data_3SKW # _entry.id 3SKW # _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 3SKW pdb_00003skw 10.2210/pdb3skw/pdb NDB NA1182 ? ? RCSB RCSB066328 ? ? WWPDB D_1000066328 ? ? # 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 3SKW _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 3SKI . unspecified PDB 3SKT . unspecified PDB 3SKL . unspecified PDB 3SKR . 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 (66-MER)' 2 non-polymer syn "2'-DEOXY-GUANOSINE" 267.241 2 ? ? ? 'in vitro transcribed RNA' 3 non-polymer syn 'CESIUM ION' 132.905 6 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 5 water nat water 18.015 2 ? ? ? ? # _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 'CESIUM ION' CS 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 transcribed RNA' # 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 CS non-polymer . 'CESIUM ION' ? 'Cs 1' 132.905 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 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 CS 1 201 201 CS CS A . E 3 CS 1 202 202 CS CS A . F 3 CS 1 203 203 CS CS A . G 3 CS 1 204 204 CS CS A . H 3 CS 1 205 205 CS CS A . I 4 MG 1 206 206 MG MG A . J 3 CS 1 304 304 CS CS A . K 4 MG 1 305 305 MG MG A . L 2 GNG 1 120 120 GNG GNG B . M 5 HOH 1 307 307 HOH HOH B . M 5 HOH 2 308 308 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 MOLREP phasing . ? 2 PHENIX refinement '(phenix.refine: 1.7_650)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 3SKW _cell.length_a 102.376 _cell.length_b 35.414 _cell.length_c 119.269 _cell.angle_alpha 90.00 _cell.angle_beta 95.18 _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 3SKW _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 3SKW _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.52 _exptl_crystal.density_percent_sol 51.17 _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, 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 2010-04-13 _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 1.4 _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 1.4 # _reflns.entry_id 3SKW _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 2.95 _reflns.number_obs 8847 _reflns.number_all 8847 _reflns.percent_possible_obs 95.7 _reflns.pdbx_Rmerge_I_obs 0.108 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 19.6 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.3 _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 2.95 _reflns_shell.d_res_low 3.06 _reflns_shell.percent_possible_all 98.4 _reflns_shell.Rmerge_I_obs 0.335 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.7 _reflns_shell.pdbx_redundancy 3.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 882 _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 3SKW _refine.ls_number_reflns_obs 8847 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.92 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.646 _refine.ls_d_res_high 2.95 _refine.ls_percent_reflns_obs 87.98 _refine.ls_R_factor_obs 0.2242 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2170 _refine.ls_R_factor_R_free 0.2873 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.97 _refine.ls_number_reflns_R_free 1556 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] -5.1870 _refine.aniso_B[2][2] -14.8741 _refine.aniso_B[3][3] 20.0611 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -27.3295 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.210 _refine.solvent_model_param_bsol 60.252 _refine.pdbx_solvent_vdw_probe_radii 1.30 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 1.06 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.41 _refine.pdbx_overall_phase_error 36.76 _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 2826 _refine_hist.pdbx_number_atoms_ligand 46 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 2874 _refine_hist.d_res_high 2.95 _refine_hist.d_res_low 19.646 # 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 f_bond_d 0.006 ? ? 3208 ? 'X-RAY DIFFRACTION' f_angle_d 1.045 ? ? 4979 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 24.869 ? ? 1610 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.061 ? ? 662 ? 'X-RAY DIFFRACTION' f_plane_restr 0.006 ? ? 136 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _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 . 2.9373 3.0317 1032 0.3523 73.00 0.4164 . . 129 . . . . 'X-RAY DIFFRACTION' . 3.0317 3.1397 1262 0.3130 89.00 0.3625 . . 162 . . . . 'X-RAY DIFFRACTION' . 3.1397 3.2649 1271 0.2425 85.00 0.3160 . . 118 . . . . 'X-RAY DIFFRACTION' . 3.2649 3.4127 1256 0.2431 87.00 0.3488 . . 160 . . . . 'X-RAY DIFFRACTION' . 3.4127 3.5916 1274 0.2267 86.00 0.2768 . . 111 . . . . 'X-RAY DIFFRACTION' . 3.5916 3.8151 1250 0.2346 87.00 0.3325 . . 139 . . . . 'X-RAY DIFFRACTION' . 