data_3SKL # _entry.id 3SKL # _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 3SKL pdb_00003skl 10.2210/pdb3skl/pdb NDB NA1179 ? ? RCSB RCSB066317 ? ? WWPDB D_1000066317 ? ? # 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 # _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' # 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 # 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3SKL _pdbx_database_status.recvd_initial_deposition_date 2011-06-22 _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 3SKR . 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 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 6 ? ? ? ? 4 non-polymer syn 'IRIDIUM HEXAMMINE ION' 294.400 10 ? ? ? ? 5 water nat water 18.015 5 ? ? ? ? # _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 'MAGNESIUM ION' MG 4 'IRIDIUM HEXAMMINE ION' IRI 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 # 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 IRI non-polymer . 'IRIDIUM HEXAMMINE ION' ? 'H18 Ir N6 3' 294.400 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 22 22 GTP GTP A . n A 1 2 G 2 23 23 G G A . n A 1 3 C 3 24 24 C C A . n A 1 4 U 4 25 25 U U A . n A 1 5 U 5 26 26 U U A . n A 1 6 A 6 27 27 A A A . n A 1 7 U 7 28 28 U U A . n A 1 8 A 8 29 29 A A A . n A 1 9 C 9 30 30 C C A . n A 1 10 A 10 31 31 A A A . n A 1 11 G 11 32 32 G G A . n A 1 12 G 12 33 33 G G A . n A 1 13 G 13 34 34 G G A . n A 1 14 U 14 35 35 U U A . n A 1 15 A 15 36 36 A A A . n A 1 16 G 16 37 37 G G A . n A 1 17 C 17 38 38 C C A . n A 1 18 A 18 39 39 A A A . n A 1 19 U 19 40 40 U U A . n A 1 20 A 20 41 41 A A A . n A 1 21 A 21 42 42 A A A . n A 1 22 U 22 43 43 U U A . n A 1 23 G 23 44 44 G G A . n A 1 24 G 24 45 45 G G A . n A 1 25 G 25 46 46 G G A . n A 1 26 C 26 47 47 C C A . n A 1 27 U 27 48 48 U U A . n A 1 28 A 28 49 49 A A A . n A 1 29 C 29 50 50 C C A . n A 1 30 U 30 51 51 U U A . n A 1 31 G 31 52 52 G G A . n A 1 32 A 32 53 53 A A A . n A 1 33 C 33 54 54 C C A . n A 1 34 C 34 55 55 C C A . n A 1 35 C 35 56 56 C C A . n A 1 36 C 36 57 57 C C A . n A 1 37 G 37 58 58 G G A . n A 1 38 C 38 59 59 C C A . n A 1 39 C 39 60 60 C C A . n A 1 40 U 40 61 61 U U A . n A 1 41 U 41 62 62 U U A . n A 1 42 C 42 63 63 C C A . n A 1 43 A 43 64 64 A A A . n A 1 44 A 44 65 65 A A A . n A 1 45 A 45 66 66 A A A . n A 1 46 C 46 67 67 C C A . n A 1 47 C 47 68 68 C C A . n A 1 48 U 48 69 69 U U A . n A 1 49 A 49 70 70 A A A . n A 1 50 U 50 71 71 U U A . n A 1 51 U 51 72 72 U U A . n A 1 52 U 52 73 73 U U A . n A 1 53 G 53 74 74 G G A . n A 1 54 G 54 75 75 G G A . n A 1 55 A 55 76 76 A A A . n A 1 56 G 56 77 77 G G A . n A 1 57 A 57 78 78 A A A . n A 1 58 C 58 79 79 C C A . n A 1 59 U 59 80 80 U U A . n A 1 60 A 60 81 81 A A A . n A 1 61 U 61 82 82 U U A . n A 1 62 A 62 83 83 A A A . n A 1 63 A 63 84 84 A A A . n A 1 64 G 64 85 85 G G A . n A 1 65 U 65 86 86 U U A . n A 1 66 CCC 66 87 87 CCC CCC A . n B 1 1 GTP 1 22 22 GTP GTP B . n B 1 2 G 2 23 23 G G B . n B 1 3 C 3 24 24 C C B . n B 1 4 U 4 25 25 U U B . n B 1 5 U 5 26 26 U U B . n B 1 6 A 6 27 27 A A B . n B 1 7 U 7 28 28 U U B . n B 1 8 A 8 29 29 A A B . n B 1 9 C 9 30 30 C C B . n B 1 10 A 10 31 31 A A B . n B 1 11 G 11 32 32 G G B . n B 1 12 G 12 33 33 G G B . n B 1 13 G 13 34 34 G G B . n B 1 14 U 14 35 35 U U B . n B 1 15 A 15 36 36 A A B . n B 1 16 G 16 37 37 G G B . n B 1 17 C 17 38 38 C C B . n B 1 18 A 18 39 39 A A B . n B 1 19 U 19 40 40 U U B . n B 1 20 A 20 41 41 A A B . n B 1 21 A 21 42 42 A A B . n B 1 22 U 22 43 43 U U B . n B 1 23 G 23 44 44 G G B . n B 1 24 G 24 45 45 G G B . n B 1 25 G 25 46 46 G G B . n B 1 26 C 26 47 47 C C B . n B 1 27 U 27 48 48 U U B . n B 1 28 A 28 49 49 A A B . n B 1 29 C 29 50 50 C C B . n B 1 30 U 30 51 51 U U B . n B 1 31 G 31 52 52 G G B . n B 1 32 A 32 53 53 A A B . n B 1 33 C 33 54 54 C C B . n B 1 34 C 34 55 55 C C B . n B 1 35 C 35 56 56 C C B . n B 1 36 C 36 57 57 C C B . n B 1 37 G 37 58 58 G G B . n B 1 38 C 38 59 59 C C B . n B 1 39 C 39 60 60 C C B . n B 1 40 U 40 61 61 U U B . n B 1 41 U 41 62 62 U U B . n B 1 42 C 42 63 63 C C B . n B 1 43 A 43 64 64 A A B . n B 1 44 A 44 65 65 A A B . n B 1 45 A 45 66 66 A A B . n B 1 46 C 46 67 67 C C B . n B 1 47 C 47 68 68 C C B . n B 1 48 U 48 69 69 U U B . n B 1 49 A 49 70 70 A A B . n B 1 50 U 50 71 71 U U B . n B 1 51 U 51 72 72 U U B . n B 1 52 U 52 73 73 U U B . n B 1 53 G 53 74 74 G G B . n B 1 54 G 54 75 75 G G B . n B 1 55 A 55 76 76 A A B . n B 1 56 G 56 77 77 G G B . n B 1 57 A 57 78 78 A A B . n B 1 58 C 58 79 79 C C B . n B 1 59 U 59 80 80 U U B . n B 1 60 A 60 81 81 A A B . n B 1 61 U 61 82 82 U U B . n B 1 62 A 62 83 83 A A B . n B 1 63 A 63 84 84 A A B . n B 1 64 G 64 85 85 G G B . n B 1 65 U 65 86 86 U U B . n B 1 66 CCC 66 87 87 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 MG 1 201 201 MG MG A . E 4 IRI 1 402 402 IRI IRI A . F 4 IRI 1 403 403 IRI IRI A . G 4 IRI 1 405 405 IRI IRI A . H 4 IRI 1 409 409 IRI IRI A . I 4 IRI 1 411 411 IRI IRI A . J 2 GNG 1 120 120 GNG GNG B . K 3 MG 1 202 202 MG MG B . L 3 MG 1 203 203 MG MG B . M 3 MG 1 204 204 MG MG B . N 3 MG 1 205 205 MG MG B . O 3 MG 1 206 206 MG MG B . P 4 IRI 1 404 404 IRI IRI B . Q 4 IRI 1 406 406 IRI IRI B . R 4 IRI 1 407 407 IRI IRI B . S 4 IRI 1 408 408 IRI IRI B . T 4 IRI 1 410 410 IRI IRI B . U 5 HOH 1 501 501 HOH HOH A . U 5 HOH 2 503 503 HOH HOH A . U 5 HOH 3 505 505 HOH HOH A . V 5 HOH 1 502 502 HOH HOH B . V 5 HOH 2 504 504 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHENIX 'model building' . