data_3U08 # _entry.id 3U08 # _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 3U08 pdb_00003u08 10.2210/pdb3u08/pdb NDB NA1306 ? ? RCSB RCSB068141 ? ? WWPDB D_1000068141 ? ? # 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 2012-09-12 2 'Structure model' 1 1 2014-01-08 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' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 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' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.value' 10 3 'Structure model' '_struct_conn.pdbx_dist_value' 11 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 12 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 15 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 16 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3U08 _pdbx_database_status.recvd_initial_deposition_date 2011-09-28 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3U05 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wei, D.G.' 1 'Neidle, S.' 2 # _citation.id primary _citation.title 'Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 135 _citation.page_first 1369 _citation.page_last 1377 _citation.year 2013 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23276263 _citation.pdbx_database_id_DOI 10.1021/ja308952y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wei, D.' 1 ? primary 'Wilson, W.D.' 2 ? primary 'Neidle, S.' 3 ? # 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 "5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'" 3663.392 2 ? ? ? ? 2 non-polymer syn "4'-(5-carbamimidoyl-1H-benzimidazol-2-yl)biphenyl-4-carboxamide" 355.393 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 water nat water 18.015 150 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _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 "4'-(5-carbamimidoyl-1H-benzimidazol-2-yl)biphenyl-4-carboxamide" D63 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG 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 'This sequence occurs naturally in humans.' # 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 D63 non-polymer . "4'-(5-carbamimidoyl-1H-benzimidazol-2-yl)biphenyl-4-carboxamide" ? 'C21 H17 N5 O' 355.393 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 DG 4 16 16 DG DG B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DC 9 21 21 DC DC B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG 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 D63 1 13 1 D63 963 A . D 3 MG 1 14 1 MG MG A . E 3 MG 1 15 1 MG MG A . F 4 HOH 1 16 16 HOH HOH A . F 4 HOH 2 17 17 HOH HOH A . F 4 HOH 3 18 1 HOH HOH A . F 4 HOH 4 19 3 HOH HOH A . F 4 HOH 5 20 5 HOH HOH A . F 4 HOH 6 21 21 HOH HOH A . F 4 HOH 7 22 6 HOH HOH A . F 4 HOH 8 23 23 HOH HOH A . F 4 HOH 9 24 24 HOH HOH A . F 4 HOH 10 25 8 HOH HOH A . F 4 HOH 11 26 26 HOH HOH A . F 4 HOH 12 27 27 HOH HOH A . F 4 HOH 13 28 9 HOH HOH A . F 4 HOH 14 29 29 HOH HOH A . F 4 HOH 15 30 30 HOH HOH A . F 4 HOH 16 31 31 HOH HOH A . F 4 HOH 17 32 11 HOH HOH A . F 4 HOH 18 33 33 HOH HOH A . F 4 HOH 19 34 12 HOH HOH A . F 4 HOH 20 35 35 HOH HOH A . F 4 HOH 21 36 36 HOH HOH A . F 4 HOH 22 37 37 HOH HOH A . F 4 HOH 23 38 13 HOH HOH A . F 4 HOH 24 39 39 HOH HOH A . F 4 HOH 25 40 40 HOH HOH A . F 4 HOH 26 41 41 HOH HOH A . F 4 HOH 27 42 42 HOH HOH A . F 4 HOH 28 43 43 HOH HOH A . F 4 HOH 29 44 44 HOH HOH