3.8151 4.1072 1309 0.2201 88.00 0.3012 . . 125 . . . . 'X-RAY DIFFRACTION' . 4.1072 4.5160 1293 0.2182 90.00 0.2940 . . 174 . . . . 'X-RAY DIFFRACTION' . 4.5160 5.1591 1368 0.2003 95.00 0.2175 . . 137 . . . . 'X-RAY DIFFRACTION' . 5.1591 6.4612 1370 0.1632 95.00 0.2832 . . 151 . . . . 'X-RAY DIFFRACTION' . 6.4612 19.6464 1364 0.2080 93.00 0.2546 . . 150 . . . . 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3SKW _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 3SKW _struct.title ;Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cesium soak ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3SKW _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;three-way RNA junction, riboswitch, 2'-deoxy guanosine, 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 3 ? K N N 4 ? L N N 2 ? M N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3SKW _struct_ref.pdbx_db_accession 3SKW _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _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 3SKW A 1 ? 66 ? 3SKW 23 ? 88 ? 23 88 2 1 3SKW B 1 ? 66 ? 3SKW 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 2 1 B,L,M # _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 ? ? ? ? ? ? ? 1.594 ? ? covale2 covale both ? A U 65 "O3'" ? ? ? 1_555 A CCC 66 P ? ? A U 87 A CCC 88 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale3 covale both ? B GTP 1 "O3'" ? ? ? 1_555 B G 2 P ? ? B GTP 23 B G 24 1_555 ? ? ? ? ? ? ? 1.599 ? ? 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 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A GTP 1 N2 ? ? ? 1_555 A CCC 66 O2 ? ? A GTP 23 A CCC 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A GTP 1 O6 ? ? ? 1_555 A CCC 66 N4 ? ? A GTP 23 A CCC 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 65 O2 ? ? A G 24 A U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 65 N3 ? ? A G 24 A U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 64 N1 ? ? A C 25 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 64 O6 ? ? A C 25 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 64 N2 ? ? A C 25 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 62 N6 ? ? A U 26 A A 84 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog10 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 63 N1 ? ? A U 26 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 63 N6 ? ? A U 26 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 62 N1 ? ? A U 27 A A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 62 N6 ? ? A U 27 A A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 61 N3 ? ? A A 28 A U 83 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog15 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 60 N1 ? ? A U 29 A A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 60 N6 ? ? A U 29 A A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 59 N3 ? ? A A 30 A U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 59 O4 ? ? A A 30 A U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 37 N1 ? ? A C 31 A G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 37 O6 ? ? A C 31 A G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 37 N2 ? ? A C 31 A G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 10 N1 ? ? ? 1_555 A G 31 N2 ? ? A A 32 A G 53 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog23 hydrog ? ? A G 11 N2 ? ? ? 1_555 A U 30 O4 ? ? A G 33 A U 52 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 A U 30 O2 ? ? A G 34 A U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog25 hydrog ? ? A G 12 O6 ? ? ? 1_555 A U 30 N3 ? ? A G 34 A U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog26 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 35 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 35 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 35 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 36 A A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 36 A A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 15 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 37 A U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A A 15 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 37 A U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 16 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 38 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 16 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 38 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 16 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 38 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 17 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 39 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 17 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 39 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 17 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 39 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A A 20 N1 ? ? ? 