 1 'BINDING SITE FOR RESIDUE MG B 203' BC5 Software A MG 204 ? 2 'BINDING SITE FOR RESIDUE MG A 204' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 A A 8 ? A A 30 . ? 1_555 ? 2 AC1 6 C A 9 ? C A 31 . ? 1_555 ? 3 AC1 6 C A 34 ? C A 56 . ? 1_555 ? 4 AC1 6 G A 37 ? G A 59 . ? 1_555 ? 5 AC1 6 C A 58 ? C A 80 . ? 1_555 ? 6 AC1 6 MG I . ? MG A 201 . ? 1_555 ? 7 AC2 8 A B 8 ? A B 30 . ? 1_555 ? 8 AC2 8 C B 9 ? C B 31 . ? 1_555 ? 9 AC2 8 C B 34 ? C B 56 . ? 1_555 ? 10 AC2 8 C B 35 ? C B 57 . ? 1_555 ? 11 AC2 8 C B 36 ? C B 58 . ? 1_555 ? 12 AC2 8 G B 37 ? G B 59 . ? 1_555 ? 13 AC2 8 C B 58 ? C B 80 . ? 1_555 ? 14 AC2 8 U B 59 ? U B 81 . ? 1_555 ? 15 AC3 3 A A 10 ? A A 32 . ? 1_555 ? 16 AC3 3 A A 55 ? A A 77 . ? 1_555 ? 17 AC3 3 G A 56 ? G A 78 . ? 1_555 ? 18 AC4 4 C A 3 ? C A 25 . ? 1_555 ? 19 AC4 4 U A 4 ? U A 26 . ? 1_555 ? 20 AC4 4 U A 19 ? U A 41 . ? 4_546 ? 21 AC4 4 A A 20 ? A A 42 . ? 4_546 ? 22 AC5 2 G A 23 ? G A 45 . ? 1_555 ? 23 AC5 2 G A 24 ? G A 46 . ? 1_555 ? 24 AC6 5 G B 11 ? G B 33 . ? 1_555 ? 25 AC6 5 C B 26 ? C B 48 . ? 1_555 ? 26 AC6 5 U B 27 ? U B 49 . ? 1_555 ? 27 AC6 5 C B 38 ? C B 60 . ? 1_555 ? 28 AC6 5 C B 39 ? C B 61 . ? 1_555 ? 29 AC7 5 G A 11 ? G A 33 . ? 1_555 ? 30 AC7 5 C A 26 ? C A 48 . ? 1_555 ? 31 AC7 5 U A 27 ? U A 49 . ? 1_555 ? 32 AC7 5 C A 38 ? C A 60 . ? 1_555 ? 33 AC7 5 C A 39 ? C A 61 . ? 1_555 ? 34 AC8 6 G A 11 ? G A 33 . ? 1_555 ? 35 AC8 6 U A 41 ? U A 63 . ? 1_555 ? 36 AC8 6 U A 52 ? U A 74 . ? 1_555 ? 37 AC8 6 G A 53 ? G A 75 . ? 1_555 ? 38 AC8 6 G A 54 ? G A 76 . ? 1_555 ? 39 AC8 6 A A 55 ? A A 77 . ? 1_555 ? 40 AC9 5 GTP B 1 ? GTP B 23 . ? 1_555 ? 41 AC9 5 G B 2 ? G B 24 . ? 1_555 ? 42 AC9 5 C B 3 ? C B 25 . ? 1_555 ? 43 AC9 5 G B 64 ? G B 86 . ? 1_555 ? 44 AC9 5 U B 65 ? U B 87 . ? 1_555 ? 45 BC1 2 G B 23 ? G B 45 . ? 1_555 ? 46 BC1 2 G B 24 ? G B 46 . ? 1_555 ? 47 BC2 5 G B 11 ? G B 33 . ? 1_555 ? 48 BC2 5 U B 41 ? U B 63 . ? 1_555 ? 49 BC2 5 U B 52 ? U B 74 . ? 1_555 ? 50 BC2 5 G B 53 ? G B 75 . ? 1_555 ? 51 BC2 5 G B 54 ? G B 76 . ? 1_555 ? 52 BC3 3 C A 9 ? C A 31 . ? 1_555 ? 53 BC3 3 A A 10 ? A A 32 . ? 1_555 ? 54 BC3 3 GNG C . ? GNG A 120 . ? 1_555 ? 55 BC4 1 A B 18 ? A B 40 . ? 1_555 ? 56 BC5 2 G A 37 ? G A 59 . ? 1_555 ? 57 BC5 2 C A 38 ? C A 60 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A GTP 23 ? ? "O3'" A GTP 23 ? ? P A G 24 ? ? 104.05 119.70 -15.65 1.20 Y 2 1 "C3'" B GTP 23 ? ? "O3'" B GTP 23 ? ? P B G 24 ? ? 109.47 119.70 -10.23 1.20 Y # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A GTP 1 A GTP 23 ? G "GUANOSINE-5'-TRIPHOSPHATE" 2 A CCC 66 A CCC 88 ? C ? 3 B GTP 1 B GTP 23 ? G "GUANOSINE-5'-TRIPHOSPHATE" 4 B CCC 66 B CCC 88 ? C ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 306 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id R _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CCC PC P N S 73 CCC O1C O N N 74 CCC O2C O N N 75 CCC P P N N 76 CCC OP1 O N N 77 CCC OP2 O N N 78 CCC OP3 O N N 79 CCC "O5'" O N N 80 CCC "C5'" C N N 81 CCC "C4'" C N R 82 CCC "O4'" O N N 83 CCC "C3'" C N R 84 CCC "O3'" O N N 85 CCC "C2'" C N R 86 CCC "O2'" O N N 87 CCC "C1'" C N R 88 CCC N1 N N N 89 CCC C2 C N N 90 CCC O2 O N N 91 CCC N3 N N N 92 CCC C4 C N N 93 CCC N4 N N N 94 CCC C5 C N N 95 CCC C6 C N N 96 CCC HOC2 H N N 97 CCC HOP2 H N N 98 