data_109D # _entry.id 109D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 109D pdb_0000109d 10.2210/pdb109d/pdb RCSB GDL033 ? ? WWPDB D_1000170023 ? ? # 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 1995-05-08 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.value' 6 4 'Structure model' '_struct_conn.pdbx_dist_value' 7 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 8 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 9 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 10 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 109D _pdbx_database_status.recvd_initial_deposition_date 1995-02-15 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Czarny, A.' 1 'Boykin, D.W.' 2 'Wood, A.A.' 3 'Nunn, C.M.' 4 'Neidle, S.' 5 'Zhao, M.' 6 'Wilson, W.D.' 7 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2. ; 'Nucleic Acids Res.' 23 3678 3684 1995 NARHAD UK 0305-1048 0389 ? 7478996 10.1093/nar/23.18.3678 1 'Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA' J.Am.Chem.Soc. 117 4716 4717 1995 JACSAT US 0002-7863 0004 ? ? ? 2 ;Low Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G ; Biochemistry 30 10294 ? 1991 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wood, A.A.' 1 ? primary 'Nunn, C.M.' 2 ? primary 'Czarny, A.' 3 ? primary 'Boykin, D.W.' 4 ? primary 'Neidle, S.' 5 ? 1 'Czarny, A.' 6 ? 1 'Boykin, D.W.' 7 ? 1 'Wood, A.A.' 8 ? 1 'Nunn, C.M.' 9 ? 1 'Neidle, S.' 10 ? 1 'Zhao, M.' 11 ? 1 'Wilson, W.D.' 12 ? 2 'Quintana, J.R.' 13 ? 2 'Lipanov, A.A.' 14 ? 2 'Dickerson, R.E.' 15 ? # 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 ;DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') ; 3663.392 2 ? ? ? ? 2 non-polymer syn '5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE' 396.445 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 90 ? ? ? ? # _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 '5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE' IBB 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 # 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 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 IBB non-polymer . '5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE' ? 'C23 H20 N6 O' 396.445 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 C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G 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 IBB 1 25 25 IBB IBB A . D 3 MG 1 26 26 MG MO6 A . E 4 HOH 1 29 29 HOH HOH A . E 4 HOH 2 30 30 HOH HOH A . E 4 HOH 3 31 31 HOH HOH A . E 4 HOH 4 33 33 HOH HOH A . E 4 HOH 5 34 34 HOH HOH A . E 4 HOH 6 37 37 HOH HOH A . E 4 HOH 7 38 38 HOH HOH A . E 4 HOH 8 40 40 HOH HOH A . E 4 HOH 9 41 41 HOH HOH A . E 4 HOH 10 42 42 HOH HOH A . E 4 HOH 11 43 43 HOH HOH A . E 4 HOH 12 44 44 HOH HOH A . E 4 HOH 13 45 45 HOH HOH A . E 4 HOH 14 47 47 HOH HOH A . E 4 HOH 15 49 49 HOH HOH A . E 4 HOH 16 50 50 HOH HOH A . E 4 HOH 17 52 52 HOH HOH A . E 4 HOH 18 54 54 HOH HOH A . E 4 HOH 19 55 55 HOH HOH A . E 4 HOH 20 58 58 HOH HOH A . E 4 HOH 21 60 60 HOH HOH A . E 4 HOH 22 62 62 HOH HOH A . E 4 HOH 23 63 