1_555 A G 23 N2 ? ? A A 42 A G 45 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog40 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 47 N3 ? ? A G 45 A C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 47 O2 ? ? A G 45 A C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 47 N4 ? ? A G 45 A C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 24 N1 ? ? ? 1_555 A C 46 N3 ? ? A G 46 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 24 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 46 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 24 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 46 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 53 A C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 53 A C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 53 A C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 35 N4 ? ? ? 1_555 A U 59 O2 ? ? A C 57 A U 81 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog50 hydrog ? ? A C 39 N3 ? ? ? 1_555 A G 56 N1 ? ? A C 61 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 39 N4 ? ? ? 1_555 A G 56 O6 ? ? A C 61 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 39 O2 ? ? ? 1_555 A G 56 N2 ? ? A C 61 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A U 40 N3 ? ? ? 1_555 A A 55 N1 ? ? A U 62 A A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A U 40 O4 ? ? ? 1_555 A A 55 N6 ? ? A U 62 A A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A U 41 N3 ? ? ? 1_555 A G 54 O6 ? ? A U 63 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog56 hydrog ? ? A U 41 O2 ? ? ? 1_555 A G 54 N1 ? ? A U 63 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog57 hydrog ? ? A C 42 N3 ? ? ? 1_555 A G 53 N1 ? ? A C 64 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 42 N4 ? ? ? 1_555 A G 53 O6 ? ? A C 64 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A C 42 O2 ? ? ? 1_555 A G 53 N2 ? ? A C 64 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A A 43 N1 ? ? ? 1_555 A U 52 N3 ? ? A A 65 A U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A A 43 N6 ? ? ? 1_555 A U 52 O4 ? ? A A 65 A U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A A 44 N1 ? ? ? 1_555 A U 51 N3 ? ? A A 66 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A A 44 N6 ? ? ? 1_555 A U 51 O4 ? ? A A 66 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A A 45 N1 ? ? ? 1_555 A U 50 N3 ? ? A A 67 A U 72 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog65 hydrog ? ? B GTP 1 N2 ? ? ? 1_555 B CCC 66 O2 ? ? B GTP 23 B CCC 88 1_555 ? ? ? ? ? ? 'GTP-CCC PAIR' ? ? ? hydrog66 hydrog ? ? B G 2 N1 ? ? ? 1_555 B U 65 O2 ? ? B G 24 B U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog67 hydrog ? ? B G 2 O6 ? ? ? 1_555 B U 65 N3 ? ? B G 24 B U 87 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog68 hydrog ? ? B C 3 N3 ? ? ? 1_555 B G 64 N1 ? ? B C 25 B G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? B C 3 N4 ? ? ? 1_555 B G 64 O6 ? ? B C 25 B G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? B C 3 O2 ? ? ? 1_555 B G 64 N2 ? ? B C 25 B G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? B U 4 N3 ? ? ? 1_555 B A 63 N1 ? ? B U 26 B A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? B U 4 O4 ? ? ? 1_555 B A 63 N6 ? ? B U 26 B A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? B U 5 N3 ? ? ? 1_555 B A 62 N1 ? ? B U 27 B A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? B U 5 O4 ? ? ? 1_555 B A 62 N6 ? ? B U 27 B A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? B A 6 N1 ? ? ? 1_555 B U 61 N3 ? ? B A 28 B U 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? B A 6 N6 ? ? ? 1_555 B U 61 O4 ? ? B A 28 B U 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? B U 7 N3 ? ? ? 1_555 B A 60 N1 ? ? B U 29 B A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? B U 7 O4 ? ? ? 1_555 B A 60 N6 ? ? B U 29 B A 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? B A 8 N1 ? ? ? 1_555 B U 59 N3 ? ? B A 30 B U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? B A 8 N6 ? ? ? 1_555 B U 59 O4 ? ? B A 30 B U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 31 N3 ? ? B C 31 B G 53 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog82 hydrog ? ? B C 9 N3 ? ? ? 1_555 B G 37 N1 ? ? B C 31 B G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 37 O6 ? ? B C 31 B G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? B C 9 O2 ? ? ? 1_555 B G 37 N2 ? ? B C 31 B G 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? B A 10 N1 ? ? ? 