CCC HOP3 H N N 99 CCC "H5'" H N N 100 CCC "H5''" H N N 101 CCC "H4'" H N N 102 CCC "H3'" H N N 103 CCC "H2'" H N N 104 CCC "H1'" H N N 105 CCC H41 H N N 106 CCC H42 H N N 107 CCC H5 H N N 108 CCC H6 H N N 109 G OP3 O N N 110 G P P N N 111 G OP1 O N N 112 G OP2 O N N 113 G "O5'" O N N 114 G "C5'" C N N 115 G "C4'" C N R 116 G "O4'" O N N 117 G "C3'" C N S 118 G "O3'" O N N 119 G "C2'" C N R 120 G "O2'" O N N 121 G "C1'" C N R 122 G N9 N Y N 123 G C8 C Y N 124 G N7 N Y N 125 G C5 C Y N 126 G C6 C N N 127 G O6 O N N 128 G N1 N N N 129 G C2 C N N 130 G N2 N N N 131 G N3 N N N 132 G C4 C Y N 133 G HOP3 H N N 134 G HOP2 H N N 135 G "H5'" H N N 136 G "H5''" H N N 137 G "H4'" H N N 138 G "H3'" H N N 139 G "HO3'" H N N 140 G "H2'" H N N 141 G "HO2'" H N N 142 G "H1'" H N N 143 G H8 H N N 144 G H1 H N N 145 G H21 H N N 146 G H22 H N N 147 GNG "O5'" O N N 148 GNG "C5'" C N N 149 GNG "C4'" C N R 150 GNG "O4'" O N N 151 GNG "C1'" C N R 152 GNG N9 N Y N 153 GNG C8 C Y N 154 GNG N7 N Y N 155 GNG C5 C Y N 156 GNG C4 C Y N 157 GNG N3 N N N 158 GNG C2 C N N 159 GNG N1 N N N 160 GNG C6 C N N 161 GNG O6 O N N 162 GNG N2 N N N 163 GNG "C2'" C N N 164 GNG "C3'" C N S 165 GNG "O3'" O N N 166 GNG "H5'" H N N 167 GNG "H5'1" H N N 168 GNG "H5'2" H N N 169 GNG "H4'" H N N 170 GNG "H1'" H N N 171 GNG H8 H N N 172 GNG HN3 H N N 173 GNG HN21 H N N 174 GNG HN22 H N N 175 GNG "H2'1" H N N 176 GNG "H2'2" H N N 177 GNG "H3'" H N N 178 GNG H1 H N N 179 GTP PG P N N 180 GTP O1G O N N 181 GTP O2G O N N 182 GTP O3G O N N 183 GTP O3B O N N 184 GTP PB P N N 185 GTP O1B O N N 186 GTP O2B O N N 187 GTP O3A O N N 188 GTP PA P N N 189 GTP O1A O N N 190 GTP O2A O N N 191 GTP "O5'" O N N 192 GTP "C5'" C N N 193 GTP "C4'" C N R 194 GTP "O4'" O N N 195 GTP "C3'" C N S 196 GTP "O3'" O N N 197 GTP "C2'" C N R 198 GTP "O2'" O N N 199 GTP "C1'" C N R 200 GTP N9 N Y N 201 GTP C8 C Y N 202 GTP N7 N Y N 203 GTP C5 C Y N 204 GTP C6 C N N 205 GTP O6 O N N 206 GTP N1 N N N 207 GTP C2 C N N 208 GTP N2 N N N 209 GTP N3 N N N 210 GTP C4 C Y N 211 GTP HOG2 H N N 212 GTP HOG3 H N N 213 GTP HOB2 H N N 214 GTP HOA2 H N N 215 GTP "H5'" H N N 216 GTP "H5''" H N N 217 GTP "H4'" H N N 218 GTP "H3'" H N N 219 GTP "HO3'" H N N 220 GTP "H2'" H N N 221 GTP "HO2'" H N N 222 GTP "H1'" H N N 223 GTP H8 H N N 224 GTP HN1 H N N 225 GTP HN21 H N N 226 GTP HN22 H N N 227 HOH O O N N 228 HOH H1 H N N 229 HOH H2 H N N 230 MG MG MG N N 231 NCO CO CO N N 232 NCO N1 N N N 233 NCO N2 N N N 234 NCO N3 N N N 235 NCO N4 N N N 236 NCO N5 N N N 237 NCO N6 N N N 238 NCO HN11 H N N 239 NCO HN12 H N N 240 NCO HN13 H N N 241 NCO HN21 H N N 242 NCO HN22 H N N 243 NCO HN23 H N N 244 NCO HN31 H N N 245 NCO HN32 H N N 246 NCO HN33 H N N 247 NCO HN41 H N N 248 NCO HN42 H N N 249 NCO HN43 H N N 250 NCO HN51 H N N 251 NCO HN52 H N N 252 NCO HN53 H N N 253 NCO HN61 H N N 254 NCO HN62 H N N 255 NCO HN63 H N N 256 U OP3 O N N 257 U P P N N 258 U OP1 O N N 259 U OP2 O N N 260 U "O5'" O N N 261 U "C5'" C N N 262 U "C4'" C N R 263 U "O4'" O N N 264 U "C3'" C N S 265 U "O3'" O N N 266 U "C2'" C N R 267 U "O2'" O N N 268 U "C1'" C N R 269 U N1 N N N 270 U C2 C N N 271 U O2 O N N 272 U N3 N N N 273 U C4 C N N 274 U O4 O N N 275 U C5 C N N 276 U C6 C N N 277 U HOP3 H N N 278 U HOP2 H N N 279 U "H5'" H N N 280 U "H5''" H