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 3SKL _cell.length_a 98.002 _cell.length_b 34.955 _cell.length_c 111.057 _cell.angle_alpha 90.00 _cell.angle_beta 92.45 _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 3SKL _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 3SKL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.22 _exptl_crystal.density_percent_sol 44.68 _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 potassium chloride and 0.0-2.0 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 2010-02-03 _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 1.1052 _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 1.1052 # _reflns.entry_id 3SKL _reflns.observed_criterion_sigma_I 3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 2.9 _reflns.number_obs 8487 _reflns.number_all 8590 _reflns.percent_possible_obs 98.8 _reflns.pdbx_Rmerge_I_obs 0.102 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.5 _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 2.9 _reflns_shell.d_res_low 3.0 _reflns_shell.percent_possible_all 92.3 _reflns_shell.Rmerge_I_obs 0.18 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 5.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 764 _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 3SKL _refine.ls_number_reflns_obs 8178 _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 2.90 _refine.ls_percent_reflns_obs 99.61 _refine.ls_R_factor_obs 0.22079 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21863 _refine.ls_R_factor_R_free 0.26371 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 405 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.948 _refine.correlation_coeff_Fo_to_Fc_free 0.926 _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 SAD _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 0.467 _refine.overall_SU_ML 0.454 _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 2826 _refine_hist.pdbx_number_atoms_ligand 114 _refine_hist.number_atoms_solvent 5 _refine_hist.number_atoms_total 2945 _refine_hist.d_res_high 2.90 _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 ? 3264 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.008 3.000 ? 5124 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.003 0.020 ? 1382 ? 'X-RAY DIFFRACTION' r_nbd_refined 0.170 0.200 ? 1255 ? 'X-RAY DIFFRACTION' r_nbtor_refined 0.280 0.200 ? 1969 ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined 0.150 0.200 ? 99 ? 'X-RAY DIFFRACTION' r_metal_ion_refined 0.011 0.200 ? 1 ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined 0.183 0.200 ? 33 ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined 0.225 0.200 ? 4 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.900 _refine_ls_shell.d_res_low 2.974 _refine_ls_shell.number_reflns_R_work 551 _refine_ls_shell.R_factor_R_work 0.306 _refine_ls_shell.percent_reflns_obs 96.14 _refine_ls_shell.R_factor_R_free 0.476 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _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 3SKL _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 3SKL _struct.title ;Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'-deoxyguanosine, iridium hexammine soak ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3SKL _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 4 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 2 ? K N N 3 ? L N N 3 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 4 ? Q N N 4 ? R N N 4 ? S N N 4 ? T N N 4 ? U N N 5 ? V N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3SKL _struct_ref.pdbx_db_accession 3SKL _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 3SKL A 1 ? 66 ? 3SKL 22 ? 87 ? 22 87 2 1 3SKL B 1 ? 66 ? 3SKL 22 ? 87 ? 22 87 # 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,U 2 1 B,J,K,L,M,N,O,P,Q,R,S,T,V # _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 22 A G 23 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale2 covale both ? A U 65 "O3'" ? ? ? 1_555 A CCC 66 P ? ? A U 86 A CCC 87 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale3 covale both ? B GTP 1 "O3'" ? ? ? 1_555 B G 2 P ? ? B GTP 22 B G 23 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale4 covale both ? B U 65 "O3'" ? ? ? 1_555 B CCC 66 P ? ? B U 86 B CCC 87 1_555 ? ? ? ? ? ? ? 1.596 ? ? hydrog1 hydrog ? ? A GTP 1 N1 ? ? ? 1_555 A CCC 66 N3 ? ? A GTP 22 A CCC 87 1_555 ? ? ? ? ? ? 