A . F 4 HOH 30 45 14 HOH HOH A . F 4 HOH 31 46 15 HOH HOH A . F 4 HOH 32 47 1 HOH HOH A . F 4 HOH 33 48 48 HOH HOH A . F 4 HOH 34 49 49 HOH HOH A . F 4 HOH 35 50 50 HOH HOH A . F 4 HOH 36 51 1 HOH HOH A . F 4 HOH 37 52 52 HOH HOH A . F 4 HOH 38 53 53 HOH HOH A . F 4 HOH 39 54 54 HOH HOH A . F 4 HOH 40 55 55 HOH HOH A . F 4 HOH 41 56 56 HOH HOH A . F 4 HOH 42 57 57 HOH HOH A . F 4 HOH 43 58 58 HOH HOH A . F 4 HOH 44 59 59 HOH HOH A . F 4 HOH 45 61 61 HOH HOH A . F 4 HOH 46 62 62 HOH HOH A . F 4 HOH 47 63 63 HOH HOH A . F 4 HOH 48 64 64 HOH HOH A . F 4 HOH 49 65 65 HOH HOH A . F 4 HOH 50 70 70 HOH HOH A . F 4 HOH 51 72 72 HOH HOH A . F 4 HOH 52 73 73 HOH HOH A . F 4 HOH 53 74 74 HOH HOH A . F 4 HOH 54 75 75 HOH HOH A . F 4 HOH 55 77 77 HOH HOH A . F 4 HOH 56 78 78 HOH HOH A . F 4 HOH 57 81 81 HOH HOH A . F 4 HOH 58 82 82 HOH HOH A . F 4 HOH 59 83 83 HOH HOH A . F 4 HOH 60 85 85 HOH HOH A . F 4 HOH 61 86 86 HOH HOH A . F 4 HOH 62 87 87 HOH HOH A . F 4 HOH 63 90 90 HOH HOH A . F 4 HOH 64 94 94 HOH HOH A . F 4 HOH 65 95 95 HOH HOH A . F 4 HOH 66 98 98 HOH HOH A . F 4 HOH 67 99 99 HOH HOH A . F 4 HOH 68 100 100 HOH HOH A . F 4 HOH 69 103 103 HOH HOH A . F 4 HOH 70 105 105 HOH HOH A . F 4 HOH 71 107 107 HOH HOH A . F 4 HOH 72 109 109 HOH HOH A . F 4 HOH 73 114 114 HOH HOH A . F 4 HOH 74 115 115 HOH HOH A . F 4 HOH 75 116 116 HOH HOH A . F 4 HOH 76 117 117 HOH HOH A . F 4 HOH 77 119 119 HOH HOH A . F 4 HOH 78 120 120 HOH HOH A . F 4 HOH 79 121 121 HOH HOH A . F 4 HOH 80 122 122 HOH HOH A . F 4 HOH 81 123 123 HOH HOH A . F 4 HOH 82 126 126 HOH HOH A . F 4 HOH 83 127 127 HOH HOH A . F 4 HOH 84 137 137 HOH HOH A . F 4 HOH 85 138 138 HOH HOH A . F 4 HOH 86 140 140 HOH HOH A . F 4 HOH 87 142 142 HOH HOH A . F 4 HOH 88 143 143 HOH HOH A . F 4 HOH 89 145 145 HOH HOH A . F 4 HOH 90 147 147 HOH HOH A . F 4 HOH 91 151 151 HOH HOH A . G 4 HOH 1 2 2 HOH HOH B . G 4 HOH 2 4 4 HOH HOH B . G 4 HOH 3 7 7 HOH HOH B . G 4 HOH 4 10 10 HOH HOH B . G 4 HOH 5 25 25 HOH HOH B . G 4 HOH 6 26 18 HOH HOH B . G 4 HOH 7 27 19 HOH HOH B . G 4 HOH 8 28 28 HOH HOH B . G 4 HOH 9 29 20 HOH HOH B . G 4 HOH 10 30 22 HOH HOH B . G 4 HOH 11 32 32 HOH HOH B . G 4 HOH 12 34 34 HOH HOH B . G 4 HOH 13 38 38 HOH HOH B . G 4 HOH 14 45 45 HOH HOH B . G 4 HOH 15 46 46 HOH HOH B . G 4 HOH 16 47 47 HOH HOH B . G 4 HOH 17 51 51 HOH HOH B . G 4 HOH 18 60 60 HOH HOH B . G 4 HOH 19 66 66 HOH HOH B . G 4 HOH 20 67 67 HOH HOH B . G 4 HOH 21 68 68 HOH HOH B . G 4 HOH 22 69 69 HOH HOH B . G 4 HOH 23 71 71 HOH HOH B . G 4 HOH 24 76 76 HOH HOH B . G 4 HOH 25 79 79 HOH HOH B . G 4 HOH 26 80 80 HOH HOH B . G 4 HOH 27 84 84 HOH HOH B . G 4 HOH 28 88 88 HOH HOH B . G 4 HOH 29 89 89 HOH HOH B . G 4 HOH 30 91 91 HOH HOH B . G 4 HOH 31 92 92 HOH HOH B . G 4 HOH 32 93 93 HOH HOH B . G 4 HOH 33 96 96 HOH HOH B . G 4 HOH 34 97 97 HOH HOH B . G 4 HOH 35 101 101 HOH HOH B . G 4 HOH 36 102 102 HOH HOH B . G 4 HOH 37 104 104 HOH HOH B . G 4 HOH 38 106 106 HOH HOH B . G 4 HOH 39 108 108 HOH HOH B . G 4 HOH 40 110 110 HOH HOH B . G 4 HOH 41 111 111 HOH HOH B . G 4 HOH 42 112 112 HOH HOH B . G 4 HOH 43 113 113 HOH HOH B . G 4 HOH 44 124 124 HOH HOH B . G 4 HOH 45 125 125 HOH HOH B . G 4 HOH 46 128 128 HOH HOH B . G 4 HOH 47 129 129 HOH HOH B . G 4 HOH 48 130 130 HOH HOH B . G 4 HOH 49 131 131 HOH HOH B . G 4 HOH 50 132 132 HOH HOH B . G 4 HOH 51 133 133 HOH HOH B . G 4 HOH 52 134 134 HOH HOH B . G 4 HOH 53 135 135 HOH HOH B . G 4 HOH 54 136 136 HOH HOH B . G 4 HOH 55 141 141 HOH HOH B . G 4 HOH 56 144 144 HOH HOH B . G 4 HOH 57 148 148 HOH HOH B . G 4 HOH 58 149 149 HOH HOH B . G 4 HOH 59 150 150 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DNA 'data collection' . ? 