N N 281 U "H4'" H N N 282 U "H3'" H N N 283 U "HO3'" H N N 284 U "H2'" H N N 285 U "HO2'" H N N 286 U "H1'" H N N 287 U H3 H N N 288 U H5 H N N 289 U H6 H N N 290 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 CCC PC O1C doub N N 76 CCC PC O2C sing N N 77 CCC PC "O3'" sing N N 78 CCC PC "O2'" sing N N 79 CCC O2C HOC2 sing N N 80 CCC P OP1 doub N N 81 CCC P OP2 sing N N 82 CCC P OP3 sing N N 83 CCC P "O5'" sing N N 84 CCC OP2 HOP2 sing N N 85 CCC OP3 HOP3 sing N N 86 CCC "O5'" "C5'" sing N N 87 CCC "C5'" "C4'" sing N N 88 CCC "C5'" "H5'" sing N N 89 CCC "C5'" "H5''" sing N N 90 CCC "C4'" "O4'" sing N N 91 CCC "C4'" "C3'" sing N N 92 CCC "C4'" "H4'" sing N N 93 CCC "O4'" "C1'" sing N N 94 CCC "C3'" "O3'" sing N N 95 CCC "C3'" "C2'" sing N N 96 CCC "C3'" "H3'" sing N N 97 CCC "C2'" "O2'" sing N N 98 CCC "C2'" "C1'" sing N N 99 CCC "C2'" "H2'" sing N N 100 CCC "C1'" N1 sing N N 101 CCC "C1'" "H1'" sing N N 102 CCC N1 C2 sing N N 103 CCC N1 C6 sing N N 104 CCC C2 O2 doub N N 105 CCC C2 N3 sing N N 106 CCC N3 C4 doub N N 107 CCC C4 N4 sing N N 108 CCC C4 C5 sing N N 109 CCC N4 H41 sing N N 110 CCC N4 H42 sing N N 111 CCC C5 C6 doub N N 112 CCC C5 H5 sing N N 113 CCC C6 H6 sing N N 114 G OP3 P sing N N 115 G OP3 HOP3 sing N N 116 G P OP1 doub N N 117 G P OP2 sing N N 118 G P "O5'" sing N N 119 G OP2 HOP2 sing N N 120 G "O5'" "C5'" sing N N 121 G "C5'" "C4'" sing N N 122 G "C5'" "H5'" sing N N 123 G "C5'" "H5''" sing N N 124 G "C4'" "O4'" sing N N 125 G "C4'" "C3'" sing N N 126 G "C4'" "H4'" sing N N 127 G "O4'" "C1'" sing N N 128 G "C3'" "O3'" sing N N 129 G "C3'" "C2'" sing N N 130 G "C3'" "H3'" sing N N 131 G "O3'" "HO3'" sing N N 132 G "C2'" "O2'" sing N N 133 G "C2'" "C1'" sing N N 134 G "C2'" "H2'" sing N N 135 G "O2'" "HO2'" sing N N 136 G "C1'" N9 sing N N 137 G "C1'" "H1'" sing N N 138 G N9 C8 sing Y N 139 G N9 C4 sing Y N 140 G C8 N7 doub Y N 141 G C8 H8 sing N N 142 G N7 C5 sing Y N 143 G C5 C6 sing N N 144 G C5 C4 doub Y N 145 G C6 O6 doub N N 146 G C6 N1 sing N N 147 G N1 C2 sing N N 148 G N1 H1 sing N N 149 G C2 N2 sing N N 150 G C2 N3 doub N N 151 G N2 H21 sing N N 152 G N2 H22 sing N N 153 G N3 C4 sing N N 154 GNG "O5'" "C5'" sing N N 155 GNG "O5'" "H5'" sing N N 156 GNG "C5'" "C4'" sing N N 157 GNG "C5'" "H5'1" sing N N 158 GNG "C5'" "H5'2" sing N N 159 GNG "C4'" "O4'" sing N N 160 GNG "C4'" "C3'" sing N N 161 GNG "C4'" "H4'" sing N N 162 GNG "O4'" "C1'" sing N N 163 GNG "C1'" N9 sing N N 164 GNG "C1'" "C2'" sing N N 165 GNG "C1'" "H1'" sing N N 166 GNG N9 C8 sing Y N 167 GNG N9 C4 sing Y N 168 GNG C8 N7 doub Y N 169 GNG C8 H8 sing N N 170 GNG N7 C5 sing Y N 171 GNG C5 C4 doub Y N 172 GNG C5 C6 sing N N 173 GNG C4 N3 sing N N 174 GNG N3 C2 sing N N 175 GNG N3 HN3 sing N N 176 GNG C2 N1 doub N N 177 GNG C2 N2 sing N N 178 GNG N1 C6 sing N N 179 GNG C6 O6 doub N N 180 GNG N2 HN21 sing N N 181 GNG N2 HN22 sing N N 182 GNG "C2'" "C3'" sing N N 183 GNG "C2'" "H2'1" sing N N 184 GNG "C2'" "H2'2" sing N N 185 GNG "C3'" "O3'" sing N N 186 GNG "C3'" "H3'" sing N N 187 GNG "O3'" H1 sing N N 188 GTP PG O1G doub N N 189 GTP PG O2G sing N N 190 GTP PG O3G sing N N 191 GTP PG O3B sing N N 192 GTP O2G HOG2 sing N N 193 GTP O3G HOG3 sing N N 194 GTP O3B PB sing N N 195 GTP PB O1B doub N N 196 GTP PB O2B sing