'GTP-CCC PAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 65 O2 ? ? A G 23 A U 86 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 65 N3 ? ? A G 23 A U 86 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 64 N1 ? ? A C 24 A G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 64 O6 ? ? A C 24 A G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 64 N2 ? ? A C 24 A G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 63 N1 ? ? A U 25 A A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 63 N6 ? ? A U 25 A A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 62 N1 ? ? A U 26 A A 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 62 N6 ? ? A U 26 A A 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 61 N3 ? ? A A 27 A U 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 61 O4 ? ? A A 27 A U 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 60 N1 ? ? A U 28 A A 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 60 N6 ? ? A U 28 A A 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 59 N3 ? ? A A 29 A U 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 59 O4 ? ? A A 29 A U 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 37 N2 ? ? A C 30 A G 58 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog18 hydrog ? ? A G 11 N2 ? ? ? 1_555 A G 12 O6 ? ? A G 32 A G 33 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog19 hydrog ? ? A G 11 N2 ? ? ? 1_555 A U 30 O4 ? ? A G 32 A U 51 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog20 hydrog ? ? A G 12 N1 ? ? ? 1_555 A U 30 O2 ? ? A G 33 A U 51 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 12 O6 ? ? ? 1_555 A U 30 N3 ? ? A G 33 A U 51 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 34 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 34 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 34 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 35 A A 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 35 A A 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 15 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 36 A U 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 15 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 36 A U 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 16 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 37 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 16 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 37 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 16 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 37 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 17 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 38 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 17 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 38 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 17 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 38 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 20 N1 ? ? ? 1_555 A G 23 N2 ? ? A A 41 A G 44 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog36 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 47 N3 ? ? A G 44 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 47 O2 ? ? A G 44 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 47 N4 ? ? A G 44 A C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 24 N1 ? ? ? 1_555 A C 46 N3 ? ? A G 45 A C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 24 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 45 A C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 24 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 45 A C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 52 A C 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 52 A C 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 52 A C 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 35 N4 ? ? ? 1_555 A U 59 O2 ? ? A C 56 A U 80 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog46 hydrog ? ? A C 39 N3 ? ? ? 1_555 A G 56 N1 ? ? A C 60 A G 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 39 N4 ? ? ? 1_555 A G 56 O6 ? ? A C 60 A G 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 39 O2 ? ? ? 1_555 A G 56 N2 ? ? A C 60 A G 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A U 40 N3 ? ? ? 1_555 A A 55 N1 ? ? A U 61 A A 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A U 40 O4 ? ? ? 1_555 A A 55 N6 ? ? A U 61 A A 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A U 41 N3 ? ? ? 1_555 A G 54 O6 ? ? A U 62 A G 75 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog52 hydrog ? ? A U 41 O2 ? ? ? 1_555 A G 54 N1 ? ? A U 62 A G 75 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog53 hydrog ? ? A C 42 N4 ? ? ? 1_555 A G 53 O6 ? ? A C 63 A G 74 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog54 hydrog ? ? A A 43 N1 ? ? ? 1_555 A U 52 N3 ? ? A A 64 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A A 43 N6 ? ? ? 1_555 A U 52 O4 ? ? A A 64 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A A 44 N1 ? ? ? 1_555 A U 51 N3 ? ? A A 65 A U 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A A 44 N6 ? ? ? 1_555 A U 51 O4 ? ? A A 65 A U 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A A 45 N1 ? ? ? 1_555 A U 50 N3 ? ? A A 66 A U 71 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog59 hydrog ? ? B GTP 1 N1 ? ? ? 1_555 B CCC 66 N3 ? ? B GTP 22 B CCC 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B GTP 1 N2 ? ? ? 1_555 B CCC 66 O2 ? ? B GTP 22 B CCC 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B GTP 1 O6 ? ? ? 1_555 B CCC 66 N4 ? ? B GTP 22 B CCC 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B G 2 N1 ? ? ? 