1_555 B G 31 N2 ? ? B A 32 B G 53 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog86 hydrog ? ? B G 11 N2 ? ? ? 1_555 B U 30 O4 ? ? B G 33 B U 52 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog87 hydrog ? ? B G 12 N1 ? ? ? 1_555 B U 30 O2 ? ? B G 34 B U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog88 hydrog ? ? B G 12 O6 ? ? ? 1_555 B U 30 N3 ? ? B G 34 B U 52 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog89 hydrog ? ? B G 13 N1 ? ? ? 1_555 B C 29 N3 ? ? B G 35 B C 51 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog90 hydrog ? ? B U 14 N3 ? ? ? 1_555 B A 28 N1 ? ? B U 36 B A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? B U 14 O4 ? ? ? 1_555 B A 28 N6 ? ? B U 36 B A 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? B A 15 N1 ? ? ? 1_555 B U 27 N3 ? ? B A 37 B U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? B A 15 N6 ? ? ? 1_555 B U 27 O4 ? ? B A 37 B U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? B G 16 N1 ? ? ? 1_555 B C 26 N3 ? ? B G 38 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? B G 16 N2 ? ? ? 1_555 B C 26 O2 ? ? B G 38 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog96 hydrog ? ? B G 16 O6 ? ? ? 1_555 B C 26 N4 ? ? B G 38 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog97 hydrog ? ? B C 17 N3 ? ? ? 1_555 B G 25 N1 ? ? B C 39 B G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog98 hydrog ? ? B C 17 N4 ? ? ? 1_555 B G 25 O6 ? ? B C 39 B G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog99 hydrog ? ? B C 17 O2 ? ? ? 1_555 B G 25 N2 ? ? B C 39 B G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog100 hydrog ? ? B A 18 N3 ? ? ? 1_555 B A 49 N6 ? ? B A 40 B A 71 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog101 hydrog ? ? B A 20 N1 ? ? ? 1_555 B G 23 N2 ? ? B A 42 B G 45 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog102 hydrog ? ? B G 23 N1 ? ? ? 1_555 B C 47 N3 ? ? B G 45 B C 69 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog103 hydrog ? ? B G 24 N2 ? ? ? 1_555 B C 46 N3 ? ? B G 46 B C 68 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog104 hydrog ? ? B G 31 N1 ? ? ? 1_555 B G 37 O6 ? ? B G 53 B G 59 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog105 hydrog ? ? B G 31 N1 ? ? ? 1_555 B C 38 N3 ? ? B G 53 B C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog106 hydrog ? ? B G 31 N2 ? ? ? 1_555 B C 38 O2 ? ? B G 53 B C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog107 hydrog ? ? B G 31 O6 ? ? ? 1_555 B C 38 N4 ? ? B G 53 B C 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog108 hydrog ? ? B C 39 N3 ? ? ? 1_555 B G 56 N1 ? ? B C 61 B G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog109 hydrog ? ? B C 39 N4 ? ? ? 1_555 B G 56 O6 ? ? B C 61 B G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog110 hydrog ? ? B C 39 O2 ? ? ? 1_555 B G 56 N2 ? ? B C 61 B G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog111 hydrog ? ? B U 40 N3 ? ? ? 1_555 B A 55 N1 ? ? B U 62 B A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog112 hydrog ? ? B U 40 O4 ? ? ? 1_555 B A 55 N6 ? ? B U 62 B A 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog113 hydrog ? ? B U 41 N3 ? ? ? 1_555 B G 54 O6 ? ? B U 63 B G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog114 hydrog ? ? B U 41 O2 ? ? ? 1_555 B G 54 N1 ? ? B U 63 B G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog115 hydrog ? ? B C 42 O2 ? ? ? 1_555 B G 53 N2 ? ? B C 64 B G 75 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog116 hydrog ? ? B A 43 N1 ? ? ? 1_555 B U 52 N3 ? ? B A 65 B U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog117 hydrog ? ? B A 43 N6 ? ? ? 1_555 B U 52 O4 ? ? B A 65 B U 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 ? 9 'BINDING SITE FOR RESIDUE GNG A 120' AC2 Software A CS 201 ? 4 'BINDING SITE FOR RESIDUE CS A 201' AC3 Software A CS 202 ? 3 'BINDING SITE FOR RESIDUE CS A 202' AC4 Software A CS 203 ? 3 'BINDING SITE FOR RESIDUE CS A 203' AC5 Software A CS 204 ? 6 'BINDING SITE FOR RESIDUE CS A 204' AC6 Software A CS 205 ? 2 'BINDING SITE FOR RESIDUE CS A 205' AC7 Software A MG 206 ? 2 'BINDING SITE FOR RESIDUE MG A 206' AC8 Software A MG 305 ? 3 'BINDING SITE FOR RESIDUE MG A 305' AC9 Software B GNG 120 ? 9 'BINDING SITE FOR RESIDUE GNG B 120' # 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 9 A A 8 ? A A 30 . ? 1_555 ? 2 AC1 9 C A 9 ? C A 31 . ? 1_555 ? 3 AC1 9 C A 34 ? C A 56 . ? 1_555 ? 4 AC1 9 C A 35 ? C A 57 . ? 1_555 ? 5 AC1 9 C A 36 ? C A 58 . ? 1_555 ? 6 AC1 9 G A 37 ? G A 59 . ? 1_555 ? 7 AC1 9 C A 58 ? C A 80 . ? 1_555 ? 8 AC1 9 U A 59 ? U A 81 . ? 1_555 ? 9 AC1 9 CS E . ? CS A 202 . ? 1_555 ? 10 AC2 4 G A 24 ? G A 46 . ? 1_555 ? 11 AC2 4 G A 25 ? G A 47 . ? 1_555 ? 12 AC2 4 A A 49 ? A A 71 . ? 1_555 ? 13 AC2 4 U A 50 ? U A 72 . ? 