63 HOH HOH A . E 4 HOH 24 65 65 HOH HOH A . E 4 HOH 25 66 66 HOH HOH A . E 4 HOH 26 67 67 HOH HOH A . E 4 HOH 27 69 69 HOH HOH A . E 4 HOH 28 70 70 HOH HOH A . E 4 HOH 29 72 72 HOH HOH A . E 4 HOH 30 75 75 HOH HOH A . E 4 HOH 31 76 76 HOH HOH A . E 4 HOH 32 78 78 HOH HOH A . E 4 HOH 33 79 79 HOH HOH A . E 4 HOH 34 80 80 HOH HOH A . E 4 HOH 35 83 83 HOH HOH A . E 4 HOH 36 86 86 HOH HOH A . E 4 HOH 37 87 87 HOH HOH A . E 4 HOH 38 88 88 HOH HOH A . E 4 HOH 39 89 89 HOH HOH A . E 4 HOH 40 90 90 HOH HOH A . E 4 HOH 41 91 91 HOH HOH A . E 4 HOH 42 92 92 HOH HOH A . E 4 HOH 43 93 93 HOH HOH A . E 4 HOH 44 94 94 HOH HOH A . E 4 HOH 45 95 95 HOH HOH A . E 4 HOH 46 100 100 HOH HOH A . E 4 HOH 47 101 101 HOH HOH A . E 4 HOH 48 102 102 HOH HOH A . E 4 HOH 49 103 103 HOH HOH A . E 4 HOH 50 104 104 HOH HOH A . E 4 HOH 51 105 105 HOH HOH A . E 4 HOH 52 106 106 HOH HOH A . E 4 HOH 53 107 107 HOH HOH A . E 4 HOH 54 108 108 HOH HOH A . E 4 HOH 55 109 109 HOH HOH A . E 4 HOH 56 111 26 HOH MO6 A . E 4 HOH 57 112 26 HOH MO6 A . E 4 HOH 58 113 26 HOH MO6 A . E 4 HOH 59 114 26 HOH MO6 A . E 4 HOH 60 115 26 HOH MO6 A . E 4 HOH 61 116 26 HOH MO6 A . F 4 HOH 1 27 27 HOH HOH B . F 4 HOH 2 28 28 HOH HOH B . F 4 HOH 3 32 32 HOH HOH B . F 4 HOH 4 35 35 HOH HOH B . F 4 HOH 5 36 36 HOH HOH B . F 4 HOH 6 39 39 HOH HOH B . F 4 HOH 7 46 46 HOH HOH B . F 4 HOH 8 48 48 HOH HOH B . F 4 HOH 9 51 51 HOH HOH B . F 4 HOH 10 53 53 HOH HOH B . F 4 HOH 11 56 56 HOH HOH B . F 4 HOH 12 57 57 HOH HOH B . F 4 HOH 13 59 59 HOH HOH B . F 4 HOH 14 61 61 HOH HOH B . F 4 HOH 15 64 64 HOH HOH B . F 4 HOH 16 68 68 HOH HOH B . F 4 HOH 17 71 71 HOH HOH B . F 4 HOH 18 73 73 HOH HOH B . F 4 HOH 19 74 74 HOH HOH B . F 4 HOH 20 77 77 HOH HOH B . F 4 HOH 21 81 81 HOH HOH B . F 4 HOH 22 82 82 HOH HOH B . F 4 HOH 23 84 84 HOH HOH B . F 4 HOH 24 85 85 HOH HOH B . F 4 HOH 25 96 96 HOH HOH B . F 4 HOH 26 97 97 HOH HOH B . F 4 HOH 27 98 98 HOH HOH B . F 4 HOH 28 99 99 HOH HOH B . F 4 HOH 29 110 110 HOH HOH B . # _software.name X-PLOR _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 109D _cell.length_a 24.590 _cell.length_b 40.440 _cell.length_c 65.760 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 109D _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 # _exptl.entry_id 109D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.23 _exptl_crystal.density_percent_sol 44.88 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type XENTRONICS _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ENRAF-NONIUS _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 109D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high ? _reflns.number_obs ? _reflns.number_all ? _reflns.percent_possible_obs 87.000 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 109D _refine.ls_number_reflns_obs 4016 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 2.000 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1970000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1970000 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 37 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 