1_555 B U 65 O2 ? ? B G 23 B U 86 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog63 hydrog ? ? B G 2 O6 ? ? ? 1_555 B U 65 N3 ? ? B G 23 B U 86 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog64 hydrog ? ? B C 3 N3 ? ? ? 1_555 B G 64 N1 ? ? B C 24 B G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B C 3 N4 ? ? ? 1_555 B G 64 O6 ? ? B C 24 B G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B C 3 O2 ? ? ? 1_555 B G 64 N2 ? ? B C 24 B G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? B U 4 N3 ? ? ? 1_555 B A 63 N1 ? ? B U 25 B A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? B U 4 O4 ? ? ? 1_555 B A 63 N6 ? ? B U 25 B A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? B U 5 N3 ? ? ? 1_555 B A 62 N1 ? ? B U 26 B A 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? B U 5 O4 ? ? ? 1_555 B A 62 N6 ? ? B U 26 B A 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? B A 6 N1 ? ? ? 1_555 B U 61 N3 ? ? B A 27 B U 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? B A 6 N6 ? ? ? 1_555 B U 61 O4 ? ? B A 27 B U 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? B U 7 N3 ? ? ? 1_555 B A 60 N1 ? ? B U 28 B A 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? B U 7 O4 ? ? ? 1_555 B A 60 N6 ? ? B U 28 B A 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? B A 8 N1 ? ? ? 1_555 B U 59 N3 ? ? B A 29 B U 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? B A 8 N6 ? ? ? 1_555 B U 59 O4 ? ? B A 29 B U 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 31 N3 ? ? B C 30 B G 52 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog78 hydrog ? ? B C 9 N3 ? ? ? 1_555 B G 37 N1 ? ? B C 30 B G 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 37 O6 ? ? B C 30 B G 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? B C 9 O2 ? ? ? 1_555 B G 37 N2 ? ? B C 30 B G 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? B G 11 N2 ? ? ? 1_555 B G 12 O6 ? ? B G 32 B G 33 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog82 hydrog ? ? B G 11 N2 ? ? ? 1_555 B U 30 O4 ? ? B G 32 B U 51 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog83 hydrog ? ? B G 12 N1 ? ? ? 1_555 B U 30 O2 ? ? B G 33 B U 51 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog84 hydrog ? ? B G 12 O6 ? ? ? 1_555 B U 30 N3 ? ? B G 33 B U 51 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog85 hydrog ? ? B G 13 N1 ? ? ? 1_555 B C 29 N3 ? ? B G 34 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? B G 13 N2 ? ? ? 1_555 B C 29 O2 ? ? B G 34 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? B G 13 O6 ? ? ? 1_555 B C 29 N4 ? ? B G 34 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? B U 14 N3 ? ? ? 1_555 B A 28 N1 ? ? B U 35 B A 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? B U 14 O4 ? ? ? 1_555 B A 28 N6 ? ? B U 35 B A 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? B A 15 N1 ? ? ? 1_555 B U 27 N3 ? ? B A 36 B U 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? B A 15 N6 ? ? ? 1_555 B U 27 O4 ? ? B A 36 B U 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? B G 16 N1 ? ? ? 1_555 B C 26 N3 ? ? B G 37 B C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? B G 16 N2 ? ? ? 1_555 B C 26 O2 ? ? B G 37 B C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? B G 16 O6 ? ? ? 1_555 B C 26 N4 ? ? B G 37 B C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? B C 17 O2 ? ? ? 1_555 B G 25 N2 ? ? B C 38 B G 46 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog96 hydrog ? ? B A 20 N1 ? ? ? 1_555 B G 23 N2 ? ? B A 41 B G 44 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog97 hydrog ? ? B G 23 N1 ? ? ? 1_555 B C 47 N3 ? ? B G 44 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog98 hydrog ? ? B G 23 N2 ? ? ? 1_555 B C 47 O2 ? ? B G 44 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog99 hydrog ? ? B G 23 O6 ? ? ? 1_555 B C 47 N4 ? ? B G 44 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog100 hydrog ? ? B G 24 N1 ? ? ? 1_555 B C 46 N3 ? ? B G 45 B C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog101 hydrog ? ? B G 24 N2 ? ? ? 1_555 B C 46 O2 ? ? B G 45 B C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog102 hydrog ? ? B G 24 O6 ? ? ? 1_555 B C 46 N4 ? ? B G 45 B C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog103 hydrog ? ? B G 24 N1 ? ? ? 1_555 B C 47 N3 ? ? B G 45 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog104 hydrog ? ? B G 24 N2 ? ? ? 1_555 B C 47 O2 ? ? B G 45 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog105 hydrog ? ? B G 24 O6 ? ? ? 1_555 B C 47 N4 ? ? B G 45 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog106 hydrog ? ? B G 31 N1 ? ? ? 1_555 B C 38 N3 ? ? B G 52 B C 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog107 hydrog ? ? B G 31 N2 ? ? ? 1_555 B C 38 O2 ? ? B G 52 B C 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog108 hydrog ? ? B G 31 O6 ? ? ? 1_555 B C 38 N4 ? ? B G 52 B C 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog109 hydrog ? ? B C 35 N4 ? ? ? 1_555 B U 59 O2 ? ? B C 56 B U 80 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog110 hydrog ? ? B C 39 N3 ? ? ? 1_555 B G 56 N1 ? ? B C 60 B G 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog111 hydrog ? ? B C 39 N4 ? ? ? 