N N 197 GTP PB O3A sing N N 198 GTP O2B HOB2 sing N N 199 GTP O3A PA sing N N 200 GTP PA O1A doub N N 201 GTP PA O2A sing N N 202 GTP PA "O5'" sing N N 203 GTP O2A HOA2 sing N N 204 GTP "O5'" "C5'" sing N N 205 GTP "C5'" "C4'" sing N N 206 GTP "C5'" "H5'" sing N N 207 GTP "C5'" "H5''" sing N N 208 GTP "C4'" "O4'" sing N N 209 GTP "C4'" "C3'" sing N N 210 GTP "C4'" "H4'" sing N N 211 GTP "O4'" "C1'" sing N N 212 GTP "C3'" "O3'" sing N N 213 GTP "C3'" "C2'" sing N N 214 GTP "C3'" "H3'" sing N N 215 GTP "O3'" "HO3'" sing N N 216 GTP "C2'" "O2'" sing N N 217 GTP "C2'" "C1'" sing N N 218 GTP "C2'" "H2'" sing N N 219 GTP "O2'" "HO2'" sing N N 220 GTP "C1'" N9 sing N N 221 GTP "C1'" "H1'" sing N N 222 GTP N9 C8 sing Y N 223 GTP N9 C4 sing Y N 224 GTP C8 N7 doub Y N 225 GTP C8 H8 sing N N 226 GTP N7 C5 sing Y N 227 GTP C5 C6 sing N N 228 GTP C5 C4 doub Y N 229 GTP C6 O6 doub N N 230 GTP C6 N1 sing N N 231 GTP N1 C2 sing N N 232 GTP N1 HN1 sing N N 233 GTP C2 N2 sing N N 234 GTP C2 N3 doub N N 235 GTP N2 HN21 sing N N 236 GTP N2 HN22 sing N N 237 GTP N3 C4 sing N N 238 HOH O H1 sing N N 239 HOH O H2 sing N N 240 NCO CO N1 sing N N 241 NCO CO N2 sing N N 242 NCO CO N3 sing N N 243 NCO CO N4 sing N N 244 NCO CO N5 sing N N 245 NCO CO N6 sing N N 246 NCO N1 HN11 sing N N 247 NCO N1 HN12 sing N N 248 NCO N1 HN13 sing N N 249 NCO N2 HN21 sing N N 250 NCO N2 HN22 sing N N 251 NCO N2 HN23 sing N N 252 NCO N3 HN31 sing N N 253 NCO N3 HN32 sing N N 254 NCO N3 HN33 sing N N 255 NCO N4 HN41 sing N N 256 NCO N4 HN42 sing N N 257 NCO N4 HN43 sing N N 258 NCO N5 HN51 sing N N 259 NCO N5 HN52 sing N N 260 NCO N5 HN53 sing N N 261 NCO N6 HN61 sing N N 262 NCO N6 HN62 sing N N 263 NCO N6 HN63 sing N N 264 U OP3 P sing N N 265 U OP3 HOP3 sing N N 266 U P OP1 doub N N 267 U P OP2 sing N N 268 U P "O5'" sing N N 269 U OP2 HOP2 sing N N 270 U "O5'" "C5'" sing N N 271 U "C5'" "C4'" sing N N 272 U "C5'" "H5'" sing N N 273 U "C5'" "H5''" sing N N 274 U "C4'" "O4'" sing N N 275 U "C4'" "C3'" sing N N 276 U "C4'" "H4'" sing N N 277 U "O4'" "C1'" sing N N 278 U "C3'" "O3'" sing N N 279 U "C3'" "C2'" sing N N 280 U "C3'" "H3'" sing N N 281 U "O3'" "HO3'" sing N N 282 U "C2'" "O2'" sing N N 283 U "C2'" "C1'" sing N N 284 U "C2'" "H2'" sing N N 285 U "O2'" "HO2'" sing N N 286 U "C1'" N1 sing N N 287 U "C1'" "H1'" sing N N 288 U N1 C2 sing N N 289 U N1 C6 sing N N 290 U C2 O2 doub N N 291 U C2 N3 sing N N 292 U N3 C4 sing N N 293 U N3 H3 sing N N 294 U C4 O4 doub N N 295 U C4 C5 sing N N 296 U C5 C6 doub N N 297 U C5 H5 sing N N 298 U C6 H6 sing N N 299 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3SKR 'double helix' 3SKR 'a-form double helix' 3SKR 'b-form double helix' 3SKR 'mismatched base pair' 3SKR 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A GTP 1 1_555 A CCC 66 1_555 -0.303 -0.002 0.048 -0.798 -13.388 -11.867 1 A_GTP23:CCC88_A A 23 ? A 88 ? ? 1 1 A G 2 1_555 A U 65 1_555 -2.041 -0.495 0.789 10.750 -24.580 -1.696 2 A_G24:U87_A A 24 ? A 87 ? 28 1 1 A C 3 1_555 A G 64 1_555 -1.590 0.176 0.891 -6.358 -18.718 -11.252 3 A_C25:G86_A A 25 ? A 86 ? ? 1 1 A U 4 1_555 A A 63 1_555 0.399 -0.531 0.556 -1.622 -13.376 -3.318 4 A_U26:A85_A A 26 ? A 85 ? 20 1 1 A U 5 1_555 A A 62 1_555 0.701 -0.118 -0.087 -0.465 -19.817 -0.170 5 A_U27:A84_A A 27 ? A 84 ? 