607 _refine_hist.d_res_high 2.000 _refine_hist.d_res_low 8.000 # 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_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.020 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 4.30 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 109D _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 109D _struct.title ;VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2 ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 109D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, 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 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 109D _struct_ref.pdbx_db_accession 109D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 109D A 1 ? 12 ? 109D 1 ? 12 ? 1 12 2 1 109D B 1 ? 12 ? 109D 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # _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 # 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 E HOH . O ? ? A MG 26 A HOH 111 1_555 ? ? ? ? ? ? ? 2.179 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 112 1_555 ? ? ? ? ? ? ? 2.192 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 113 1_555 ? ? ? ? ? ? ? 2.200 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 114 1_555 ? ? ? ? ? ? ? 2.305 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 115 1_555 ? ? ? ? ? ? ? 2.206 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 116 1_555 ? ? ? ? ? ? ? 2.251 ? ? 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 N6 ? ? ? 1_555 B DA 6 N1 ? ? A DA 6 B DA 18 1_555 ? ? ? ? ? ? 'DA-DA MISPAIR' ? ? ? hydrog16 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 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 ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 112 ? 1_555 93.1 ? 2 O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 113 ? 1_555 95.5 ? 3 O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 113 ? 1_555 87.0 ? 4 O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 114 ? 1_555 174.7 ? 5 O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 114 ? 1_555 91.3 ? 6 O ? E HOH . ? A HOH 113 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 114 ? 1_555 87.5 ? 7 O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 90.9 ? 8 O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 171.6 ? 9 O ? E HOH . ? A HOH 113 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 85.3 ? 10 O ? E HOH . ? A HOH 114 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 85.0 ? 11 O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 93.6 ? 12 O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 91.1 ? 13 O ? E HOH . ? A HOH 113 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 170.7 ? 14 O ? E HOH . ? A HOH 114 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 83.5 ? 15 O ? E HOH . ? A HOH 115 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 96.0 ? # 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 IBB 25 ? 12 'BINDING SITE FOR RESIDUE IBB A 25' AC2 Software A MG 26 ? 