1 PHASES phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 xia2 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # _cell.entry_id 3U08 _cell.length_a 24.070 _cell.length_b 39.760 _cell.length_c 65.700 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _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 3U08 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3U08 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.67 _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 283 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'MAGNESIUM CHLORIDE, DNA, DB1963, MPD, SODIUM CACODYLATE BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K' _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 PIXEL _diffrn_detector.type 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date 2011-08-07 _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 'Si 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9796 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I24' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I24 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9796 # _reflns.entry_id 3U08 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 24.07 _reflns.d_resolution_high 1.15 _reflns.number_obs 32077 _reflns.number_all 43205 _reflns.percent_possible_obs 74.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.15 1.18 8.2 ? ? ? ? ? 3172 ? ? ? ? 1 1 1.18 1.21 25.1 ? ? ? ? ? 3134 ? ? ? ? 2 1 1.21 1.25 40.1 ? ? ? ? ? 3035 ? ? ? ? 3 1 1.25 1.29 53.6 ? ? ? ? ? 2932 ? ? ? ? 4 1 1.29 1.33 65.6 ? ? ? ? ? 2865 ? ? ? ? 5 1 1.33 1.38 79.4 ? ? ? ? ? 2734 ? ? ? ? 6 1 # _refine.entry_id 3U08 _refine.ls_number_reflns_obs 15560 _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 15.33 _refine.ls_d_res_high 1.25 _refine.ls_percent_reflns_obs 89.60 _refine.ls_R_factor_obs 0.20508 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20305 _refine.ls_R_factor_R_free 0.24339 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 831 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.956 _refine.correlation_coeff_Fo_to_Fc_free 0.936 _refine.B_iso_mean 18.462 _refine.aniso_B[1][1] 0.00 _refine.aniso_B[2][2] 0.00 _refine.aniso_B[3][3] 0.00 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _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 'MOLECULAR REPLACEMENT' _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 0.066 _refine.overall_SU_ML 0.039 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 0.863 _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 486 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 150 _refine_hist.number_atoms_total 665 _refine_hist.d_res_high 1.25 _refine_hist.d_res_low 15.33 # 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 0.009 0.021 ? 575 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.347 3.000 ? 880 ? 'X-RAY DIFFRACTION' r_angle_other_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_chiral_restr 0.056 0.200 ? 94 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.013 0.020 ? 287 ? 