1_555 ? 14 AC3 3 C A 9 ? C A 31 . ? 1_555 ? 15 AC3 3 A A 10 ? A A 32 . ? 1_555 ? 16 AC3 3 GNG C . ? GNG A 120 . ? 1_555 ? 17 AC4 3 G A 11 ? G A 33 . ? 1_555 ? 18 AC4 3 G A 12 ? G A 34 . ? 1_555 ? 19 AC4 3 G A 13 ? G A 35 . ? 1_555 ? 20 AC5 6 G A 16 ? G A 38 . ? 1_555 ? 21 AC5 6 C A 17 ? C A 39 . ? 1_555 ? 22 AC5 6 G A 25 ? G A 47 . ? 1_555 ? 23 AC5 6 C A 26 ? C A 48 . ? 1_555 ? 24 AC5 6 A A 44 ? A A 66 . ? 1_545 ? 25 AC5 6 A A 45 ? A A 67 . ? 1_545 ? 26 AC6 2 C A 46 ? C A 68 . ? 1_555 ? 27 AC6 2 U A 50 ? U A 72 . ? 1_555 ? 28 AC7 2 G A 23 ? G A 45 . ? 1_555 ? 29 AC7 2 G A 24 ? G A 46 . ? 1_555 ? 30 AC8 3 U A 41 ? U A 63 . ? 1_555 ? 31 AC8 3 G A 53 ? G A 75 . ? 1_555 ? 32 AC8 3 G A 54 ? G A 76 . ? 1_555 ? 33 AC9 9 A B 8 ? A B 30 . ? 1_555 ? 34 AC9 9 C B 9 ? C B 31 . ? 1_555 ? 35 AC9 9 C B 34 ? C B 56 . ? 1_555 ? 36 AC9 9 C B 35 ? C B 57 . ? 1_555 ? 37 AC9 9 C B 36 ? C B 58 . ? 1_555 ? 38 AC9 9 G B 37 ? G B 59 . ? 1_555 ? 39 AC9 9 C B 58 ? C B 80 . ? 1_555 ? 40 AC9 9 U B 59 ? U B 81 . ? 1_555 ? 41 AC9 9 HOH M . ? HOH B 307 . ? 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 ? ? 105.72 119.70 -13.98 1.20 Y 2 1 C6 A G 47 ? ? C5 A G 47 ? ? N7 A G 47 ? ? 126.77 130.40 -3.63 0.60 N 3 1 "C3'" B GTP 23 ? ? "O3'" B GTP 23 ? ? P B G 24 ? ? 127.57 119.70 7.87 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 ? # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 4.7059 8.6471 37.4505 0.9956 1.5067 0.7281 0.4790 0.0973 0.1147 0.0146 0.0754 0.0314 -0.0320 0.0165 -0.0475 -0.0457 -0.0090 0.0359 0.1072 0.1199 0.1281 0.2135 0.0430 -0.0284 'X-RAY DIFFRACTION' 2 ? refined 2.6500 9.2905 33.6996 0.6868 1.6470 0.7232 0.1582 0.0888 -0.1478 0.2546 0.5223 0.0826 0.1772 0.1287 0.0340 -0.0099 -0.0683 0.0087 0.1315 0.0682 0.1401 0.0547 0.0669 -0.0377 'X-RAY DIFFRACTION' 3 ? refined 30.1539 16.2886 43.5886 0.9172 1.2291 0.7468 0.2602 -0.1487 -0.1030 0.6593 0.4993 0.0493 0.2859 -0.1092 0.0651 0.1682 -0.4999 0.1323 0.1119 -0.1273 -0.2200 -0.2945 0.0970 -0.0185 'X-RAY DIFFRACTION' 4 ? refined 26.4512 5.0532 52.7252 0.9168 1.3351 0.6720 -0.0217 -0.1789 0.0512 0.0157 0.1273 0.3560 0.0463 0.0025 0.0699 0.1116 -0.1023 -0.0745 0.2757 -0.1696 -0.0530 0.2278 -0.1554 0.0362 'X-RAY DIFFRACTION' 5 ? refined 38.1615 3.0366 24.8377 0.5361 0.8928 0.5340 -0.1276 0.0264 0.1631 0.3755 0.1561 1.2519 0.1638 -0.2463 0.0405 -0.1833 -0.0453 0.0376 0.0390 -0.1022 -0.0656 0.1174 0.1101 0.1198 'X-RAY DIFFRACTION' 6 ? refined 42.2918 1.5844 24.8284 0.3333 0.8505 0.6466 -0.0263 -0.0254 -0.0678 0.2364 0.0842 0.0586 0.1359 0.1174 0.0673 0.0113 0.0105 -0.0077 0.0359 0.2386 -0.1330 -0.0901 0.2839 -0.1300 'X-RAY DIFFRACTION' 7 ? refined 17.5641 -6.3307 8.5685 0.1275 -0.2134 0.2149 0.1256 0.1597 -0.1105 0.1319 0.1464 0.0511 -0.1384 -0.0804 0.1078 -0.1607 0.0630 -0.3174 -0.0684 -0.0580 0.0286 0.1233 0.0802 -0.3238 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(chain A and resid 23:30)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(chain A and resid 81:88)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(chain A and resid 31:60)' 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? '(chain A and resid 61:80)' 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? '(chain B and resid 23:30)' 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? '(chain B and resid 81:88)' 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? '(chain B and resid 31:60)' # 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 CS CS CS N N 110 G OP3 O N N 111 G P P N N 112 G OP1 O N N 113 G OP2 O N N 114 G "O5'" O N N 115 G "C5'" C N N 116 G "C4'" C N R 117 G "O4'" O N N 118 G "C3'" C N S 119 G "O3'" O N N 120 G "C2'" C N R 121 G "O2'" O N N 122 G "C1'" C N R 123 G N9 N Y N 124 G C8 C Y N 125 G N7 N Y N 126 G C5 C Y N 127 G C6 C N N 128 G O6 O N N 129 G N1 N N N 130 G C2 C N N 131 G N2 N N N 132 G N3 N N N 133 G C4 C Y N 134 G HOP3 H N N 135 G HOP2 H N N 136 G "H5'" H N N 137 G "H5''" H N N 138 G "H4'" H N N 139 G "H3'" H N N 140 G "HO3'" H N N 141 G "H2'" H N N 142 G "HO2'" H N N 143 G "H1'" H N N 144 G H8 H N N 145 G H1 H N N 146 G H21 H N N 147 G H22 H N N 148 GNG "O5'" O N N 149 GNG "C5'" C N N 150 GNG "C4'" C N R 151 GNG "O4'" O N N 152 GNG "C1'" C N R 153 GNG N9 N Y N 154 GNG C8 C Y N 155 GNG N7 N Y N 156 GNG C5 C Y N 157 GNG C4 C Y N 158 GNG N3 N N N 159 GNG C2 C N N 160 GNG N1 N N N 161 GNG C6 C N N 162 GNG O6 O N N 163 GNG N2 N N N 164 GNG "C2'" C N N 165 GNG "C3'" C N S 166 GNG "O3'" O N N 167 GNG "H5'" H N N 168 GNG "H5'1" H N N 169 GNG "H5'2" H N N 170 GNG "H4'" H N N 171 GNG "H1'" H N N 172 GNG H8 H N N 173 GNG HN3 H N N 174 GNG HN21 H N N 175 GNG HN22 H N N 176 GNG "H2'1" H N N 177 GNG "H2'2" H N N 178 GNG "H3'" H N N 179 GNG H1 H N N 180 GTP PG P N N 181 GTP O1G O N N 182 GTP O2G