6 'BINDING SITE FOR RESIDUE MG A 26' 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 12 DA A 5 ? DA A 5 . ? 1_555 ? 2 AC1 12 DA A 6 ? DA A 6 . ? 1_555 ? 3 AC1 12 DT A 7 ? DT A 7 . ? 1_555 ? 4 AC1 12 DT A 8 ? DT A 8 . ? 1_555 ? 5 AC1 12 DC A 9 ? DC A 9 . ? 1_555 ? 6 AC1 12 HOH E . ? HOH A 40 . ? 1_555 ? 7 AC1 12 HOH E . ? HOH A 62 . ? 1_555 ? 8 AC1 12 HOH E . ? HOH A 66 . ? 1_555 ? 9 AC1 12 DA B 6 ? DA B 18 . ? 1_555 ? 10 AC1 12 DT B 7 ? DT B 19 . ? 1_555 ? 11 AC1 12 DT B 8 ? DT B 20 . ? 1_555 ? 12 AC1 12 DC B 9 ? DC B 21 . ? 1_555 ? 13 AC2 6 HOH E . ? HOH A 111 . ? 1_555 ? 14 AC2 6 HOH E . ? HOH A 112 . ? 1_555 ? 15 AC2 6 HOH E . ? HOH A 113 . ? 1_555 ? 16 AC2 6 HOH E . ? HOH A 114 . ? 1_555 ? 17 AC2 6 HOH E . ? HOH A 115 . ? 1_555 ? 18 AC2 6 HOH E . ? HOH A 116 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C3'" A DC 3 ? ? "C2'" A DC 3 ? ? 1.464 1.516 -0.052 0.008 N 2 1 C5 A DG 4 ? ? N7 A DG 4 ? ? 1.347 1.388 -0.041 0.006 N 3 1 C6 A DA 6 ? ? N1 A DA 6 ? ? 1.414 1.351 0.063 0.007 N 4 1 N9 A DA 6 ? ? C4 A DA 6 ? ? 1.416 1.374 0.042 0.006 N 5 1 C5 A DG 10 ? ? N7 A DG 10 ? ? 1.351 1.388 -0.037 0.006 N 6 1 N1 B DA 18 ? ? C2 B DA 18 ? ? 1.225 1.339 -0.114 0.009 N 7 1 C2 B DA 18 ? ? N3 B DA 18 ? ? 1.174 1.331 -0.157 0.009 N 8 1 N3 B DA 18 ? ? C4 B DA 18 ? ? 1.470 1.344 0.126 0.006 N 9 1 C6 B DA 18 ? ? N1 B DA 18 ? ? 1.275 1.351 -0.076 0.007 N 10 1 C5 B DA 18 ? ? N7 B DA 18 ? ? 1.348 1.388 -0.040 0.006 N 11 1 N9 B DA 18 ? ? C4 B DA 18 ? ? 1.473 1.374 0.099 0.006 N 12 1 C5 B DG 22 ? ? N7 B DG 22 ? ? 1.345 1.388 -0.043 0.006 N 13 1 C5 B DG 24 ? ? N7 B DG 24 ? ? 1.345 1.388 -0.043 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 103.46 108.00 -4.54 0.70 N 2 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DC 3 ? ? 128.57 119.70 8.87 1.20 Y 3 1 P A DC 3 ? ? "O5'" A DC 3 ? ? "C5'" A DC 3 ? ? 109.68 120.90 -11.22 1.60 N 4 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 99.90 105.90 -6.00 0.80 N 5 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 113.26 108.30 4.96 0.30 N 6 1 "O4'" A DA 6 ? ? "C4'" A DA 6 ? ? "C3'" A DA 6 ? ? 101.02 104.50 -3.48 0.40 N 7 1 "C1'" A DA 6 ? ? "O4'" A DA 6 ? ? "C4'" A DA 6 ? ? 116.89 110.30 6.59 0.70 N 8 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? "C2'" A DA 6 ? ? 99.87 105.90 -6.03 0.80 N 9 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.39 108.30 3.09 0.30 N 10 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 105.50 118.60 -13.10 0.60 N 11 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 136.72 129.30 7.42 0.50 N 12 1 N3 A DA 6 ? ? C4 A DA 6 ? ? C5 A DA 6 ? ? 121.93 126.80 -4.87 0.70 N 13 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N1 A DA 6 ? ? 124.46 117.70 6.76 0.50 N 14 1 C5 A DA 6 ? ? N7 A DA 6 ? ? C8 A DA 6 ? ? 107.41 103.90 3.51 0.50 N 15 1 N9 A DA 6 ? ? C4 A DA 6 ? ? C5 A DA 6 ? ? 108.20 105.80 2.40 0.40 N 16 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N6 A DA 6 ? ? 117.36 123.70 -6.34 0.80 N 17 1 "C3'" A DA 6 ? ? "O3'" A DA 6 ? ? P A DT 7 ? ? 129.35 119.70 9.65 1.20 Y 18 1 "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? "C3'" A DT 7 ? ? 