'X-RAY DIFFRACTION' r_gen_planes_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_it 1.452 3.000 ? 575 ? 'X-RAY DIFFRACTION' r_scangle_it 2.234 4.500 ? 880 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.246 _refine_ls_shell.d_res_low 1.278 _refine_ls_shell.number_reflns_R_work 693 _refine_ls_shell.R_factor_R_work 0.281 _refine_ls_shell.percent_reflns_obs 55.98 _refine_ls_shell.R_factor_R_free 0.238 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 47 _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 3U08 _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 3U08 _struct.title 'Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3U08 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'double helix, DNA minor groove-ligand binder, DB1963, DNA' # 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 4 ? G N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3U08 _struct_ref.pdbx_db_accession 3U08 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGCGAATTCGCG _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 3U08 A 1 ? 12 ? 3U08 1 ? 12 ? 1 12 2 1 3U08 B 1 ? 12 ? 3U08 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1570 ? 1 MORE -12 ? 1 'SSA (A^2)' 4490 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _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 metalc1 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 14 A HOH 18 1_555 ? ? ? ? ? ? ? 2.077 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 14 A HOH 83 1_555 ? ? ? ? ? ? ? 2.062 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 14 A HOH 85 1_555 ? ? ? ? ? ? ? 2.056 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 14 B HOH 4 1_555 ? ? ? ? ? ? ? 2.047 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 14 B HOH 84 1_555 ? ? ? ? ? ? ? 2.055 ? ? metalc6 metalc ? ? E MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 15 A HOH 54 1_555 ? ? ? ? ? ? ? 2.236 ? ? metalc7 metalc ? ? E MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 15 A HOH 64 1_555 ? ? ? ? ? ? ? 2.264 ? ? metalc8 metalc ? ? E MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 15 A HOH 81 1_555 ? ? ? ? ? ? ? 2.104 ? ? metalc9 metalc ? ? E MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 15 A HOH 107 1_555 ? ? ? ? ? ? ? 2.669 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? F HOH . ? A HOH 18 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? F HOH . ? A HOH 83 ? 1_555 90.1 ? 2 O ? F HOH . ? A HOH 18 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? F HOH . ? A HOH 85 ? 1_555 88.2 ? 3 O ? F HOH . ? A HOH 83 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? F HOH . ? A HOH 85 ? 1_555 96.5 ? 4 O ? F HOH . ? A HOH 18 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 4 ? 1_555 94.8 ? 5 O ? F HOH . ? A HOH 83 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 4 ? 1_555 87.0 ? 6 O ? F HOH . ? A HOH 85 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 4 ? 1_555 175.4 ? 7 O ? F HOH . ? A HOH 18 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 84 ? 1_555 91.8 ? 8 O ? F HOH . ? A HOH 83 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 84 ? 1_555 173.5 ? 9 O ? F HOH . ? A HOH 85 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 84 ? 1_555 89.8 ? 10 O ? G HOH . ? B HOH 4 ? 1_555 MG ? D MG . ? A MG 14 ? 1_555 O ? G HOH . ? B HOH 84 ? 1_555 86.6 ? 