O N N 183 GTP O3G O N N 184 GTP O3B O N N 185 GTP PB P N N 186 GTP O1B O N N 187 GTP O2B O N N 188 GTP O3A O N N 189 GTP PA P N N 190 GTP O1A O N N 191 GTP O2A O N N 192 GTP "O5'" O N N 193 GTP "C5'" C N N 194 GTP "C4'" C N R 195 GTP "O4'" O N N 196 GTP "C3'" C N S 197 GTP "O3'" O N N 198 GTP "C2'" C N R 199 GTP "O2'" O N N 200 GTP "C1'" C N R 201 GTP N9 N Y N 202 GTP C8 C Y N 203 GTP N7 N Y N 204 GTP C5 C Y N 205 GTP C6 C N N 206 GTP O6 O N N 207 GTP N1 N N N 208 GTP C2 C N N 209 GTP N2 N N N 210 GTP N3 N N N 211 GTP C4 C Y N 212 GTP HOG2 H N N 213 GTP HOG3 H N N 214 GTP HOB2 H N N 215 GTP HOA2 H N N 216 GTP "H5'" H N N 217 GTP "H5''" H N N 218 GTP "H4'" H N N 219 GTP "H3'" H N N 220 GTP "HO3'" H N N 221 GTP "H2'" H N N 222 GTP "HO2'" H N N 223 GTP "H1'" H N N 224 GTP H8 H N N 225 GTP HN1 H N N 226 GTP HN21 H N N 227 GTP HN22 H N N 228 HOH O O N N 229 HOH H1 H N N 230 HOH H2 H N N 231 MG MG MG N N 232 U OP3 O N N 233 U P P N N 234 U OP1 O N N 235 U OP2 O N N 236 U "O5'" O N N 237 U "C5'" C N N 238 U "C4'" C N R 239 U "O4'" O N N 240 U "C3'" C N S 241 U "O3'" O N N 242 U "C2'" C N R 243 U "O2'" O N N 244 U "C1'" C N R 245 U N1 N N N 246 U C2 C N N 247 U O2 O N N 248 U N3 N N N 249 U C4 C N N 250 U O4 O N N 251 U C5 C N N 252 U C6 C N N 253 U HOP3 H N N 254 U HOP2 H N N 255 U "H5'" H N N 256 U "H5''" H N N 257 U "H4'" H N N 258 U "H3'" H N N 259 U "HO3'" H N N 260 U "H2'" H N N 261 U "HO2'" H N N 262 U "H1'" H N N 263 U H3 H N N 264 U H5 H N N 265 U H6 H N N 266 # 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 U OP3 P sing N N 241 U OP3 HOP3 sing N N 242 U P OP1 doub N N 243 U P OP2 sing N N 244 U P "O5'" sing N N 245 U OP2 HOP2 sing N N 246 U "O5'" "C5'" sing N N 247 U "C5'" "C4'" sing N N 248 U "C5'" "H5'" sing N N 249 U "C5'" "H5''" sing N N 250 U "C4'" "O4'" sing N N 251 U "C4'" "C3'" sing N N 252 U "C4'" "H4'" sing N N 253 U "O4'" "C1'" sing N N 254 U "C3'" "O3'" sing N N 255 U "C3'" "C2'" sing N N 256 U "C3'" "H3'" sing N N 257 U "O3'" "HO3'" sing N N 258 U "C2'" "O2'" sing N N 259 U "C2'" "C1'" sing N N 260 U "C2'" "H2'" sing N N 261 U "O2'" "HO2'" sing N N 262 U "C1'" N1 sing N N 263 U "C1'" "H1'" sing N N 264 U N1 C2 sing N N 265 U N1 C6 sing N N 266 U C2 O2 doub N N 267 U C2 N3 sing N N 268 U N3 C4 sing N N 269 U N3 H3 sing N N 270 U C4 O4 doub N N 271 U C4 C5 sing N N 272 U C5 C6 doub N N 273 U C5 H5 sing N N 274 U C6 H6 sing N N 275 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3SKW 'double helix' 3SKW 'a-form double helix' 3SKW 'bulge loop' 3SKW 'mismatched base pair' 3SKW '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 -0.989 -0.575 0.260 -4.700 -2.662 -6.064 1 A_GTP23:CCC88_A A 23 ? A 88 ? 19 1 1 A G 2 1_555 A U 65 1_555 -1.076 -0.647 -0.101 -6.298 -8.633 -10.158 2 A_G24:U87_A A 24 ? A 87 ? 28 1 1 A C 3 1_555 A G 64 1_555 -0.094 -0.370 0.452 -4.296 -10.301 -3.496 3 A_C25:G86_A A 25 ? A 86 ? 19 1 1 A U 4 1_555 A A 63 1_555 0.573 -0.530 0.942 -10.468 -8.261 -4.918 4 A_U26:A85_A A 26 ? A 85 ? 20 1 1 A U 5 1_555 A A 62 1_555 0.097 -0.462 0.309 -5.484 -10.074 -3.108 5 A_U27:A84_A A 27 ? A 84 ? 20 1 1 A A 6 1_555 A U 61 1_555 -0.225 0.234 0.208 -8.609 -17.483 6.667 6 A_A28:U83_A A 28 ? A 83 ? ? ? 1 A U 7 1_555 A A 60 1_555 0.327 -0.324 0.128 -6.186 -8.061 -1.366 7 A_U29:A82_A A 29 ? A 82 ? 20 1 1 A A 8 1_555 A U 59 1_555 -0.486 -0.372 0.319 6.820 -3.945 -8.357 8 A_A30:U81_A A 30 ? A 81 ? 20 1 1 A G 25 1_555 A C 17 1_555 0.812 -0.508 0.629 2.199 -6.025 -1.106 9 A_G47:C39_A A 47 ? A 39 ? 19 1 1 A C 26 1_555 A G 16 1_555 1.505 -0.636 0.503 0.238 6.544 -8.089 10 A_C48:G38_A A 48 ? A 38 ? 19 1 1 A U 27 1_555 A A 15 1_555 0.474 -0.518 0.273 -0.720 -0.509 1.944 11 A_U49:A37_A A 49 ? A 37 ? 20 1 1 A A 28 1_555 A U 14 1_555 0.236 -0.114 0.912 10.426 -2.941 -19.228 12 A_A50:U36_A A 50 ? A 36 ? 20 1 1 A C 29 1_555 A G 13 1_555 1.674 -0.455 0.378 2.009 -17.508 -0.325 13 A_C51:G35_A A 51 ? A 35 ? 19 1 1 A U 30 1_555 A G 12 1_555 2.988 -0.771 0.047 -9.193 -4.616 4.161 14 A_U52:G34_A A 52 ? A 34 ? 28 1 1 A G 31 1_555 A C 38 1_555 0.364 -0.036 0.473 5.584 -8.395 -2.937 15 A_G53:C60_A A 53 ? A 60 ? 19 1 1 A C 9 1_555 A G 37 1_555 0.521 -0.333 -0.375 7.935 -18.518 -4.495 16 A_C31:G59_A A 31 ? A 59 ? 19 1 1 A G 23 1_555 A C 47 1_555 0.003 -0.379 0.238 -10.531 5.425 -1.579 17 A_G45:C69_A A 45 ? A 69 ? 19 1 1 A G 24 1_555 A C 46 1_555 -0.009 -0.428 0.265 -5.042 -6.883 0.758 18 A_G46:C68_A A 46 ? A 68 ? 19 1 1 A U 50 1_555 A A 45 1_555 -0.149 0.457 0.197 0.181 -6.621 22.892 19 A_U72:A67_A A 72 ? A 67 ? ? 1 1 A U 51 1_555 A A 44 1_555 0.360 -0.129 0.237 1.912 -14.733 -0.958 20 A_U73:A66_A A 73 ? A 66 ? 20 1 1 A U 52 1_555 A A 43 1_555 -0.390 -0.120 -0.347 -1.489 -13.278 -0.104 21 A_U74:A65_A A 74 ? A 65 ? 