101.04 104.50 -3.46 0.40 N 19 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 113.53 108.30 5.23 0.30 N 20 1 C6 A DT 7 ? ? N1 A DT 7 ? ? C2 A DT 7 ? ? 118.05 121.30 -3.25 0.50 N 21 1 N3 A DT 7 ? ? C4 A DT 7 ? ? C5 A DT 7 ? ? 109.49 115.20 -5.71 0.60 N 22 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C6 A DT 7 ? ? 124.03 118.00 6.03 0.60 N 23 1 N3 A DT 7 ? ? C2 A DT 7 ? ? O2 A DT 7 ? ? 115.73 122.30 -6.57 0.60 N 24 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 116.75 122.90 -6.15 0.60 N 25 1 "O4'" A DT 8 ? ? "C4'" A DT 8 ? ? "C3'" A DT 8 ? ? 101.84 104.50 -2.66 0.40 N 26 1 N1 A DT 8 ? ? C2 A DT 8 ? ? N3 A DT 8 ? ? 118.41 114.60 3.81 0.60 N 27 1 C4 A DT 8 ? ? C5 A DT 8 ? ? C6 A DT 8 ? ? 122.77 118.00 4.77 0.60 N 28 1 N3 A DT 8 ? ? C2 A DT 8 ? ? O2 A DT 8 ? ? 118.14 122.30 -4.16 0.60 N 29 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 101.07 108.00 -6.93 0.70 N 30 1 "O4'" A DG 12 ? ? "C4'" A DG 12 ? ? "C3'" A DG 12 ? ? 101.56 104.50 -2.94 0.40 N 31 1 "C3'" B DC 13 ? ? "O3'" B DC 13 ? ? P B DG 14 ? ? 127.56 119.70 7.86 1.20 Y 32 1 "O4'" B DC 15 ? ? "C4'" B DC 15 ? ? "C3'" B DC 15 ? ? 101.34 104.50 -3.16 0.40 N 33 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? "C2'" B DC 15 ? ? 100.85 105.90 -5.05 0.80 N 34 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 110.88 108.30 2.58 0.30 N 35 1 C2 B DC 15 ? ? N3 B DC 15 ? ? C4 B DC 15 ? ? 124.02 119.90 4.12 0.50 N 36 1 N3 B DC 15 ? ? C4 B DC 15 ? ? C5 B DC 15 ? ? 118.42 121.90 -3.48 0.40 N 37 1 "C3'" B DA 17 ? ? "O3'" B DA 17 ? ? P B DA 18 ? ? 131.17 119.70 11.47 1.20 Y 38 1 "C1'" B DA 18 ? ? "O4'" B DA 18 ? ? "C4'" B DA 18 ? ? 118.54 110.30 8.24 0.70 N 39 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? "C2'" B DA 18 ? ? 95.20 105.90 -10.70 0.80 N 40 1 C6 B DA 18 ? ? N1 B DA 18 ? ? C2 B DA 18 ? ? 132.96 118.60 14.36 0.60 N 41 1 N1 B DA 18 ? ? C2 B DA 18 ? ? N3 B DA 18 ? ? 120.94 129.30 -8.36 0.50 N 42 1 C2 B DA 18 ? ? N3 B DA 18 ? ? C4 B DA 18 ? ? 116.87 110.60 6.27 0.50 N 43 1 N3 B DA 18 ? ? C4 B DA 18 ? ? C5 B DA 18 ? ? 121.41 126.80 -5.39 0.70 N 44 1 C4 B DA 18 ? ? C5 B DA 18 ? ? C6 B DA 18 ? ? 111.72 117.00 -5.28 0.50 N 45 1 N9 B DA 18 ? ? C4 B DA 18 ? ? C5 B DA 18 ? ? 100.33 105.80 -5.47 0.40 N 46 1 N3 B DA 18 ? ? C4 B DA 18 ? ? N9 B DA 18 ? ? 138.24 127.40 10.84 0.80 N 47 1 N1 B DA 18 ? ? C6 B DA 18 ? ? N6 B DA 18 ? ? 106.90 118.60 -11.70 0.60 N 48 1 C5 B DA 18 ? ? C6 B DA 18 ? ? N6 B DA 18 ? ? 137.03 123.70 13.33 0.80 N 49 1 P B DT 19 ? ? "O5'" B DT 19 ? ? "C5'" B DT 19 ? ? 108.26 120.90 -12.64 1.60 N 50 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 110.93 108.30 2.63 0.30 N 51 1 N3 B DT 19 ? ? C4 B DT 19 ? ? C5 B DT 19 ? ? 110.65 115.20 -4.55 0.60 N 52 1 C4 B DT 19 ? ? C5 B DT 19 ? ? C6 B DT 19 ? ? 122.15 118.00 4.15 0.60 N 53 1 "O4'" B DT 20 ? ? "C4'" B DT 20 ? ? "C3'" B DT 20 ? ? 100.26 104.50 -4.24 0.40 N 54 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 102.92 108.00 -5.08 0.70 N 55 1 P B DC 21 ? ? "O5'" B DC 21 ? ? "C5'" B DC 21 ? ? 111.19 120.90 -9.71 1.60 N 56 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 102.63 108.00 -5.37 0.70 N 57 1 N1 B DC 21 ? ? C2 B DC 21 ? ? O2 B DC 21 ? ? 