20 1 1 A A 6 1_555 A U 61 1_555 -0.679 -0.060 0.327 -7.163 -5.681 -6.816 6 A_A28:U83_A A 28 ? A 83 ? 20 1 1 A U 7 1_555 A A 60 1_555 -0.045 -0.114 0.574 -12.431 -6.914 -18.059 7 A_U29:A82_A A 29 ? A 82 ? 20 1 1 A A 8 1_555 A U 59 1_555 -0.333 0.138 0.911 16.703 -3.546 0.381 8 A_A30:U81_A A 30 ? A 81 ? 20 1 1 A G 25 1_555 A C 17 1_555 -0.562 -0.313 -0.038 -5.207 -6.763 -3.309 9 A_G47:C39_A A 47 ? A 39 ? 19 1 1 A C 26 1_555 A G 16 1_555 -0.724 0.077 0.197 4.524 -8.066 5.945 10 A_C48:G38_A A 48 ? A 38 ? 19 1 1 A U 27 1_555 A A 15 1_555 -1.230 -0.238 0.765 -4.402 -2.529 -1.229 11 A_U49:A37_A A 49 ? A 37 ? 20 1 1 A A 28 1_555 A U 14 1_555 -0.209 -0.349 0.583 14.647 -4.831 -7.075 12 A_A50:U36_A A 50 ? A 36 ? 20 1 1 A C 29 1_555 A G 13 1_555 -0.833 -0.208 0.126 9.806 -7.948 0.925 13 A_C51:G35_A A 51 ? A 35 ? 19 1 1 A U 30 1_555 A G 12 1_555 1.625 -0.607 0.217 -8.817 -10.705 -3.178 14 A_U52:G34_A A 52 ? A 34 ? 28 1 1 A G 31 1_555 A C 38 1_555 0.803 0.218 0.387 17.759 -17.175 -4.731 15 A_G53:C60_A A 53 ? A 60 ? 19 1 1 A C 9 1_555 A G 37 1_555 0.704 -0.197 -0.458 16.248 -6.019 -13.161 16 A_C31:G59_A A 31 ? A 59 ? 19 1 1 A G 23 1_555 A C 47 1_555 0.235 0.068 -0.680 -20.234 -1.669 5.070 17 A_G45:C69_A A 45 ? A 69 ? 19 1 1 A G 24 1_555 A C 46 1_555 -0.796 -0.403 -0.068 -7.644 -12.130 -4.804 18 A_G46:C68_A A 46 ? A 68 ? 19 1 1 A U 50 1_555 A A 45 1_555 0.814 -0.057 -0.173 -3.176 -5.608 10.173 19 A_U72:A67_A A 72 ? A 67 ? 20 1 1 A U 51 1_555 A A 44 1_555 0.629 -0.409 -0.559 7.146 -20.047 -9.336 20 A_U73:A66_A A 73 ? A 66 ? 20 1 1 A U 52 1_555 A A 43 1_555 0.447 -0.245 0.167 -0.864 -5.874 -2.055 21 A_U74:A65_A A 74 ? A 65 ? 20 1 1 A G 53 1_555 A C 42 1_555 0.014 -0.007 0.188 3.610 0.717 -2.234 22 A_G75:C64_A A 75 ? A 64 ? 19 1 1 A G 54 1_555 A U 41 1_555 -1.592 -0.615 -0.133 2.878 -4.270 -6.254 23 A_G76:U63_A A 76 ? A 63 ? 28 1 1 A A 55 1_555 A U 40 1_555 0.289 -0.445 0.048 -4.239 1.257 -8.508 24 A_A77:U62_A A 77 ? A 62 ? 20 1 1 A G 56 1_555 A C 39 1_555 -0.382 -0.164 0.528 -0.203 -4.237 -10.619 25 A_G78:C61_A A 78 ? A 61 ? 19 1 1 B GTP 1 1_555 B CCC 66 1_555 1.604 0.310 0.082 -2.006 1.891 -13.474 26 B_GTP23:CCC88_B B 23 ? B 88 ? ? 1 1 B G 2 1_555 B U 65 1_555 -2.047 -0.727 0.070 1.636 -20.131 -11.777 27 B_G24:U87_B B 24 ? B 87 ? 28 1 1 B C 3 1_555 B G 64 1_555 1.344 -0.408 0.546 4.687 -21.841 6.444 28 B_C25:G86_B B 25 ? B 86 ? 19 1 1 B U 4 1_555 B A 63 1_555 -0.600 -0.404 1.001 -9.536 -9.626 -3.719 29 B_U26:A85_B B 26 ? B 85 ? 20 1 1 B U 5 1_555 B A 62 1_555 0.136 -0.064 -0.185 9.591 -17.133 1.560 30 B_U27:A84_B B 27 ? B 84 ? 20 1 1 B A 6 1_555 B U 61 1_555 -0.287 0.280 0.736 5.903 5.210 1.448 31 B_A28:U83_B B 28 ? B 83 ? 20 1 1 B U 7 1_555 B A 60 1_555 -0.158 0.133 -0.072 -3.738 -20.350 -12.112 32 B_U29:A82_B B 29 ? B 82 ? 20 1 1 B A 8 1_555 B U 59 1_555 -0.662 -0.166 0.165 15.702 -5.497 -1.186 33 B_A30:U81_B B 30 ? B 81 ? 20 1 1 B G 25 1_555 B C 17 1_555 1.442 0.132 -1.286 -26.297 -4.300 7.675 34 B_G47:C39_B B 47 ? B 39 ? ? 1 1 B C 26 1_555 B G 16 1_555 0.786 -0.152 -0.153 -7.421 -0.933 -16.043 35 B_C48:G38_B B 48 ? B 38 ? ? 1 1 B U 27 1_555 B A 15 1_555 0.648 0.024 -0.090 -1.439 -3.389 0.545 36 B_U49:A37_B B 49 ? B 37 ? 20 1 1 B A 28 1_555 B U 14 1_555 -0.094 -0.162 0.037 2.991 -9.429 -9.538 37 B_A50:U36_B B 50 ? B 36 ? 