1_555 B G 56 O6 ? ? B C 60 B G 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog112 hydrog ? ? B C 39 O2 ? ? ? 1_555 B G 56 N2 ? ? B C 60 B G 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog113 hydrog ? ? B U 40 N3 ? ? ? 1_555 B A 55 N1 ? ? B U 61 B A 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog114 hydrog ? ? B U 40 O4 ? ? ? 1_555 B A 55 N6 ? ? B U 61 B A 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog115 hydrog ? ? B U 41 N3 ? ? ? 1_555 B G 54 O6 ? ? B U 62 B G 75 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog116 hydrog ? ? B U 41 O2 ? ? ? 1_555 B G 54 N1 ? ? B U 62 B G 75 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog117 hydrog ? ? B C 42 N3 ? ? ? 1_555 B G 53 N1 ? ? B C 63 B G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog118 hydrog ? ? B C 42 N4 ? ? ? 1_555 B G 53 O6 ? ? B C 63 B G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog119 hydrog ? ? B C 42 O2 ? ? ? 1_555 B G 53 N2 ? ? B C 63 B G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog120 hydrog ? ? B A 43 N1 ? ? ? 1_555 B U 52 N3 ? ? B A 64 B U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog121 hydrog ? ? B A 43 N6 ? ? ? 1_555 B U 52 O4 ? ? B A 64 B U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog122 hydrog ? ? B A 44 N1 ? ? ? 1_555 B U 51 N3 ? ? B A 65 B U 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog123 hydrog ? ? B A 44 N6 ? ? ? 1_555 B U 51 O4 ? ? B A 65 B U 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog124 hydrog ? ? B A 45 N1 ? ? ? 1_555 B U 50 N3 ? ? B A 66 B U 71 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 ? 8 'BINDING SITE FOR RESIDUE GNG A 120' AC2 Software B GNG 120 ? 9 'BINDING SITE FOR RESIDUE GNG B 120' AC3 Software A MG 201 ? 1 'BINDING SITE FOR RESIDUE MG A 201' AC4 Software B MG 202 ? 3 'BINDING SITE FOR RESIDUE MG B 202' AC5 Software B MG 203 ? 5 'BINDING SITE FOR RESIDUE MG B 203' AC6 Software B MG 205 ? 3 'BINDING SITE FOR RESIDUE MG B 205' AC7 Software B MG 206 ? 4 'BINDING SITE FOR RESIDUE MG B 206' AC8 Software A IRI 402 ? 2 'BINDING SITE FOR RESIDUE IRI A 402' AC9 Software A IRI 403 ? 8 'BINDING SITE FOR RESIDUE IRI A 403' BC1 Software B IRI 404 ? 4 'BINDING SITE FOR RESIDUE IRI B 404' BC2 Software A IRI 405 ? 5 'BINDING SITE FOR RESIDUE IRI A 405' BC3 Software B IRI 406 ? 4 'BINDING SITE FOR RESIDUE IRI B 406' BC4 Software B IRI 407 ? 2 'BINDING SITE FOR RESIDUE IRI B 407' BC5 Software B IRI 408 ? 3 'BINDING SITE FOR RESIDUE IRI B 408' BC6 Software A IRI 409 ? 5 'BINDING SITE FOR RESIDUE IRI A 409' BC7 Software B IRI 410 ? 5 'BINDING SITE FOR RESIDUE IRI B 410' BC8 Software A IRI 411 ? 3 'BINDING SITE FOR RESIDUE IRI A 411' # 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 8 A A 8 ? A A 29 . ? 1_555 ? 2 AC1 8 C A 9 ? C A 30 . ? 1_555 ? 3 AC1 8 C A 34 ? C A 55 . ? 1_555 ? 4 AC1 8 C A 35 ? C A 56 . ? 1_555 ? 5 AC1 8 C A 36 ? C A 57 . ? 1_555 ? 6 AC1 8 G A 37 ? G A 58 . ? 1_555 ? 7 AC1 8 C A 58 ? C A 79 . ? 1_555 ? 8 AC1 8 U A 59 ? U A 80 . ? 1_555 ? 9 AC2 9 A B 8 ? A B 29 . ? 1_555 ? 10 AC2 9 C B 9 ? C B 30 . ? 1_555 ? 11 AC2 9 C B 34 ? C B 55 . ? 1_555 ? 12 AC2 9 C B 35 ? C B 56 . ? 1_555 ? 13 AC2 9 C B 36 ? C B 57 . ? 1_555 ? 14 AC2 9 G B 37 ? G B 58 . ? 1_555 ? 15 AC2 9 C B 58 ? C B 79 . ? 1_555 ? 16 AC2 9 U B 59 ? U B 80 . ? 1_555 ? 17 AC2 9 MG K . ? MG B 202 . ? 1_555 ? 18 AC3 1 GTP A 1 ? GTP A 22 . ? 1_555 ? 19 AC4 3 C B 9 ? C B 30 . ? 1_555 ? 20 AC4 3 A B 10 ? A B 31 . ? 1_555 ? 21 AC4 3 GNG J . ? GNG B 120 . ? 1_555 ? 22 AC5 5 GTP B 1 ? GTP B 22 . ? 1_555 ? 23 AC5 5 G B 2 ? G B 23 . ? 1_555 ? 24 AC5 5 C B 3 ? C B 24 . ? 1_555 ? 25 AC5 5 G B 64 ? G B 85 . ? 1_555 ? 26 AC5 5 U B 65 ? U B 86 . ? 1_555 ? 27 AC6 3 G B 11 ? G B 32 . ? 1_555 ? 28 AC6 3 G B 12 ? G B 33 . ? 1_555 ? 29 AC6 3 G B 13 ? G B 34 . ? 1_555 ? 30 AC7 4 C B 47 ? C B 68 . ? 1_555 ? 31 AC7 4 C B 47 ? C B 68 . ? 2_656 ? 32 AC7 4 U B 48 ? U B 69 . ? 2_656 ? 33 AC7 4 U B 48 ? U B 69 . ? 1_555 ? 34 AC8 2 G A 23 ? G A 44 . ? 1_555 ? 35 AC8 2 G A 24 ? G A 45 . ? 1_555 ? 36 AC9 8 A A 10 ? A A 31 . ? 1_555 ? 37 AC9 8 G A 11 ? G A 32 . ? 1_555 ? 38 AC9 8 U A 40 ? U A 61 . ? 1_555 ? 39 AC9 8 U A 41 ? U A 62 . ? 1_555 ? 40 AC9 8 C A 42 ? C A 63 . ? 1_555 ? 41 AC9 8 U A 52 ? U A 73 . ? 1_555 ? 42 AC9 8 G A 53 ? G A 74 . ? 1_555 ? 43 AC9 8 G A 54 ? G A 75 . ? 1_555 ? 44 BC1 4 U B 30 ? U B 51 . ? 1_555 ? 45 BC1 4 G B 31 ? G B 52 . ? 1_555 ? 46 BC1 4 C B 33 ? C B 54 . ? 1_555 ? 47 BC1 4 C B 35 ? C B 56 . ? 1_555 ? 48 BC2 5 G A 11 ? G A 32 . ? 1_555 ? 49 BC2 5 C A 26 ? C A 47 . ? 1_555 ? 50 BC2 5 U A 27 ? U A 48 . ? 1_555 ? 51 BC2 5 C A 38 ? C A 59 . ? 1_555 ? 52 BC2 5 C A 39 ? C A 60 . ? 1_555 ? 53 BC3 4 G B 37 ? G B 58 . ? 1_555 ? 54 BC3 4 C B 38 ? C B 59 . ? 1_555 ? 55 BC3 4 C B 39 ? C B 60 . ? 1_555 ? 56 BC3 4 C B 42 ? C B 63 . ? 4_556 ? 57 BC4 2 G B 23 ? G B 44 . ? 1_555 ? 58 BC4 2 G B 24 ? G B 45 . ? 1_555 ? 59 BC5 3 A B 10 ? A B 31 . ? 1_555 ? 60 BC5 3 A B 55 ? A B 76 . ? 1_555 ? 61 BC5 3 G B 56 ? G B 77 . ? 1_555 ? 62 BC6 5 U A 30 ? U A 51 . ? 1_555 ? 63 BC6 5 G A 31 ? G A 52 . ? 1_555 ? 64 BC6 5 C A 33 ? C A 54 . ? 1_555 ? 65 BC6 5 C A 34 ? C A 55 . ? 1_555 ? 66 BC6 5 C A 35 ? C A 56 . ? 