122.51 118.90 3.61 0.60 N 58 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 111.21 108.30 2.91 0.30 N 59 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1 B DC 23 ? ? 111.96 108.30 3.66 0.30 N 60 1 N9 B DG 24 ? ? "C1'" B DG 24 ? ? "C2'" B DG 24 ? ? 100.93 112.60 -11.67 1.90 N 61 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 116.31 108.30 8.01 0.30 N 62 1 N7 B DG 24 ? ? C8 B DG 24 ? ? N9 B DG 24 ? ? 116.65 113.10 3.55 0.50 N 63 1 C8 B DG 24 ? ? N9 B DG 24 ? ? C4 B DG 24 ? ? 103.30 106.40 -3.10 0.40 N 64 1 N3 B DG 24 ? ? C2 B DG 24 ? ? N2 B DG 24 ? ? 114.82 119.90 -5.08 0.70 N 65 1 N1 B DG 24 ? ? C6 B DG 24 ? ? O6 B DG 24 ? ? 123.63 119.90 3.73 0.60 N # _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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 IBB C1 C N N 147 IBB C2 C N N 148 IBB C3 C N N 149 IBB C4 C Y N 150 IBB C5 C Y N 151 IBB C6 C Y N 152 IBB C7 C Y N 153 IBB C8 C Y N 154 IBB C9 C Y N 155 IBB C10 C Y N 156 IBB C11 C Y N 157 IBB C12 C Y N 158 IBB C13 C Y N 159 IBB C14 C Y N 160 IBB C15 C Y N 161 IBB C16 C Y N 162 IBB C17 C Y N 163 IBB C18 C Y N 164 IBB C19 C Y N 165 IBB C20 C Y N 166 IBB C21 C Y N 167 IBB C22 C Y N 168 IBB C23 C Y N 169 IBB N1 N N N 170 IBB N2 N N N 171 IBB N3 N Y N 172 IBB N4 N Y N 173 IBB N5 N Y N 174 IBB N6 N Y N 175 IBB O1 O N N 176 IBB H1 H N N 177 IBB H21A H N N 178 IBB H22 H N N 179 IBB H31 H N N 180 IBB H32 H N N 181 IBB H5 H N N 182 IBB H6 H N N 183 IBB H9 H N N 184 IBB H13 H N N 185 IBB H14 H N N 186 IBB H17 H N N 187 IBB H18 H N N 188 IBB H20 H N N 189 IBB H21 H N N 190 IBB H23 H N N 191 IBB HN1 H N N 192 IBB HN2 H N N 193 IBB HN3 H N N 194 IBB HN6 H N N 195 IBB HO1 H N N 196 MG MG MG N N 197 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 IBB C1 C4 sing N N 152 IBB C1 N1 sing N N 153 IBB C1 N2 sing N N 154 IBB C1 H1 sing N N 155 IBB C2 C3 sing N N 156 IBB C2 N1 sing N N 157 IBB C2 H21A sing N N 158 IBB C2 H22 sing N N 159 IBB C3 N2 sing N N 160 IBB C3 H31 sing N N 161 IBB C3 H32 sing N N 162 IBB C4 C5 sing Y N 163 IBB C4 C9 doub Y N 164 IBB C5 C6 doub Y N 165 IBB C5 H5 sing N N 166 IBB C6 C7 sing Y N 167 IBB C6 H6 sing N N 168 IBB C7 C8 doub Y N 169 IBB C7 N4 sing Y N 170 IBB C8 C9 sing Y N 171 IBB C8 N3 sing Y N 172 IBB C9 H9 sing N N 173 IBB C10 C22 sing Y N 174 IBB C10 N3 sing Y N 175 IBB C10 N4 doub Y N 176 IBB C11 C12 doub Y N 177 IBB C11 C23 sing Y N 178 IBB C11 N6 sing Y N 179 IBB C12 C13 sing Y N 180 IBB C12 N5 sing Y N 181 IBB C13 C14 doub Y N 182 IBB C13 H13 sing N N 183 IBB C14 C22 sing Y N 184 IBB C14 H14 sing N N 185 IBB C15 C16 sing Y N 186 IBB C15 N5 doub Y N 187 IBB C15 N6 sing Y N 188 IBB C16 C17 sing Y N 189 IBB C16 C21 doub Y N 190 IBB C17 C18 doub Y N 191 IBB C17 H17 sing N N 192 IBB C18 C19 sing Y N 193 IBB C18 H18 sing N N 194 IBB C19 C20 doub Y N 195 IBB C19 O1 sing N N 196 IBB C20 C21 sing Y N 197 IBB C20 H20 sing N N 198 IBB C21 H21 sing N N 199 IBB C22 C23 doub Y N 200 IBB C23 H23 sing N N 201 IBB N1 HN1 sing N N 202 IBB N2 HN2 sing N N 