20 1 1 B C 29 1_555 B G 13 1_555 1.588 -0.327 -0.332 3.624 -2.808 9.935 38 B_C51:G35_B B 51 ? B 35 ? 19 1 1 B U 30 1_555 B G 12 1_555 2.340 0.022 -0.217 -7.268 -7.883 7.878 39 B_U52:G34_B B 52 ? B 34 ? 28 1 1 B G 31 1_555 B C 38 1_555 -0.386 -0.153 0.538 9.580 -16.864 -1.239 40 B_G53:C60_B B 53 ? B 60 ? 19 1 1 B C 9 1_555 B G 37 1_555 -0.690 -0.121 -0.131 5.972 -22.460 -0.116 41 B_C31:G59_B B 31 ? B 59 ? 19 1 1 B G 23 1_555 B C 47 1_555 -0.498 -0.371 -0.296 -12.687 5.984 -0.174 42 B_G45:C69_B B 45 ? B 69 ? 19 1 1 B G 24 1_555 B C 46 1_555 0.184 0.313 -0.425 -15.576 -18.618 5.154 43 B_G46:C68_B B 46 ? B 68 ? 19 1 1 B U 50 1_555 B A 45 1_555 0.149 0.287 -0.234 3.576 -9.151 10.972 44 B_U72:A67_B B 72 ? B 67 ? ? ? 1 B U 51 1_555 B A 44 1_555 -0.015 -0.059 0.295 -0.360 -23.173 0.810 45 B_U73:A66_B B 73 ? B 66 ? 20 1 1 B U 52 1_555 B A 43 1_555 0.464 -0.249 0.270 -5.505 -11.280 -0.678 46 B_U74:A65_B B 74 ? B 65 ? 20 1 1 B G 53 1_555 B C 42 1_555 0.415 0.010 -0.726 -11.692 -14.988 -8.375 47 B_G75:C64_B B 75 ? B 64 ? 19 1 1 B G 54 1_555 B U 41 1_555 -2.090 -0.691 0.154 2.912 -6.392 -9.329 48 B_G76:U63_B B 76 ? B 63 ? 28 1 1 B A 55 1_555 B U 40 1_555 0.213 -0.151 -0.166 -2.165 -2.697 -9.208 49 B_A77:U62_B B 77 ? B 62 ? 20 1 1 B G 56 1_555 B C 39 1_555 -0.416 -0.040 -0.135 4.259 -4.372 5.197 50 B_G78:C61_B B 78 ? B 61 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A GTP 1 1_555 A CCC 66 1_555 A G 2 1_555 A U 65 1_555 0.235 -2.480 2.361 -9.054 10.786 28.991 -5.602 -1.369 1.255 20.116 16.886 32.164 1 AA_GTP23G24:U87CCC88_AA A 23 ? A 88 ? A 24 ? A 87 ? 1 A G 2 1_555 A U 65 1_555 A C 3 1_555 A G 64 1_555 -0.566 -1.529 3.552 -6.020 10.166 35.255 -3.814 0.053 3.062 16.232 9.613 37.123 2 AA_G24C25:G86U87_AA A 24 ? A 87 ? A 25 ? A 86 ? 1 A C 3 1_555 A G 64 1_555 A U 4 1_555 A A 63 1_555 0.167 -1.733 3.133 1.866 -0.187 44.466 -2.272 -0.056 3.144 -0.247 -2.464 44.504 3 AA_C25U26:A85G86_AA A 25 ? A 86 ? A 26 ? A 85 ? 1 A U 4 1_555 A A 63 1_555 A U 5 1_555 A A 62 1_555 0.301 -0.927 3.259 5.320 5.372 34.211 -2.336 0.286 3.093 8.996 -8.909 35.012 4 AA_U26U27:A84A85_AA A 26 ? A 85 ? A 27 ? A 84 ? 1 A U 5 1_555 A A 62 1_555 A A 6 1_555 A U 61 1_555 -0.470 -1.663 3.079 -5.208 13.340 27.359 -5.323 0.027 2.112 26.062 10.176 30.817 5 AA_U27A28:U83A84_AA A 27 ? A 84 ? A 28 ? A 83 ? 1 A A 6 1_555 A U 61 1_555 A U 7 1_555 A A 60 1_555 -0.314 -1.484 3.524 0.266 5.594 41.433 -2.695 0.470 3.303 7.863 -0.374 41.793 6 AA_A28U29:A82U83_AA A 28 ? A 83 ? A 29 ? A 82 ? 1 A U 7 1_555 A A 60 1_555 A A 8 1_555 A U 59 1_555 0.489 -1.543 2.235 0.290 2.397 28.535 -3.481 -0.945 2.105 4.853 -0.587 28.635 7 AA_U29A30:U81A82_AA A 29 ? A 82 ? A 30 ? A 81 ? 1 A G 25 1_555 A C 17 1_555 A C 26 1_555 A G 16 1_555 0.705 -2.196 2.884 -0.392 0.511 30.708 -4.234 -1.399 2.839 0.966 0.740 30.715 8 AA_G47C48:G38C39_AA A 47 ? A 39 ? A 48 ? A 38 ? 1 A C 26 1_555 A G 16 1_555 A U 27 1_555 A A 15 1_555 -0.497 -1.943 3.346 -4.766 6.924 27.440 -5.430 -0.035 2.826 14.181 9.761 28.675 9 AA_C48U49:A37G38_AA A 48 ? A 38 ? A 49 ? A 37 ? 1 A U 27 1_555 A A 15 1_555 A A 28 1_555 A U 14 1_555 -0.100 -1.536 2.427 0.896 3.485 35.080 -2.907 0.260 2.266 5.764 -1.482 35.258 10 AA_U49A50:U36A37_AA A 49 ? A 37 ? A 50 ? A 36 ? 