20 1 1 A G 53 1_555 A C 42 1_555 0.137 -0.345 -0.044 -2.899 -9.650 -2.339 22 A_G75:C64_A A 75 ? A 64 ? 19 1 1 A G 54 1_555 A U 41 1_555 -1.194 -0.745 0.113 4.165 -1.659 -20.046 23 A_G76:U63_A A 76 ? A 63 ? 28 1 1 A A 55 1_555 A U 40 1_555 0.252 0.025 0.244 5.119 -5.383 1.765 24 A_A77:U62_A A 77 ? A 62 ? 20 1 1 A G 56 1_555 A C 39 1_555 -0.076 -0.283 0.106 -5.856 -10.429 -6.712 25 A_G78:C61_A A 78 ? A 61 ? 19 1 1 B GTP 1 1_555 B CCC 66 1_555 -0.707 0.658 0.206 -6.007 -12.221 15.800 26 B_GTP23:CCC88_B B 23 ? B 88 ? ? ? 1 B G 2 1_555 B U 65 1_555 -1.653 -0.631 -0.341 2.203 -10.573 -0.982 27 B_G24:U87_B B 24 ? B 87 ? 28 1 1 B C 3 1_555 B G 64 1_555 -0.048 -0.065 0.016 0.737 -23.219 -2.797 28 B_C25:G86_B B 25 ? B 86 ? 19 1 1 B U 4 1_555 B A 63 1_555 0.516 -0.467 0.849 -9.079 -4.258 -7.761 29 B_U26:A85_B B 26 ? B 85 ? 20 1 1 B U 5 1_555 B A 62 1_555 -0.160 -0.149 -0.527 1.774 -21.652 2.365 30 B_U27:A84_B B 27 ? B 84 ? 20 1 1 B A 6 1_555 B U 61 1_555 0.014 -0.164 0.617 -6.915 -0.006 -0.849 31 B_A28:U83_B B 28 ? B 83 ? 20 1 1 B U 7 1_555 B A 60 1_555 -0.928 -0.325 0.550 -7.563 -11.602 -3.166 32 B_U29:A82_B B 29 ? B 82 ? 20 1 1 B A 8 1_555 B U 59 1_555 -0.203 0.123 -0.946 -15.977 -19.550 0.069 33 B_A30:U81_B B 30 ? B 81 ? 20 1 1 B G 37 1_555 B C 9 1_555 0.535 -0.011 -0.080 -15.486 -3.328 -1.523 34 B_G59:C31_B B 59 ? B 31 ? 19 1 1 B C 38 1_555 B G 31 1_555 0.330 0.203 0.441 0.962 -16.083 -4.863 35 B_C60:G53_B B 60 ? B 53 ? 19 1 1 B G 12 1_555 B U 30 1_555 -2.845 -0.647 0.708 15.334 -7.321 4.628 36 B_G34:U52_B B 34 ? B 52 ? 28 1 1 B G 13 1_555 B C 29 1_555 -0.207 0.146 0.161 -9.284 -13.974 13.274 37 B_G35:C51_B B 35 ? B 51 ? ? 1 1 B U 14 1_555 B A 28 1_555 -0.823 -0.299 1.169 -17.208 -0.312 1.969 38 B_U36:A50_B B 36 ? B 50 ? 20 1 1 B A 15 1_555 B U 27 1_555 0.515 0.161 0.748 19.142 5.712 -7.534 39 B_A37:U49_B B 37 ? B 49 ? 20 1 1 B G 16 1_555 B C 26 1_555 0.000 0.221 -0.145 9.604 -3.798 -3.458 40 B_G38:C48_B B 38 ? B 48 ? 19 1 1 B C 17 1_555 B G 25 1_555 -0.093 0.065 -0.754 16.913 -8.140 2.456 41 B_C39:G47_B B 39 ? B 47 ? 19 1 1 B A 18 1_555 B A 49 1_555 3.664 -4.355 -2.320 10.908 27.834 -68.973 42 B_A40:A71_B B 40 ? B 71 ? ? 10 1 B G 23 1_555 B C 47 1_555 0.372 0.352 0.234 -16.542 -8.071 -19.752 43 B_G45:C69_B B 45 ? B 69 ? ? 1 1 B G 24 1_555 B C 46 1_555 1.329 0.324 0.587 1.868 -20.953 -11.072 44 B_G46:C68_B B 46 ? B 68 ? ? 1 1 B C 39 1_555 B G 56 1_555 -1.005 -0.334 -0.324 5.517 -5.098 -11.662 45 B_C61:G78_B B 61 ? B 78 ? 19 1 1 B U 40 1_555 B A 55 1_555 -0.161 0.147 0.048 -5.008 5.447 -7.161 46 B_U62:A77_B B 62 ? B 77 ? 20 1 1 B U 41 1_555 B G 54 1_555 1.267 -0.391 -0.196 11.516 -2.611 3.095 47 B_U63:G76_B B 63 ? B 76 ? 28 1 1 B C 42 1_555 B G 53 1_555 -0.520 0.284 -0.225 7.209 -12.409 18.257 48 B_C64:G75_B B 64 ? B 75 ? ? 1 1 B A 43 1_555 B U 52 1_555 -0.167 0.047 0.282 3.969 5.761 -16.411 49 B_A65:U74_B B 65 ? B 74 ? 20 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 -0.388 -1.998 3.269 -4.779 9.045 39.431 -3.818 0.059 2.790 13.139 6.943 40.685 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 0.117 -1.722 2.972 -4.882 3.647 37.658 -3.043 -0.724 2.763 5.605 7.503 38.130 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 -0.112 -1.643 3.172 -2.619 10.768 38.616 -3.510 -0.107 2.641 15.888 3.864 40.116 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 0.161 -1.207 2.933 2.922 0.784 27.766 -2.668 0.289 2.900 1.627 -6.067 27.927 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 0.122 -1.136 3.060 -0.624 9.956 33.160 -3.273 -0.291 2.617 16.973 1.063 34.588 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 -0.500 -0.937 3.314 -0.223 3.092 36.805 -1.898 0.759 3.231 4.887 0.352 36.931 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 -0.180 -1.866 2.899 2.632 13.206 24.387 -6.243 0.845 1.659 28.638 -5.709 27.808 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 -0.558 -2.076 3.260 3.791 6.897 30.734 -4.967 1.664 2.657 12.752 -7.009 31.702 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 0.169 -1.812 3.060 3.768 4.277 22.721 -5.756 0.720 2.670 10.643 -9.376 23.416 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 -1.162 -1.475 2.871 -5.159 4.211 28.939 -3.656 1.317 2.794 8.288 10.154 29.679 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 0.640 -1.902 3.268 5.755 10.618 44.121 -3.332 -0.347 2.819 13.829 -7.496 45.664 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 0.207 -1.778 3.583 2.407 -0.671 39.483 -2.540 0.004 3.618 -0.991 -3.559 39.558 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 2.561 -2.366 2.667 2.762 5.102 50.000 -3.075 -2.854 2.559 6.012 -3.256 50.314 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 -1.957 -0.876 2.860 -0.116 7.821 53.489 -1.378 2.149 2.720 8.637 0.128 54.016 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 