1_555 ? 67 BC7 5 G B 11 ? G B 32 . ? 1_555 ? 68 BC7 5 C B 26 ? C B 47 . ? 1_555 ? 69 BC7 5 U B 27 ? U B 48 . ? 1_555 ? 70 BC7 5 C B 38 ? C B 59 . ? 1_555 ? 71 BC7 5 C B 39 ? C B 60 . ? 1_555 ? 72 BC8 3 G A 13 ? G A 34 . ? 1_555 ? 73 BC8 3 U A 14 ? U A 35 . ? 1_555 ? 74 BC8 3 U A 51 ? U A 72 . ? 1_555 ? # 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 22 ? G "GUANOSINE-5'-TRIPHOSPHATE" 2 A CCC 66 A CCC 87 ? C ? 3 B GTP 1 B GTP 22 ? G "GUANOSINE-5'-TRIPHOSPHATE" 4 B CCC 66 B CCC 87 ? C ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id MG _pdbx_struct_special_symmetry.auth_seq_id 206 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id O _pdbx_struct_special_symmetry.label_comp_id MG _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 IRI IR IR N N 231 IRI N1 N N N 232 IRI N2 N N N 233 IRI N3 N N N 234 IRI N4 N N N 235 IRI N5 N N N 236 IRI N6 N N N 237 IRI HN11 H N N 238 IRI HN12 H N N 239 IRI HN13 H N N 240 IRI HN21 H N N 241 IRI HN22 H N N 242 IRI HN23 H N N 243 IRI HN31 H N N 244 IRI HN32 H N N 245 IRI HN33 H N N 246 IRI HN41 H N N 247 IRI HN42 H N N 248 IRI HN43 H N N 249 IRI HN51 H N N 250 IRI HN52 H N N 251 IRI HN53 H N N 252 IRI HN61 H N N 253 IRI HN62 H N N 254 IRI HN63 H N N 255 MG MG MG 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 IRI IR N1 sing N N 241 IRI IR N2 sing N N 242 IRI IR N3 sing N N 243 IRI IR N4 sing N N 244 IRI IR N5 sing N N 245 IRI IR N6 sing N N 246 IRI N1 HN11 sing N N 247 IRI N1 HN12 sing N N 248 IRI N1 HN13 sing N N 249 IRI N2 HN21 sing N N 250 IRI N2 HN22 sing N N 251 IRI N2 HN23 sing N N 252 IRI N3 HN31 sing N N 253 IRI N3 HN32 sing N N 254 IRI N3 HN33 sing N N 255 IRI N4 HN41 sing N N 256 IRI N4 HN42 sing N N 257 IRI N4 HN43 sing N N 258 IRI N5 HN51 sing N N 259 IRI N5 HN52 sing N N 260 IRI N5 HN53 sing N N 261 IRI N6 HN61 sing N N 262 IRI N6 HN62 sing N N 263 IRI 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 3SKL 'double helix' 3SKL 'a-form double helix' 3SKL 'mismatched base pair' 3SKL '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 0.607 0.327 -0.399 -7.214 -11.223 -2.542 1 A_GTP22:CCC87_A A 22 ? A 87 ? ? 1 1 A G 2 1_555 A U 65 1_555 -2.594 -0.884 -0.006 5.950 -19.982 -4.920 2 A_G23:U86_A A 23 ? A 86 ? 28 1 1 A C 3 1_555 A G 64 1_555 0.344 -0.279 0.226 -0.107 -26.957 0.276 3 A_C24:G85_A A 24 ? A 85 ? 19 1 1 A U 4 1_555 A A 63 1_555 0.576 0.036 0.729 -11.312 -12.609 -2.518 4 A_U25:A84_A A 25 ? A 84 ? 20 1 1 A U 5 1_555 A A 62 1_555 0.846 -0.395 0.049 -0.435 -14.969 -5.601 5 A_U26:A83_A A 26 ? A 83 ? 20 1 1 A A 6 1_555 A U 61 1_555 -0.303 -0.199 0.165 -1.597 -15.316 -1.423 6 A_A27:U82_A A 27 ? A 82 ? 20 1 1 A U 7 1_555 A A 60 1_555 0.527 -0.011 0.515 -11.956 -25.170 1.398 7 A_U28:A81_A A 28 ? A 81 ? 20 1 1 A A 8 1_555 A U 59 1_555 -0.155 0.083 0.003 7.226 -6.702 -5.351 8 A_A29:U80_A A 29 ? A 80 ? 20 1 1 A G 25 1_555 A C 17 1_555 -0.605 -0.213 0.105 -1.891 -10.388 1.999 9 A_G46:C38_A A 46 ? A 38 ? 19 1 1 A C 26 1_555 A G 16 1_555 0.422 0.051 -0.213 2.941 -7.988 -1.035 10 A_C47:G37_A A 47 ? A 37 ? 19 1 1 A U 27 1_555 A A 15 1_555 -0.158 -0.154 0.392 -0.363 3.907 -5.833 11 A_U48:A36_A A 48 ? A 36 ? 20 1 1 A A 28 1_555 A U 14 1_555 0.040 0.019 -0.049 -4.397 -14.342 -9.040 12 A_A49:U35_A A 49 ? A 35 ? 20 1 1 A C 29 1_555 A G 13 1_555 1.173 -0.437 0.145 4.806 -17.456 2.735 13 A_C50:G34_A A 50 ? A 34 ? 19 1 1 A U 30 1_555 A G 12 1_555 3.108 -0.575 0.276 -14.634 -20.072 2.197 14 A_U51:G33_A A 51 ? A 33 ? 28 1 1 A G 31 1_555 A C 38 1_555 0.591 -0.269 0.279 9.950 -22.636 -4.840 15 A_G52:C59_A A 52 ? A 59 ? 19 1 1 A C 9 1_555 A G 37 1_555 -0.524 0.313 -0.721 19.892 -15.375 10.576 16 A_C30:G58_A A 30 ? A 58 ? ? 1 1 A G 23 1_555 A C 47 1_555 -0.015 -0.002 -0.479 -16.105 4.784 0.592 17 A_G44:C68_A A 44 ? A 68 ? 19 1 1 A G 24 1_555 A C 46 1_555 -0.975 -0.458 -0.303 -10.535 -13.256 0.896 18 A_G45:C67_A A 45 ? A 67 ? 19 1 1 A U 50 1_555 A A 45 1_555 -0.356 0.099 0.227 -2.626 -4.630 14.713 19 A_U71:A66_A A 71 ? A 66 ? ? 1 1 A U 51 1_555 A A 44 1_555 -0.429 0.143 0.035 0.443 -20.383 2.259 20 A_U72:A65_A A 72 ? A 65 ? 20 1 1 A U 52 1_555 A A 43 1_555 0.032 0.083 0.555 -7.015 -13.930 -0.243 21 A_U73:A64_A A 73 ? A 64 ? 20 1 1 A G 53 1_555 A C 42 1_555 0.054 0.033 -0.793 -9.328 -8.647 -11.759 22 A_G74:C63_A A 74 ? A 63 ? ? 1 1 A G 54 1_555 A U 41 1_555 -2.979 -0.866 0.291 4.558 -6.099 1.049 23 A_G75:U62_A A 75 ? A 62 ? 28 1 1 A A 55 1_555 A U 40 1_555 0.685 -0.278 -0.097 -3.426 -19.238 1.022 24 A_A76:U61_A A 76 ? A 61 ? 20 1 1 A G 56 1_555 A C 39 1_555 0.700 -0.128 -0.072 -1.164 -7.451 2.178 25 A_G77:C60_A A 77 ? A 60 ? 19 1 1 B GTP 1 1_555 B CCC 66 1_555 0.132 -0.174 -0.060 -3.945 -11.733 -0.902 26 B_GTP22:CCC87_B B 22 ? B 87 ? 19 1 1 B G 2 1_555 B U 65 1_555 -2.331 -0.711 0.341 6.256 -17.896 0.845 27 B_G23:U86_B B 23 ? B 86 ? 28 1 1 B C 3 1_555 B G 64 1_555 -0.330 -0.009 0.136 4.008 -23.197 6.199 28 B_C24:G85_B B 24 ? B 85 ? 19 1 1 B U 4 1_555 B A 63 1_555 -0.310 -0.236 0.293 -13.150 -16.252 -5.859 29 B_U25:A84_B B 25 ? B 84 ? 20 1 1 B U 5 1_555 B A 62 1_555 0.077 -0.137 0.257 -5.262 -13.613 -2.157 30 B_U26:A83_B B 26 ? B 83 ? 20 1 1 B A 6 1_555 B U 61 1_555 0.632 0.009 0.490 -0.427 -6.435 -2.283 31 B_A27:U82_B B 27 ? B 82 ? 