11 O ? F HOH . ? A HOH 54 ? 1_555 MG ? E MG . ? A MG 15 ? 1_555 O ? F HOH . ? A HOH 64 ? 1_555 73.2 ? 12 O ? F HOH . ? A HOH 54 ? 1_555 MG ? E MG . ? A MG 15 ? 1_555 O ? F HOH . ? A HOH 81 ? 1_555 88.8 ? 13 O ? F HOH . ? A HOH 64 ? 1_555 MG ? E MG . ? A MG 15 ? 1_555 O ? F HOH . ? A HOH 81 ? 1_555 99.8 ? 14 O ? F HOH . ? A HOH 54 ? 1_555 MG ? E MG . ? A MG 15 ? 1_555 O ? F HOH . ? A HOH 107 ? 1_555 72.4 ? 15 O ? F HOH . ? A HOH 64 ? 1_555 MG ? E MG . ? A MG 15 ? 1_555 O ? F HOH . ? A HOH 107 ? 1_555 81.1 ? 16 O ? F HOH . ? A HOH 81 ? 1_555 MG ? E MG . ? A MG 15 ? 1_555 O ? F HOH . ? A HOH 107 ? 1_555 160.2 ? # 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 D63 13 ? 16 'BINDING SITE FOR RESIDUE D63 A 13' AC2 Software A MG 14 ? 6 'BINDING SITE FOR RESIDUE MG A 14' AC3 Software A MG 15 ? 6 'BINDING SITE FOR RESIDUE MG A 15' 1 ? ? ? ? ? ? ? # 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 16 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 16 DT A 7 ? DT A 7 . ? 1_555 ? 3 AC1 16 DT A 8 ? DT A 8 . ? 1_555 ? 4 AC1 16 DC A 9 ? DC A 9 . ? 1_555 ? 5 AC1 16 HOH F . ? HOH A 21 . ? 1_555 ? 6 AC1 16 HOH F . ? HOH A 37 . ? 1_555 ? 7 AC1 16 HOH F . ? HOH A 47 . ? 1_555 ? 8 AC1 16 HOH F . ? HOH A 87 . ? 1_555 ? 9 AC1 16 HOH F . ? HOH A 95 . ? 1_555 ? 10 AC1 16 HOH F . ? HOH A 103 . ? 1_555 ? 11 AC1 16 HOH F . ? HOH A 105 . ? 1_555 ? 12 AC1 16 DA B 6 ? DA B 18 . ? 1_555 ? 13 AC1 16 DT B 7 ? DT B 19 . ? 1_555 ? 14 AC1 16 DT B 8 ? DT B 20 . ? 1_555 ? 15 AC1 16 DC B 9 ? DC B 21 . ? 1_555 ? 16 AC1 16 DG B 10 ? DG B 22 . ? 1_555 ? 17 AC2 6 HOH F . ? HOH A 18 . ? 1_555 ? 18 AC2 6 HOH F . ? HOH A 19 . ? 3_655 ? 19 AC2 6 HOH F . ? HOH A 83 . ? 1_555 ? 20 AC2 6 HOH F . ? HOH A 85 . ? 1_555 ? 21 AC2 6 HOH G . ? HOH B 4 . ? 1_555 ? 22 AC2 6 HOH G . ? HOH B 84 . ? 1_555 ? 23 AC3 6 HOH F . ? HOH A 54 . ? 1_555 ? 24 AC3 6 HOH F . ? HOH A 64 . ? 1_555 ? 25 AC3 6 HOH F . ? HOH A 81 . ? 1_555 ? 26 AC3 6 HOH F . ? HOH A 103 . ? 2_564 ? 27 AC3 6 HOH F . ? HOH A 107 . ? 1_555 ? 28 AC3 6 DG B 10 ? DG B 22 . ? 2_564 ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # 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 D63 NAA N N N 1 D63 NAB N N N 2 D63 NAC N N N 3 D63 OAD O N N 4 D63 CAE C Y N 5 D63 CAF C Y N 6 D63 CAG C Y N 7 D63 CAH C Y N 8 D63 CAI C Y N 9 D63 CAJ C Y N 10 D63 CAK C Y N 11 D63 CAL C Y N 12 D63 CAM C Y N 13 D63 CAN C Y N 14 D63 CAO C Y N 15 D63 NAP N Y N 16 D63 NAQ N Y N 17 D63 CAR C N N 18 D63 CAS C N N 19 D63 CAT C Y N 20 D63 CAU C Y N 21 D63 CAV C Y N 22 D63 CAW C Y N 23 D63 CAX C Y N 24 D63 CAY C Y N 25 D63 CAZ C Y N 26 D63 CBA C Y N 27 D63 HNAA H N N 28 D63 HNAB H N N 29 D63 HNAC H N N 30 D63 HNAD H N N 31 D63 HNAE H N N 32 D63 HAE H N N 33 D63 HAF H N N 34 D63 HAG H N N 35 D63 HAH H N N 36 D63 HAI H N N 37 D63 HAJ H N N 38 D63 HAK H N N 39 D63 HAL H N N 40 D63 HAM H N N 41 D63 HAN H N N 42 D63 HAO H N N 43 D63 HNAP H N N 44 DA OP3 O N N 45 DA P P N N 46 DA OP1 O N N 47 DA OP2 O N N 48 DA "O5'" O N N 49 DA "C5'" C N N 50 DA "C4'" C N R 51 DA "O4'" O N N 52 DA "C3'" C N S 53 DA "O3'" O N N 54 DA "C2'" C N N 55 DA "C1'" C N R 56 DA N9 N Y N 57 DA C8 C Y N 58 DA N7 N Y N 59 DA C5 C Y N 60 DA C6 C Y N 61 DA N6 N N N 62 DA N1 N Y N 63 DA C2 C Y N 64 DA N3 N Y N 65 DA C4 C Y N 66 DA HOP3 H N N 67 DA HOP2 H N N 68 DA "H5'" H N N 69 DA "H5''" H N N 70 DA "H4'" H N N 71 DA "H3'" H N