0.502 -2.274 2.955 3.857 6.213 30.409 -5.215 -0.314 2.496 11.635 -7.223 31.256 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 -0.471 -2.542 3.126 0.555 3.788 26.903 -6.270 1.128 2.739 8.090 -1.186 27.169 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 -1.384 -1.053 3.256 -5.320 -3.621 34.355 -1.183 1.466 3.514 -6.064 8.910 34.934 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 -0.256 -1.387 3.218 4.012 11.788 34.182 -3.730 0.923 2.571 19.280 -6.561 36.315 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 -0.349 -1.613 3.350 -3.142 10.384 22.689 -6.550 -0.056 2.415 24.665 7.463 25.118 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 0.145 -2.132 3.063 -4.852 3.983 28.193 -5.063 -1.250 2.680 8.051 9.808 28.869 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 0.445 -2.233 3.231 1.485 1.700 35.018 -3.951 -0.522 3.139 2.822 -2.464 35.089 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 0.662 -2.394 3.340 3.422 10.086 29.765 -6.116 -0.634 2.476 18.890 -6.409 31.573 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 -0.714 -1.359 2.688 -9.282 14.098 29.389 -4.088 0.076 1.983 25.327 16.676 33.799 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 -0.644 -1.383 3.198 -2.357 2.436 38.742 -2.365 0.689 3.141 3.663 3.545 38.884 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 -0.276 -1.887 3.350 -8.347 8.346 37.737 -3.753 -0.551 2.880 12.534 12.535 39.476 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 -0.065 -1.079 2.894 12.211 -0.142 32.170 -1.807 1.800 2.697 -0.245 -21.111 34.352 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 0.282 -1.119 3.184 -10.471 12.034 33.712 -3.212 -1.711 2.467 19.456 16.928 37.196 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 -0.002 -1.919 3.195 1.225 8.143 29.327 -5.121 0.225 2.579 15.697 -2.361 30.437 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 0.325 -0.824 3.711 14.046 17.456 32.278 -3.551 1.381 2.837 27.635 -22.236 39.121 29 BB_U29A30:U81A82_BB B 29 ? B 82 ? B 30 ? B 81 ? 1 B G 37 1_555 B C 9 1_555 B C 38 1_555 B G 31 1_555 2.341 -0.784 2.562 5.097 9.615 56.572 -1.228 -2.213 2.593 10.042 -5.323 57.525 30 BB_G59C60:G53C31_BB B 59 ? B 31 ? B 60 ? B 53 ? 1 B C 38 1_555 B G 31 1_555 B G 12 1_555 B U 30 1_555 -2.445 -2.036 2.478 -4.270 3.650 46.434 -2.799 2.808 2.523 4.610 5.392 46.754 31 BB_C60G34:U52G53_BB B 60 ? B 53 ? B 34 ? B 52 ? 1 B G 12 1_555 B U 30 1_555 B G 13 1_555 B C 29 1_555 -0.167 -1.212 3.537 -0.976 6.483 47.284 -2.046 0.123 3.355 8.038 1.210 47.710 32 BB_G34G35:C51U52_BB B 34 ? B 52 ? B 35 ? B 51 ? 1 B G 13 1_555 B C 29 1_555 B U 14 1_555 B A 28 1_555 -0.751 -1.658 3.227 -11.084 12.336 25.851 -5.397 -0.610 2.344 24.611 22.113 30.636 33 BB_G35U36:A50C51_BB B 35 ? B 51 ? B 36 ? B 50 ? 1 B U 14 1_555 B A 28 1_555 B A 15 1_555 B U 27 1_555 0.015 -1.146 2.045 3.233 -7.517 39.402 -1.106 0.219 2.213 -11.006 -4.733 40.209 34 BB_U36A37:U49A50_BB B 36 ? B 50 ? B 37 ? B 49 ? 1 B A 15 1_555 B U 27 1_555 B G 16 1_555 B C 26 1_555 -0.105 -2.150 3.597 6.481 6.405 28.367 -5.561 1.596 2.956 12.662 -12.814 29.766 35 BB_A37G38:C48U49_BB B 37 ? B 49 ? B 38 ? B 48 ? 1 B G 16 1_555 B C 26 1_555 B C 17 1_555 B G 25 1_555 0.969 -1.977 2.943 5.837 5.941 33.120 -4.193 -0.843 2.686 10.221 -10.043 34.123 36 BB_G38C39:G47C48_BB B 38 ? B 48 ? B 39 ? B 47 ? 1 B C 17 1_555 B G 25 1_555 B A 18 1_555 B A 49 1_555 -1.269 -0.476 4.306 8.585 -6.675 72.237 -0.117 1.432 4.178 -5.630 -7.242 72.941 37 BB_C39A40:A71G47_BB B 39 ? B 47 ? B 40 ? B 71 ? 1 B G 23 1_555 B C 47 1_555 B G 24 1_555 B C 46 1_555 0.607 -1.854 2.669 4.289 7.389 39.168 -3.363 -0.506 2.346 10.866 -6.307 40.053 38 BB_G45G46:C68C69_BB B 45 ? B 69 ? B 46 ? B 68 ? 1 B C 39 1_555 B G 56 1_555 B U 40 1_555 B A 55 1_555 -0.041 -2.688 3.562 -6.776 9.898 40.602 -4.741 -0.637 2.831 13.902 9.517 42.265 39 BB_C61U62:A77G78_BB B 61 ? B 78 ? B 62 ? B 77 ? 1 B U 40 1_555 B A 55 1_555 B U 41 1_555 B G 54 1_555 0.341 -1.435 2.805 0.365 -1.269 29.628 -2.572 -0.599 2.867 -2.480 -0.713 29.656 40 BB_U62U63:G76A77_BB B 62 ? B 77 ? B 63 ? B 76 ? 1 B U 41 1_555 B G 54 1_555 B C 42 1_555 B G 53 1_555 0.850 -2.514 2.981 3.142 7.937 28.955 -6.166 -1.105 2.304 15.454 -6.118 30.161 41 BB_U63C64:G75G76_BB B 63 ? B 76 ? B 64 ? B 75 ? 1 B C 42 1_555 B G 53 1_555 B A 43 1_555 B U 52 1_555 -1.761 -1.815 3.196 -2.831 12.941 30.324 -5.152 2.669 2.394 23.387 5.116 33.029 42 BB_C64A65:U74G75_BB B 64 ? B 75 ? B 65 ? B 74 ? # _atom_sites.entry_id 3SKW _atom_sites.fract_transf_matrix[1][1] 0.009768 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000885 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028237 _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] 0.008419 _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 CS MG N O P # loop_