20 1 1 B U 7 1_555 B A 60 1_555 1.123 0.004 0.182 -8.690 -12.276 3.461 32 B_U28:A81_B B 28 ? B 81 ? 20 1 1 B A 8 1_555 B U 59 1_555 0.147 -0.141 0.480 7.445 -3.600 -1.592 33 B_A29:U80_B B 29 ? B 80 ? 20 1 1 B G 25 1_555 B C 17 1_555 -0.652 0.192 -0.300 -12.269 -7.897 10.992 34 B_G46:C38_B B 46 ? B 38 ? ? 1 1 B C 26 1_555 B G 16 1_555 0.184 -0.239 -0.175 -0.671 -19.012 -2.068 35 B_C47:G37_B B 47 ? B 37 ? 19 1 1 B U 27 1_555 B A 15 1_555 -0.146 -0.121 0.777 2.675 -2.708 0.353 36 B_U48:A36_B B 48 ? B 36 ? 20 1 1 B A 28 1_555 B U 14 1_555 0.063 -0.031 0.270 7.798 -11.486 4.277 37 B_A49:U35_B B 49 ? B 35 ? 20 1 1 B C 29 1_555 B G 13 1_555 0.223 -0.063 -0.029 15.343 -14.176 4.251 38 B_C50:G34_B B 50 ? B 34 ? 19 1 1 B U 30 1_555 B G 12 1_555 2.345 -0.479 -0.433 -2.011 -17.614 7.312 39 B_U51:G33_B B 51 ? B 33 ? 28 1 1 B G 31 1_555 B C 38 1_555 -0.208 0.064 0.298 7.670 -21.631 3.901 40 B_G52:C59_B B 52 ? B 59 ? 19 1 1 B C 9 1_555 B G 37 1_555 -0.363 0.137 -0.674 21.067 -17.490 4.119 41 B_C30:G58_B B 30 ? B 58 ? 19 1 1 B G 23 1_555 B C 47 1_555 -0.074 -0.237 -0.798 -20.955 -3.581 -4.763 42 B_G44:C68_B B 44 ? B 68 ? 19 1 1 B G 24 1_555 B C 46 1_555 0.080 0.188 -0.609 -12.672 -14.338 1.348 43 B_G45:C67_B B 45 ? B 67 ? 19 1 1 B U 50 1_555 B A 45 1_555 -0.344 0.710 0.514 -10.906 -17.893 26.504 44 B_U71:A66_B B 71 ? B 66 ? ? 1 1 B U 51 1_555 B A 44 1_555 0.328 -0.053 0.380 -3.975 -6.169 3.909 45 B_U72:A65_B B 72 ? B 65 ? 20 1 1 B U 52 1_555 B A 43 1_555 0.014 0.001 0.242 1.186 -16.238 3.742 46 B_U73:A64_B B 73 ? B 64 ? 20 1 1 B G 53 1_555 B C 42 1_555 -0.530 -0.257 -0.092 -5.788 -11.262 4.671 47 B_G74:C63_B B 74 ? B 63 ? 19 1 1 B G 54 1_555 B U 41 1_555 -1.919 -0.626 -0.049 -3.103 -9.233 2.493 48 B_G75:U62_B B 75 ? B 62 ? 28 1 1 B A 55 1_555 B U 40 1_555 -0.415 -0.205 -0.346 -9.210 -7.791 -4.207 49 B_A76:U61_B B 76 ? B 61 ? 20 1 1 B G 56 1_555 B C 39 1_555 -0.096 -0.038 0.393 -1.528 -7.324 -8.584 50 B_G77:C60_B B 77 ? B 60 ? 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 -0.240 -1.917 2.606 -7.404 10.121 21.093 -6.659 -1.001 1.537 25.000 18.288 24.502 1 AA_GTP22G23:U86CCC87_AA A 22 ? A 87 ? A 23 ? A 86 ? 1 A G 2 1_555 A U 65 1_555 A C 3 1_555 A G 64 1_555 0.038 -1.358 3.378 -4.248 6.269 44.863 -2.313 -0.426 3.155 8.146 5.520 45.465 2 AA_G23C24:G85U86_AA A 23 ? A 86 ? A 24 ? A 85 ? 1 A C 3 1_555 A G 64 1_555 A U 4 1_555 A A 63 1_555 -0.371 -1.591 3.462 -4.892 11.663 35.512 -3.974 -0.056 2.843 18.416 7.725 37.629 3 AA_C24U25:A84G85_AA A 24 ? A 85 ? A 25 ? A 84 ? 1 A U 4 1_555 A A 63 1_555 A U 5 1_555 A A 62 1_555 -0.171 -1.320 2.889 5.639 0.381 32.831 -2.359 1.121 2.806 0.668 -9.885 33.301 4 AA_U25U26:A83A84_AA A 25 ? A 84 ? A 26 ? A 83 ? 1 A U 5 1_555 A A 62 1_555 A A 6 1_555 A U 61 1_555 0.456 -1.359 3.232 0.589 8.372 27.911 -4.408 -0.787 2.727 16.880 -1.187 29.122 5 AA_U26A27:U82A83_AA A 26 ? A 83 ? A 27 ? A 82 ? 1 A A 6 1_555 A U 61 1_555 A U 7 1_555 A A 60 1_555 0.459 -1.437 3.688 3.090 7.121 36.313 -3.300 -0.269 3.382 11.268 -4.889 37.106 6 AA_A27U28:A81U82_AA A 27 ? A 82 ? A 28 ? A 81 ? 1 A U 7 1_555 A A 60 1_555 A A 8 1_555 A U 59 1_555 -0.202 -0.924 2.746 5.212 15.952 29.542 -3.561 0.992 1.947 28.566 -9.333 33.883 7 AA_U28A29:U80A81_AA A 28 ? A 81 ? A 29 ? A 80 ? 1 A G 25 1_555 A C 17 1_555 A C 26 1_555 A G 16 1_555 0.223 -1.771 3.099 4.706 2.700 38.368 -2.979 0.201 2.978 4.083 -7.116 38.736 8 AA_G46C47:G37C38_AA A 46 ? A 38 ? A 47 ? A 37 ? 1 A C 26 1_555 A G 16 1_555 A U 27 1_555 A A 15 1_555 -0.524 -1.427 3.411 -4.177 9.956 28.604 -4.657 0.179 2.815 19.304 8.098 30.534 9 AA_C47U48:A36G37_AA A 47 ? A 37 ? A 48 ? A 36 ? 1 A U 27 1_555 A A 15 1_555 A A 28 1_555 A U 14 1_555 -0.344 -1.952 3.203 2.416 9.900 29.402 -5.314 1.051 2.399 18.806 -4.589 31.081 10 AA_U48A49:U35A36_AA A 48 ? A 36 ? A 49 ? A 35 ? 1 A A 28 1_555 A U 14 1_555 A C 29 1_555 A G 13 1_555 0.759 -1.520 2.990 -0.825 2.394 40.008 -2.463 -1.191 2.883 3.494 1.204 40.085 11 AA_A49C50:G34U35_AA A 49 ? A 35 ? A 50 ? A 34 ? 1 A C 29 1_555 A G 13 1_555 A U 30 1_555 A G 12 1_555 0.396 -1.648 3.563 7.560 9.955 43.729 -3.059 0.189 3.158 13.052 -9.911 45.396 12 AA_C50U51:G33G34_AA A 50 ? A 34 ? A 51 ? A 33 ? 1 A U 30 1_555 A G 12 1_555 A G 31 1_555 A C 38 1_555 2.362 -1.704 2.712 -0.782 2.543 46.143 -2.346 -3.064 2.581 3.241 0.996 46.215 13 AA_U51G52:C59G33_AA A 51 ? A 33 ? A 52 ? A 59 ? 1 A G 31 1_555 A C 38 1_555 A C 9 1_555 A G 37 1_555 -1.701 -0.591 2.724 2.644 11.169 48.568 -1.355 2.174 2.450 13.363 -3.163 49.825 14 AA_G52C30:G58C59_AA A 52 ? A 59 ? A 30 ? A 58 ? 1 A G 23 1_555 A C 47 1_555 A G 24 1_555 A C 46 1_555 0.412 -2.105 3.199 0.250 9.533 23.234 -7.253 -0.886 2.181 22.494 -0.590 25.090 15 AA_G44G45:C67C68_AA A 44 ? A 68 ? A 45 ? A 67 ? 1 A G 24 1_555 A C 46 1_555 A U 50 1_555 A A 45 1_555 -0.524 -2.562 2.991 -6.227 3.938 28.396 -5.810 -0.146 2.671 7.861 12.431 29.318 16 AA_G45U71:A66C67_AA A 45 ? A 67 ? A 71 ? A 66 ? 1 A U 50 1_555 A A 45 1_555 A U 51 1_555 A A 44 1_555 -1.259 -0.777 3.082 -2.793 0.601 32.258 -1.494 1.787 3.162 1.079 5.015 32.381 17 AA_U71U72:A65A66_AA A 71 ? A 66 ? A 72 ? A 65 ? 1 A U 51 1_555 A A 44 1_555 A U 52 1_555 A A 43 1_555 -0.367 -1.331 3.433 -5.821 5.159 38.566 -2.612 -0.169 3.255 7.716 8.705 39.313 18 AA_U72U73:A64A65_AA A 72 ? A 65 ? A 73 ? A 64 ? 