N 72 DA "HO3'" H N N 73 DA "H2'" H N N 74 DA "H2''" H N N 75 DA "H1'" H N N 76 DA H8 H N N 77 DA H61 H N N 78 DA H62 H N N 79 DA H2 H N N 80 DC OP3 O N N 81 DC P P N N 82 DC OP1 O N N 83 DC OP2 O N N 84 DC "O5'" O N N 85 DC "C5'" C N N 86 DC "C4'" C N R 87 DC "O4'" O N N 88 DC "C3'" C N S 89 DC "O3'" O N N 90 DC "C2'" C N N 91 DC "C1'" C N R 92 DC N1 N N N 93 DC C2 C N N 94 DC O2 O N N 95 DC N3 N N N 96 DC C4 C N N 97 DC N4 N N N 98 DC C5 C N N 99 DC C6 C N N 100 DC HOP3 H N N 101 DC HOP2 H N N 102 DC "H5'" H N N 103 DC "H5''" H N N 104 DC "H4'" H N N 105 DC "H3'" H N N 106 DC "HO3'" H N N 107 DC "H2'" H N N 108 DC "H2''" H N N 109 DC "H1'" H N N 110 DC H41 H N N 111 DC H42 H N N 112 DC H5 H N N 113 DC H6 H N N 114 DG OP3 O N N 115 DG P P N N 116 DG OP1 O N N 117 DG OP2 O N N 118 DG "O5'" O N N 119 DG "C5'" C N N 120 DG "C4'" C N R 121 DG "O4'" O N N 122 DG "C3'" C N S 123 DG "O3'" O N N 124 DG "C2'" C N N 125 DG "C1'" C N R 126 DG N9 N Y N 127 DG C8 C Y N 128 DG N7 N Y N 129 DG C5 C Y N 130 DG C6 C N N 131 DG O6 O N N 132 DG N1 N N N 133 DG C2 C N N 134 DG N2 N N N 135 DG N3 N N N 136 DG C4 C Y N 137 DG HOP3 H N N 138 DG HOP2 H N N 139 DG "H5'" H N N 140 DG "H5''" H N N 141 DG "H4'" H N N 142 DG "H3'" H N N 143 DG "HO3'" H N N 144 DG "H2'" H N N 145 DG "H2''" H N N 146 DG "H1'" H N N 147 DG H8 H N N 148 DG H1 H N N 149 DG H21 H N N 150 DG H22 H N N 151 DT OP3 O N N 152 DT P P N N 153 DT OP1 O N N 154 DT OP2 O N N 155 DT "O5'" O N N 156 DT "C5'" C N N 157 DT "C4'" C N R 158 DT "O4'" O N N 159 DT "C3'" C N S 160 DT "O3'" O N N 161 DT "C2'" C N N 162 DT "C1'" C N R 163 DT N1 N N N 164 DT C2 C N N 165 DT O2 O N N 166 DT N3 N N N 167 DT C4 C N N 168 DT O4 O N N 169 DT C5 C N N 170 DT C7 C N N 171 DT C6 C N N 172 DT HOP3 H N N 173 DT HOP2 H N N 174 DT "H5'" H N N 175 DT "H5''" H N N 176 DT "H4'" H N N 177 DT "H3'" H N N 178 DT "HO3'" H N N 179 DT "H2'" H N N 180 DT "H2''" H N N 181 DT "H1'" H N N 182 DT H3 H N N 183 DT H71 H N N 184 DT H72 H N N 185 DT H73 H N N 186 DT H6 H N N 187 HOH O O N N 188 HOH H1 H N N 189 HOH H2 H N N 190 MG MG MG N N 191 # 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 D63 NAA CAR sing N N 1 D63 NAB CAR doub N N 2 D63 CAR CAU sing N N 3 D63 CAU CAM doub Y N 4 D63 CAU CAO sing Y N 5 D63 CAM CAN sing Y N 6 D63 CAO CBA doub Y N 7 D63 CAN CAZ doub Y N 8 D63 CBA CAZ sing Y N 9 D63 CBA NAQ sing Y N 10 D63 CAZ NAP sing Y N 11 D63 NAQ CAY doub Y N 12 D63 NAP CAY sing Y N 13 D63 CAY CAX sing Y N 14 D63 CAX CAL doub Y N 15 D63 CAX CAK sing Y N 16 D63 CAL CAJ sing Y N 17 D63 CAK CAI doub Y N 18 D63 CAJ CAW doub Y N 19 D63 CAI CAW sing Y N 20 D63 CAW CAV sing Y N 21 D63 CAV CAG doub Y N 22 D63 CAV CAH sing Y N 23 D63 CAG CAE sing Y N 24 D63 CAH CAF doub Y N 25 D63 CAE CAT doub Y N 26 D63 CAF CAT sing Y N 27 D63 CAT CAS sing N N 28 D63 CAS NAC sing N N 29 D63 CAS OAD doub N N 30 D63 NAA HNAA sing N N 31 D63 NAA HNAB sing N N 32 D63 NAB HNAC sing N N 33 D63 NAC HNAD sing N N 34 D63 NAC HNAE sing N N 35 D63 CAE HAE sing N N 36 D63 CAF HAF sing N N 37 D63 CAG HAG sing N N 38 D63 CAH HAH sing N N 39 D63 CAI HAI sing N N 40 D63 CAJ HAJ sing N N 41 D63 CAK HAK sing N N 42 D63 CAL HAL sing N N 43 D63 CAM HAM sing N N 44 D63 CAN HAN sing N N 45 D63 CAO HAO sing N N 46 D63 NAP HNAP sing N N 47 DA OP3 P sing N N 48 DA OP3 HOP3 sing N N 49 DA P OP1 doub N N 50 DA P OP2 