1 A A 28 1_555 A U 14 1_555 A C 29 1_555 A G 13 1_555 0.504 -1.735 3.234 1.394 3.755 32.710 -3.674 -0.660 3.040 6.637 -2.464 32.947 11 AA_A50C51:G35U36_AA A 50 ? A 36 ? A 51 ? A 35 ? 1 A C 29 1_555 A G 13 1_555 A U 30 1_555 A G 12 1_555 0.817 -1.669 3.561 3.511 9.077 44.780 -2.976 -0.729 3.233 11.750 -4.545 45.772 12 AA_C51U52:G34G35_AA A 51 ? A 35 ? A 52 ? A 34 ? 1 A U 30 1_555 A G 12 1_555 A G 31 1_555 A C 38 1_555 2.567 -2.143 2.532 -0.594 1.050 57.125 -2.285 -2.709 2.471 1.098 0.621 57.137 13 AA_U52G53:C60G34_AA A 52 ? A 34 ? A 53 ? A 60 ? 1 A G 31 1_555 A C 38 1_555 A C 9 1_555 A G 37 1_555 -2.678 -0.770 3.020 -0.277 8.324 58.914 -1.159 2.688 2.909 8.417 0.280 59.448 14 AA_G53C31:G59C60_AA A 53 ? A 60 ? A 31 ? A 59 ? 1 A G 23 1_555 A C 47 1_555 A G 24 1_555 A C 46 1_555 -0.199 -2.483 2.822 -3.832 14.029 18.860 -8.908 -0.305 0.825 36.572 9.990 23.776 15 AA_G45G46:C68C69_AA A 45 ? A 69 ? A 46 ? A 68 ? 1 A G 24 1_555 A C 46 1_555 A U 50 1_555 A A 45 1_555 -0.441 -2.761 3.239 -0.437 1.484 30.008 -5.622 0.763 3.108 2.864 0.844 30.047 16 AA_G46U72:A67C68_AA A 46 ? A 68 ? A 72 ? A 67 ? 1 A U 50 1_555 A A 45 1_555 A U 51 1_555 A A 44 1_555 -1.839 -0.136 2.919 -1.070 0.423 39.700 -0.244 2.596 2.964 0.623 1.576 39.716 17 AA_U72U73:A66A67_AA A 72 ? A 67 ? A 73 ? A 66 ? 1 A U 51 1_555 A A 44 1_555 A U 52 1_555 A A 43 1_555 0.244 -1.846 3.589 -6.492 11.617 30.625 -5.140 -1.499 2.631 20.805 11.627 33.328 18 AA_U73U74:A65A66_AA A 73 ? A 66 ? A 74 ? A 65 ? 1 A U 52 1_555 A A 43 1_555 A G 53 1_555 A C 42 1_555 -0.656 -1.879 2.925 -1.376 10.278 29.075 -5.145 1.018 2.178 19.698 2.637 30.831 19 AA_U74G75:C64A65_AA A 74 ? A 65 ? A 75 ? A 64 ? 1 A G 53 1_555 A C 42 1_555 A G 54 1_555 A U 41 1_555 0.204 -2.502 3.182 1.866 3.833 23.475 -7.199 0.065 2.752 9.322 -4.538 23.854 20 AA_G75G76:U63C64_AA A 75 ? A 64 ? A 76 ? A 63 ? 1 A G 54 1_555 A U 41 1_555 A A 55 1_555 A U 40 1_555 0.156 -2.087 3.515 -1.967 5.834 35.968 -4.162 -0.529 3.137 9.363 3.156 36.474 21 AA_G76A77:U62U63_AA A 76 ? A 63 ? A 77 ? A 62 ? 1 A A 55 1_555 A U 40 1_555 A G 56 1_555 A C 39 1_555 0.309 -2.641 3.032 -0.186 1.271 28.076 -5.709 -0.677 2.910 2.617 0.383 28.105 22 AA_A77G78:C61U62_AA A 77 ? A 62 ? A 78 ? A 61 ? 1 B GTP 1 1_555 B CCC 66 1_555 B G 2 1_555 B U 65 1_555 0.026 -2.382 2.842 -0.342 9.563 23.375 -7.489 -0.132 1.745 22.434 0.803 25.233 23 BB_GTP23G24:U87CCC88_BB B 23 ? B 88 ? B 24 ? B 87 ? 1 B G 2 1_555 B U 65 1_555 B C 3 1_555 B G 64 1_555 1.367 -1.789 3.135 -2.462 3.913 42.284 -2.832 -2.114 2.886 5.404 3.400 42.524 24 BB_G24C25:G86U87_BB B 24 ? B 87 ? B 25 ? B 86 ? 1 B C 3 1_555 B G 64 1_555 B U 4 1_555 B A 63 1_555 -0.323 -1.265 3.238 -2.926 15.252 30.012 -4.436 0.125 2.360 27.277 5.232 33.710 25 BB_C25U26:A85G86_BB B 25 ? B 86 ? B 26 ? B 85 ? 1 B U 4 1_555 B A 63 1_555 B U 5 1_555 B A 62 1_555 0.206 -1.243 2.597 9.943 -0.093 32.382 -2.124 0.938 2.550 -0.162 -17.326 33.835 26 BB_U26U27:A84A85_BB B 26 ? B 85 ? B 27 ? B 84 ? 1 B U 5 1_555 B A 62 1_555 B A 6 1_555 B U 61 1_555 -0.021 -1.437 3.108 -9.747 9.754 31.354 -3.818 -1.338 2.464 17.053 17.042 34.183 27 BB_U27A28:U83A84_BB B 27 ? B 84 ? B 28 ? B 83 ? 1 B A 6 1_555 B U 61 1_555 B U 7 1_555 B A 60 1_555 -0.149 -1.554 3.663 8.651 6.558 39.514 -3.000 1.237 3.273 9.484 -12.512 40.920 28 BB_A28U29:A82U83_BB B 28 ? B 83 ? B 29 ? B 82 ? 