1 A U 52 1_555 A A 43 1_555 A G 53 1_555 A C 42 1_555 -0.887 -2.000 3.329 5.662 12.858 26.119 -6.244 2.761 1.924 26.179 -11.528 29.601 19 AA_U73G74:C63A64_AA A 73 ? A 64 ? A 74 ? A 63 ? 1 A G 53 1_555 A C 42 1_555 A G 54 1_555 A U 41 1_555 0.835 -1.665 2.747 -11.499 6.073 17.756 -5.988 -5.261 1.335 17.020 32.226 21.978 20 AA_G74G75:U62C63_AA A 74 ? A 63 ? A 75 ? A 62 ? 1 A G 54 1_555 A U 41 1_555 A A 55 1_555 A U 40 1_555 -0.300 -1.263 3.716 3.240 0.778 47.489 -1.635 0.666 3.669 0.965 -4.017 47.599 21 AA_G75A76:U61U62_AA A 75 ? A 62 ? A 76 ? A 61 ? 1 A A 55 1_555 A U 40 1_555 A G 56 1_555 A C 39 1_555 0.806 -2.350 3.258 2.817 7.270 27.331 -6.324 -1.049 2.626 15.002 -5.812 28.401 22 AA_A76G77:C60U61_AA A 76 ? A 61 ? A 77 ? A 60 ? 1 B GTP 1 1_555 B CCC 66 1_555 B G 2 1_555 B U 65 1_555 -0.143 -2.160 2.519 -8.496 13.216 24.511 -6.107 -0.872 1.205 27.778 17.857 29.049 23 BB_GTP22G23:U86CCC87_BB B 22 ? B 87 ? B 23 ? B 86 ? 1 B G 2 1_555 B U 65 1_555 B C 3 1_555 B G 64 1_555 0.140 -1.027 3.204 1.250 6.584 41.200 -2.105 -0.070 3.015 9.282 -1.762 41.718 24 BB_G23C24:G85U86_BB B 23 ? B 86 ? B 24 ? B 85 ? 1 B C 3 1_555 B G 64 1_555 B U 4 1_555 B A 63 1_555 -0.980 -1.392 3.656 -5.304 13.912 35.963 -3.904 0.784 3.043 21.436 8.173 38.829 25 BB_C24U25:A84G85_BB B 24 ? B 85 ? B 25 ? B 84 ? 1 B U 4 1_555 B A 63 1_555 B U 5 1_555 B A 62 1_555 0.347 -1.152 3.039 0.460 2.838 33.568 -2.410 -0.530 2.939 4.902 -0.795 33.687 26 BB_U25U26:A83A84_BB B 25 ? B 84 ? B 26 ? B 83 ? 1 B U 5 1_555 B A 62 1_555 B A 6 1_555 B U 61 1_555 -0.026 -1.285 2.955 -2.122 5.725 36.513 -2.698 -0.208 2.726 9.060 3.357 37.002 27 BB_U26A27:U82A83_BB B 26 ? B 83 ? B 27 ? B 82 ? 1 B A 6 1_555 B U 61 1_555 B U 7 1_555 B A 60 1_555 0.436 -1.411 3.534 6.403 8.350 33.843 -3.605 0.267 3.137 13.931 -10.683 35.395 28 BB_A27U28:A81U82_BB B 27 ? B 82 ? B 28 ? B 81 ? 1 B U 7 1_555 B A 60 1_555 B A 8 1_555 B U 59 1_555 -0.255 -1.150 2.686 0.380 11.656 30.597 -3.575 0.503 2.115 21.149 -0.690 32.694 29 BB_U28A29:U80A81_BB B 28 ? B 81 ? B 29 ? B 80 ? 1 B G 25 1_555 B C 17 1_555 B C 26 1_555 B G 16 1_555 -0.684 -1.521 2.952 2.204 1.798 36.532 -2.638 1.356 2.832 2.864 -3.510 36.639 30 BB_G46C47:G37C38_BB B 46 ? B 38 ? B 47 ? B 37 ? 1 B C 26 1_555 B G 16 1_555 B U 27 1_555 B A 15 1_555 -0.170 -1.996 3.250 -8.228 5.182 27.258 -5.087 -1.390 2.764 10.577 16.796 28.910 31 BB_C47U48:A36G37_BB B 47 ? B 37 ? B 48 ? B 36 ? 1 B U 27 1_555 B A 15 1_555 B A 28 1_555 B U 14 1_555 0.011 -1.221 2.933 3.426 8.370 32.611 -3.253 0.453 2.539 14.559 -5.960 33.809 32 BB_U48A49:U35A36_BB B 48 ? B 36 ? B 49 ? B 35 ? 1 B A 28 1_555 B U 14 1_555 B C 29 1_555 B G 13 1_555 0.250 -1.466 2.946 1.323 5.184 33.588 -3.226 -0.244 2.703 8.901 -2.272 33.999 33 BB_A49C50:G34U35_BB B 49 ? B 35 ? B 50 ? B 34 ? 1 B C 29 1_555 B G 13 1_555 B U 30 1_555 B G 12 1_555 0.735 -1.423 3.450 9.582 11.032 43.671 -2.806 -0.088 3.109 14.360 -12.473 45.937 34 BB_C50U51:G33G34_BB B 50 ? B 34 ? B 51 ? B 33 ? 1 B U 30 1_555 B G 12 1_555 B G 31 1_555 B C 38 1_555 2.880 -1.410 3.188 -2.653 8.045 49.303 -2.206 -3.586 2.792 9.562 3.153 49.981 35 BB_U51G52:C59G33_BB B 51 ? B 33 ? B 52 ? B 59 ? 1 B G 31 1_555 B C 38 1_555 B C 9 1_555 B G 37 1_555 -2.214 -0.448 2.537 -0.862 9.292 53.626 -0.926 2.382 2.466 10.212 0.948 54.373 36 BB_G52C30:G58C59_BB B 52 ? B 59 ? B 30 ? B 58 ? 1 B G 23 1_555 B C 47 1_555 B G 24 1_555 B C 46 1_555 0.140 -2.247 3.109 -1.568 13.680 25.383 -6.903 -0.554 1.688 28.605 3.278 28.824 37 BB_G44G45:C67C68_BB B 44 ? B 68 ? B 45 ? B 67 ? 1 B G 24 1_555 B C 46 1_555 B U 50 1_555 B A 45 1_555 -0.481 -2.494 3.338 -6.925 -2.270 28.706 -4.370 -0.623 3.537 -4.487 13.691 29.598 38 BB_G45U71:A66C67_BB B 45 ? B 67 ? B 71 ? B 66 ? 1 B U 50 1_555 B A 45 1_555 B U 51 1_555 B A 44 1_555 -1.231 -0.914 3.109 -4.242 3.904 32.855 -2.214 1.470 3.113 6.837 7.429 33.343 39 BB_U71U72:A65A66_BB B 71 ? B 66 ? B 72 ? B 65 ? 1 B U 51 1_555 B A 44 1_555 B U 52 1_555 B A 43 1_555 0.353 -1.517 3.071 2.152 4.098 31.724 -3.421 -0.286 2.875 7.447 -3.910 32.052 40 BB_U72U73:A64A65_BB B 72 ? B 65 ? B 73 ? B 64 ? 1 B U 52 1_555 B A 43 1_555 B G 53 1_555 B C 42 1_555 0.034 -1.637 3.298 1.891 12.316 26.596 -5.635 0.300 2.324 25.095 -3.853 29.322 41 BB_U73G74:C63A64_BB B 73 ? B 64 ? B 74 ? B 63 ? 1 B G 53 1_555 B C 42 1_555 B G 54 1_555 B U 41 1_555 0.300 -1.876 2.972 -3.741 11.587 27.619 -5.482 -1.182 1.985 22.912 7.398 30.136 42 BB_G74G75:U62C63_BB B 74 ? B 63 ? B 75 ? B 62 ? 1 B G 54 1_555 B U 41 1_555 B A 55 1_555 B U 40 1_555 -0.279 -1.714 3.460 0.192 6.323 35.738 -3.650 0.476 3.120 10.205 -0.310 36.276 43 BB_G75A76:U61U62_BB B 75 ? B 62 ? B 76 ? B 61 ? 1 B A 55 1_555 B U 40 1_555 B G 56 1_555 B C 39 1_555 0.380 -2.188 3.015 -2.746 3.980 32.585 -4.455 -1.081 2.696 7.046 4.861 32.933 44 BB_A76G77:C60U61_BB B 76 ? B 61 ? B 77 ? B 60 ? # _atom_sites.entry_id 3SKL _atom_sites.fract_transf_matrix[1][1] 0.010204 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000436 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028608 _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] 0.009013 _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 IR MG N O P # loop_