data_1QYK # _entry.id 1QYK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 1QYK pdb_00001qyk 10.2210/pdb1qyk/pdb NDB UD0040 ? ? RCSB RCSB020226 ? ? WWPDB D_1000020226 ? ? # 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 2003-10-21 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-02-12 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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' 'Version format compliance' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # 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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' diffrn_source 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site 8 6 'Structure model' pdbx_initial_refinement_model # 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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 19 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 20 5 'Structure model' '_pdbx_struct_conn_angle.value' 21 5 'Structure model' '_struct_conn.pdbx_dist_value' 22 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 23 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 24 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 26 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 27 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 28 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 29 5 'Structure model' '_struct_conn.ptnr1_symmetry' 30 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 31 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 32 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 33 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 34 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 35 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 36 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 37 5 'Structure model' '_struct_conn.ptnr2_symmetry' 38 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 39 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 40 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QYK _pdbx_database_status.recvd_initial_deposition_date 2003-09-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1QYL 'GCATGCT + Vanadium' unspecified PDB 1QZL 'GCATGCT + Cobalt' unspecified PDB 1R2O 'GCATGCT + Ni2+' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cardin, C.J.' 1 'Gan, Y.' 2 'Thorpe, J.H.' 3 'Teixeira, S.C.M.' 4 'Gale, B.C.' 5 'Moraes, M.I.A.' 6 # _citation.id primary _citation.title 'Metal Ion Distribution and Stabilization of the DNA Quadruplex Structure Formed by d(GCATGCT)' _citation.journal_abbrev 'To be published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cardin, C.J.' 1 ? primary 'Gan, Y.' 2 ? primary 'Thorpe, J.H.' 3 ? primary 'Teixeira, S.C.M.' 4 ? primary 'Gale, B.C.' 5 ? primary 'Moraes, M.I.A.' 6 ? # 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(*GP*CP*AP*TP*GP*CP*T)-3'" 2113.410 2 ? ? ? ? 2 non-polymer syn 'BARIUM ION' 137.327 2 ? ? ? ? 3 water nat water 18.015 41 ? ? ? ? # _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 '(DG)(DC)(DA)(DT)(DG)(DC)(DT)' _entity_poly.pdbx_seq_one_letter_code_can GCATGCT _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 'BARIUM ION' BA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DA n 1 4 DT n 1 5 DG n 1 6 DC n 1 7 DT 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 BA non-polymer . 'BARIUM ION' ? 'Ba 2' 137.327 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 # 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 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DT 7 7 7 DT T A . n B 1 1 DG 1 1 1 DG G B . n B 1 2 DC 2 2 2 DC C B . n B 1 3 DA 3 3 3 DA A B . n B 1 4 DT 4 4 4 DT T B . n B 1 5 DG 5 5 5 DG G B . n B 1 6 DC 6 6 6 DC C B . n B 1 7 DT 7 7 7 DT T 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 BA 1 8 1 BA BA A . D 2 BA 1 8 2 BA BA B . E 3 HOH 1 100 100 HOH HOH A . E 3 HOH 2 101 101 HOH HOH A . E 3 HOH 3 102 102 HOH HOH A . E 3 HOH 4 105 105 HOH HOH A . E 3 HOH 5 106 106 HOH HOH A . E 3 HOH 6 107 107 HOH HOH A . E 3 HOH 7 108 108 HOH HOH A . E 3 HOH 8 109 109 HOH HOH A . E 3 HOH 9 113 113 HOH HOH A . E 3 HOH 10 115 115 HOH HOH A . E 3 HOH 11 117 117 HOH HOH A . E 3 HOH 12 118 118 HOH HOH A . E 3 HOH 13 120 120 HOH HOH A . E 3 HOH 14 121 121 HOH HOH A . E 3 HOH 15 122 122 HOH HOH A . E 3 HOH 16 123 123 HOH HOH A . E 3 HOH 17 124 124 HOH HOH A . E 3 HOH 18 127 127 HOH HOH A . E 3 HOH 19 128 128 HOH HOH A . E 3 HOH 20 129 129 HOH HOH A . E 3 HOH 21 132 132 HOH HOH A . E 3 HOH 22 133 133 HOH HOH A . E 3 HOH 23 134 134 HOH HOH A . E 3 HOH 24 138 138 HOH HOH A . E 3 HOH 25 141 141 HOH HOH A . F 3 HOH 1 103 103 HOH HOH B . F 3 HOH 2 104 104 HOH HOH B . F 3 HOH 3 110 110 HOH HOH B . F 3 HOH 4 111 111 HOH HOH B . F 3 HOH 5 112 112 HOH HOH B . F 3 HOH 6 114 114 HOH HOH B . F 3 HOH 7 119 119 HOH HOH B . F 3 HOH 8 125 125 HOH HOH B . F 3 HOH 9 126 126 HOH HOH B . F 3 HOH 10 130 130 HOH HOH B . F 3 HOH 11 131 131 HOH HOH B . F 3 HOH 12 135 135 HOH HOH B . F 3 HOH 13 137 137 HOH HOH B . F 3 HOH 14 139 139 HOH HOH B . F 3 HOH 15 140 140 HOH HOH B . F 3 HOH 16 142 142 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 SHELXL-97 refinement . ? 2 XDS 'data reduction' . ? 3 XDS 'data scaling' . ? 4 XTALVIEW refinement . ? 