1 B U 7 1_555 B A 60 1_555 B A 8 1_555 B U 59 1_555 0.336 -1.151 2.818 1.231 13.858 28.637 -4.103 -0.436 2.067 26.156 -2.323 31.774 29 BB_U29A30:U81A82_BB B 29 ? B 82 ? B 30 ? B 81 ? 1 B G 25 1_555 B C 17 1_555 B C 26 1_555 B G 16 1_555 -1.185 -1.924 2.851 -6.270 -2.504 31.582 -3.048 1.098 3.161 -4.536 11.358 32.277 30 BB_G47C48:G38C39_BB B 47 ? B 39 ? B 48 ? B 38 ? 1 B C 26 1_555 B G 16 1_555 B U 27 1_555 B A 15 1_555 0.743 -1.841 2.978 1.667 3.736 26.960 -4.726 -1.209 2.743 7.955 -3.550 27.263 31 BB_C48U49:A37G38_BB B 48 ? B 38 ? B 49 ? B 37 ? 1 B U 27 1_555 B A 15 1_555 B A 28 1_555 B U 14 1_555 -0.449 -0.996 2.886 -0.407 19.214 25.934 -4.514 0.752 1.758 37.026 0.784 32.180 32 BB_U49A50:U36A37_BB B 49 ? B 37 ? B 50 ? B 36 ? 1 B A 28 1_555 B U 14 1_555 B C 29 1_555 B G 13 1_555 0.057 -1.710 3.248 0.710 -0.177 44.836 -2.226 -0.011 3.255 -0.233 -0.930 44.842 33 BB_A50C51:G35U36_BB B 50 ? B 36 ? B 51 ? B 35 ? 1 B C 29 1_555 B G 13 1_555 B U 30 1_555 B G 12 1_555 0.646 -1.853 3.418 5.565 11.934 33.256 -4.696 -0.273 2.686 19.909 -9.283 35.699 34 BB_C51U52:G34G35_BB B 51 ? B 35 ? B 52 ? B 34 ? 1 B U 30 1_555 B G 12 1_555 B G 31 1_555 B C 38 1_555 2.345 -1.034 2.850 -8.691 7.117 48.839 -1.631 -3.271 2.265 8.478 10.352 50.037 35 BB_U52G53:C60G34_BB B 52 ? B 34 ? B 53 ? B 60 ? 1 B G 31 1_555 B C 38 1_555 B C 9 1_555 B G 37 1_555 -2.481 -0.834 2.966 -3.588 4.718 52.082 -1.230 2.593 3.037 5.353 4.071 52.394 36 BB_G53C31:G59C60_BB B 53 ? B 60 ? B 31 ? B 59 ? 1 B G 23 1_555 B C 47 1_555 B G 24 1_555 B C 46 1_555 0.192 -2.470 3.326 3.625 15.829 27.009 -7.004 0.206 1.668 30.628 -7.014 31.437 37 BB_G45G46:C68C69_BB B 45 ? B 69 ? B 46 ? B 68 ? 1 B G 24 1_555 B C 46 1_555 B U 50 1_555 B A 45 1_555 -0.964 -2.546 2.727 -3.170 6.085 27.133 -6.374 1.418 2.211 12.713 6.624 27.971 38 BB_G46U72:A67C68_BB B 46 ? B 68 ? B 72 ? B 67 ? 1 B U 50 1_555 B A 45 1_555 B U 51 1_555 B A 44 1_555 -1.337 -0.663 3.481 -9.837 -3.240 33.556 -0.550 0.547 3.758 -5.452 16.555 35.074 39 BB_U72U73:A66A67_BB B 72 ? B 67 ? B 73 ? B 66 ? 1 B U 51 1_555 B A 44 1_555 B U 52 1_555 B A 43 1_555 0.031 -1.278 3.420 -1.199 3.414 36.340 -2.525 -0.220 3.288 5.458 1.916 36.514 40 BB_U73U74:A65A66_BB B 73 ? B 66 ? B 74 ? B 65 ? 1 B U 52 1_555 B A 43 1_555 B G 53 1_555 B C 42 1_555 -0.629 -1.862 3.419 7.169 16.651 27.441 -5.806 2.194 1.811 31.161 -13.417 32.792 41 BB_U74G75:C64A65_BB B 74 ? B 65 ? B 75 ? B 64 ? 1 B G 53 1_555 B C 42 1_555 B G 54 1_555 B U 41 1_555 -0.102 -2.048 2.723 -12.144 6.865 15.844 -7.702 -3.443 1.447 20.470 36.209 21.080 42 BB_G75G76:U63C64_BB B 75 ? B 64 ? B 76 ? B 63 ? 1 B G 54 1_555 B U 41 1_555 B A 55 1_555 B U 40 1_555 -0.055 -1.658 3.455 -0.071 -0.322 40.250 -2.370 0.071 3.467 -0.468 0.104 40.252 43 BB_G76A77:U62U63_BB B 76 ? B 63 ? B 77 ? B 62 ? 1 B A 55 1_555 B U 40 1_555 B G 56 1_555 B C 39 1_555 1.882 -2.387 3.134 3.513 3.215 28.504 -5.465 -3.029 3.057 6.472 -7.073 28.891 44 BB_A77G78:C61U62_BB B 77 ? B 62 ? B 78 ? B 61 ? # _atom_sites.entry_id 3SKR _atom_sites.fract_transf_matrix[1][1] 0.010149 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000387 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028557 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.009035 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CO MG N O P # loop_