203 IBB N3 HN3 sing N N 204 IBB N6 HN6 sing N N 205 IBB O1 HO1 sing N N 206 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 109D 'double helix' 109D 'b-form double helix' 109D 'mismatched base pair' # 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 0.227 -0.183 -0.224 5.955 -13.604 -0.490 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.035 -0.233 0.260 -0.896 -8.828 -3.452 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.013 -0.140 -0.005 -0.627 -5.057 -1.400 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.152 -0.038 -0.025 11.866 -4.328 -2.655 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.096 -0.068 -0.197 6.887 -19.745 0.156 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.047 -0.226 0.554 -6.398 -17.803 2.897 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.656 -0.184 0.761 0.750 -7.168 18.116 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.151 -0.194 -0.063 -7.253 -18.250 -2.478 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 -0.013 -0.113 -0.006 -10.992 -8.317 -1.696 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.011 -0.210 0.087 4.340 -1.819 -0.710 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.076 -0.146 0.098 5.431 -19.539 -2.624 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.154 -0.212 -0.283 4.047 8.262 -4.384 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 -0.289 0.288 3.562 -4.363 9.194 36.811 -0.845 -0.168 3.541 14.228 6.753 38.145 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 0.633 0.487 3.438 3.367 -6.420 38.769 1.517 -0.521 3.360 -9.569 -5.019 39.416 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 -0.189 0.650 3.158 1.357 7.390 29.638 -0.217 0.625 3.211 14.162 -2.600 30.555 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 0.041 0.217 3.495 2.883 1.794 36.423 0.081 0.359 3.495 2.863 -4.599 36.576 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 0.315 -0.697 3.505 -7.700 6.367 38.355 -1.811 -1.410 3.233 9.496 11.483 39.587 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 0.833 -0.212 3.120 1.365 -10.896 26.250 2.009 -1.391 3.006 -22.765 -2.853 28.417 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 -0.831 -0.433 3.311 8.910 10.172 39.651 -1.645 2.073 2.877 14.494 -12.695 41.805 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 -0.016 0.373 3.494 -0.219 0.347 41.030 0.492 -0.003 3.497 0.495 0.312 41.032 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 0.182 1.181 3.202 -2.888 3.333 29.498 1.604 -0.952 3.280 6.499 5.632 29.819 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 -0.913 0.915 3.445 -1.243 -13.319 39.261 2.744 1.156 3.019 -19.159 1.788 41.392 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 0.879 0.906 3.637 4.677 -4.249 39.507 1.867 -0.687 3.601 -6.238 -6.865 39.989 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 109D _atom_sites.fract_transf_matrix[1][1] 0.040667 _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] 0.024728 _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] 0.015207 _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_