sing N N 51 DA P "O5'" sing N N 52 DA OP2 HOP2 sing N N 53 DA "O5'" "C5'" sing N N 54 DA "C5'" "C4'" sing N N 55 DA "C5'" "H5'" sing N N 56 DA "C5'" "H5''" sing N N 57 DA "C4'" "O4'" sing N N 58 DA "C4'" "C3'" sing N N 59 DA "C4'" "H4'" sing N N 60 DA "O4'" "C1'" sing N N 61 DA "C3'" "O3'" sing N N 62 DA "C3'" "C2'" sing N N 63 DA "C3'" "H3'" sing N N 64 DA "O3'" "HO3'" sing N N 65 DA "C2'" "C1'" sing N N 66 DA "C2'" "H2'" sing N N 67 DA "C2'" "H2''" sing N N 68 DA "C1'" N9 sing N N 69 DA "C1'" "H1'" sing N N 70 DA N9 C8 sing Y N 71 DA N9 C4 sing Y N 72 DA C8 N7 doub Y N 73 DA C8 H8 sing N N 74 DA N7 C5 sing Y N 75 DA C5 C6 sing Y N 76 DA C5 C4 doub Y N 77 DA C6 N6 sing N N 78 DA C6 N1 doub Y N 79 DA N6 H61 sing N N 80 DA N6 H62 sing N N 81 DA N1 C2 sing Y N 82 DA C2 N3 doub Y N 83 DA C2 H2 sing N N 84 DA N3 C4 sing Y N 85 DC OP3 P sing N N 86 DC OP3 HOP3 sing N N 87 DC P OP1 doub N N 88 DC P OP2 sing N N 89 DC P "O5'" sing N N 90 DC OP2 HOP2 sing N N 91 DC "O5'" "C5'" sing N N 92 DC "C5'" "C4'" sing N N 93 DC "C5'" "H5'" sing N N 94 DC "C5'" "H5''" sing N N 95 DC "C4'" "O4'" sing N N 96 DC "C4'" "C3'" sing N N 97 DC "C4'" "H4'" sing N N 98 DC "O4'" "C1'" sing N N 99 DC "C3'" "O3'" sing N N 100 DC "C3'" "C2'" sing N N 101 DC "C3'" "H3'" sing N N 102 DC "O3'" "HO3'" sing N N 103 DC "C2'" "C1'" sing N N 104 DC "C2'" "H2'" sing N N 105 DC "C2'" "H2''" sing N N 106 DC "C1'" N1 sing N N 107 DC "C1'" "H1'" sing N N 108 DC N1 C2 sing N N 109 DC N1 C6 sing N N 110 DC C2 O2 doub N N 111 DC C2 N3 sing N N 112 DC N3 C4 doub N N 113 DC C4 N4 sing N N 114 DC C4 C5 sing N N 115 DC N4 H41 sing N N 116 DC N4 H42 sing N N 117 DC C5 C6 doub N N 118 DC C5 H5 sing N N 119 DC C6 H6 sing N N 120 DG OP3 P sing N N 121 DG OP3 HOP3 sing N N 122 DG P OP1 doub N N 123 DG P OP2 sing N N 124 DG P "O5'" sing N N 125 DG OP2 HOP2 sing N N 126 DG "O5'" "C5'" sing N N 127 DG "C5'" "C4'" sing N N 128 DG "C5'" "H5'" sing N N 129 DG "C5'" "H5''" sing N N 130 DG "C4'" "O4'" sing N N 131 DG "C4'" "C3'" sing N N 132 DG "C4'" "H4'" sing N N 133 DG "O4'" "C1'" sing N N 134 DG "C3'" "O3'" sing N N 135 DG "C3'" "C2'" sing N N 136 DG "C3'" "H3'" sing N N 137 DG "O3'" "HO3'" sing N N 138 DG "C2'" "C1'" sing N N 139 DG "C2'" "H2'" sing N N 140 DG "C2'" "H2''" sing N N 141 DG "C1'" N9 sing N N 142 DG "C1'" "H1'" sing N N 143 DG N9 C8 sing Y N 144 DG N9 C4 sing Y N 145 DG C8 N7 doub Y N 146 DG C8 H8 sing N N 147 DG N7 C5 sing Y N 148 DG C5 C6 sing N N 149 DG C5 C4 doub Y N 150 DG C6 O6 doub N N 151 DG C6 N1 sing N N 152 DG N1 C2 sing N N 153 DG N1 H1 sing N N 154 DG C2 N2 sing N N 155 DG C2 N3 doub N N 156 DG N2 H21 sing N N 157 DG N2 H22 sing N N 158 DG N3 C4 sing N N 159 DT OP3 P sing N N 160 DT OP3 HOP3 sing N N 161 DT P OP1 doub N N 162 DT P OP2 sing N N 163 DT P "O5'" sing N N 164 DT OP2 HOP2 sing N N 165 DT "O5'" "C5'" sing N N 166 DT "C5'" "C4'" sing N N 167 DT "C5'" "H5'" sing N N 168 DT "C5'" "H5''" sing N N 169 DT "C4'" "O4'" sing N N 170 DT "C4'" "C3'" sing N N 171 DT "C4'" "H4'" sing N N 172 DT "O4'" "C1'" sing N N 173 DT "C3'" "O3'" sing N N 174 DT "C3'" "C2'" sing N N 175 DT "C3'" "H3'" sing N N 176 DT "O3'" "HO3'" sing N N 177 DT "C2'" "C1'" sing N N 178 DT "C2'" "H2'" sing N N 179 DT "C2'" "H2''" sing N N 180 DT "C1'" N1 sing N N 181 DT "C1'" "H1'" sing N N 182 DT N1 C2 sing N N 183 DT N1 C6 sing N N 184 DT C2 O2 doub N N 185 DT C2 N3 sing N N 186 DT N3 C4 sing N N 187 DT N3 H3 sing N N 188 DT C4 O4 doub N N 189 DT C4 C5 sing N N 190 DT C5 C7 sing N N 191 DT C5 C6 doub N N 192 DT C7 H71 sing N N 193 DT C7 H72 sing N N 194 DT C7 H73 sing N N 195 DT C6 H6 sing N N 196 HOH O H1 sing N N 197 HOH O H2 sing N N 198 # _ndb_struct_conf_na.entry_id 3U08 _ndb_struct_conf_na.feature 'b-form double 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 DC 1 1_555 B DG 12 1_555 0.219 -0.160 0.081 2.434 -17.472 1.279 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.170 -0.155 0.222 2.626 -5.563 -3.043 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.226 -0.152 0.164 -1.597 -6.633 0.280 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.251 -0.114 0.021 11.881 -10.271 -0.710 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.051 -0.096 -0.095 7.264 -16.399 1.180 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.089 -0.107 -0.038 1.595 -19.827 7.709 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.142 -0.123 0.054 -2.046 -19.271 6.281 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.039 -0.186 -0.100 -4.942 -15.362 2.053 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.182 -0.186 -0.044 -9.545 -10.408 -0.368 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.167 -0.152 0.216 10.359 -2.574 0.938 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.148 -0.239 0.401 5.316 -25.013 -3.264 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.347 -0.139 -0.174 7.708 18.210 -2.521 12 A_DG12:DC13_B A 12 ? B 13 ? 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 DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.453 0.128 3.300 -1.453 6.692 33.354 -0.866 0.539 3.280 11.509 2.499 34.031 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.766 0.622 3.430 1.481 -3.004 41.654 1.201 -0.911 3.403 -4.216 -2.079 41.782 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.436 0.704 3.116 2.587 9.092 27.396 -0.567 1.435 3.131 18.512 -5.268 28.952 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 0.068 0.115 3.381 1.091 2.849 38.351 -0.191 0.037 3.381 4.328 -1.658 38.467 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.460 -0.269 3.331 -0.164 4.243 35.776 -1.045 -0.767 3.276 6.876 0.266 36.019 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.019 -0.638 3.282 -0.488 0.693 30.138 -1.367 -0.064 3.267 1.333 0.939 30.149 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.421 -0.233 3.298 1.981 1.022 36.158 -0.518 0.956 3.264 1.644 -3.188 36.225 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 0.057 0.307 3.390 0.735 -0.806 40.244 0.540 0.003 3.384 -1.170 -1.067 40.258 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.345 1.203 3.027 -3.029 6.827 26.681 0.916 -1.429 3.173 14.438 6.406 27.688 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.006 0.947 3.589 -3.026 -14.954 44.548 2.506 0.995 3.189 -19.075 3.860 46.962 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 1.518 0.698 3.500 5.491 -9.764 34.276 2.628 -1.614 3.377 -16.045 -9.023 36.008 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 3U08 _atom_sites.fract_transf_matrix[1][1] 0.041545 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.025151 _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] 0.015221 _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 MG N O P # loop_