5 # _cell.entry_id 1QYK _cell.length_a 22.015 _cell.length_b 59.536 _cell.length_c 47.667 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 1QYK _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1QYK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.85 _exptl_crystal.density_percent_sol 33.43 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.9 _exptl_crystal_grow.pdbx_details 'Sodium Cacodylate, Barium Chloride, Potassium Chloride, MPD, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 290K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'Sodium Cacodylate' ? ? ? 1 2 1 'Barium Chloride' ? ? ? 1 3 1 'Potassium Chloride' ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'Sodium Cacodylate' ? ? ? 1 7 2 'Barium Chloride' ? ? ? 1 8 2 MPD ? ? ? 1 9 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2003-08-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8416 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.8416 # _reflns.entry_id 1QYK _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20 _reflns.d_resolution_high 1.4 _reflns.number_obs 6514 _reflns.number_all ? _reflns.percent_possible_obs 98.5 _reflns.pdbx_Rmerge_I_obs 0.073 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.d_res_high 1.4 _reflns_shell.d_res_low 1.55 _reflns_shell.percent_possible_all 99.6 _reflns_shell.Rmerge_I_obs 0.256 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.94 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1686 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.entry_id 1QYK _refine.ls_number_reflns_obs 4860 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 100.00 _refine.ls_d_res_high 1.40 _refine.ls_percent_reflns_obs 98.5 _refine.ls_R_factor_obs 0.2011 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2011 _refine.ls_R_factor_R_free 0.2239 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 6.4 _refine.ls_number_reflns_R_free 311 _refine.ls_number_parameters 2909 _refine.ls_number_restraints 2843 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _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_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details 'ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)' _refine.pdbx_starting_model 'NDB entry UDG028' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model anisotropic _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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_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_analyze.entry_id 1QYK _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0.00 _refine_analyze.occupancy_sum_non_hydrogen 316.50 _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 280 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 41 _refine_hist.number_atoms_total 323 _refine_hist.d_res_high 1.40 _refine_hist.d_res_low 100.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.012 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.030 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0009 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.004 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.031 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1QYK _pdbx_refine.R_factor_all_no_cutoff 0.2011 _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff 0.2239 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 6.4 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 311 _pdbx_refine.R_factor_all_4sig_cutoff 0.1995 _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff 0.2162 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 6.3 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 266 _pdbx_refine.number_reflns_obs_4sig_cutoff 4248 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1QYK _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 1QYK _struct.title 'GCATGCT + Barium' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1QYK _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Quadruplex DNA, 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 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1QYK _struct_ref.pdbx_db_accession 1QYK _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1QYK A 1 ? 7 ? 1QYK 1 ? 7 ? 1 7 2 1 1QYK B 1 ? 7 ? 1QYK 1 ? 7 ? 1 7 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 3_555 -x,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 23.8335000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 ? ? A DT 4 O4 ? ? ? 8_456 C BA . BA ? ? A DT 4 A BA 8 1_555 ? ? ? ? ? ? ? 3.067 ? ? metalc2 metalc ? ? A DT 4 O2 ? ? ? 6_554 D BA . BA ? ? A DT 4 B BA 8 1_555 ? ? ? ? ? ? ? 2.992 ? ? metalc3 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 105 1_555 ? ? ? ? ? ? ? 2.668 ? ? metalc4 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 106 1_555 ? ? ? ? ? ? ? 2.760 ? ? metalc5 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 117 1_555 ? ? ? ? ? ? ? 2.876 ? ? metalc6 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 120 1_555 ? ? ? ? ? ? ? 3.236 ? ? metalc7 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 121 1_555 ? ? ? ? ? ? ? 2.677 ? ? metalc8 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 122 1_555 ? ? ? ? ? ? ? 2.965 ? ? metalc9 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 8 A HOH 132 1_555 ? ? ? ? ? ? ? 3.324 ? ? metalc10 metalc ? ? C BA . BA ? ? ? 1_555 B DT 4 O2 ? ? A BA 8 B DT 4 6_555 ? ? ? ? ? ? ? 2.856 ? ? metalc11 metalc ? ? B DG 1 "O3'" ? ? ? 1_555 D BA . BA ? ? B DG 1 B BA 8 1_555 ? ? ? ? ? ? ? 3.301 ? ? metalc12 metalc ? ? B DC 2 OP1 ? ? ? 1_555 D BA . BA ? ? B DC 2 B BA 8 1_555 ? ? ? ? ? ? ? 2.956 ? ? metalc13 metalc ? ? B DT 4 O4 ? ? ? 8_455 D BA . BA ? ? B DT 4 B BA 8 1_555 ? ? ? ? ? ? ? 2.791 ? ? metalc14 metalc ? ? B DG 5 "O3'" ? ? ? 1_555 D BA . BA ? ? B DG 5 B BA 8 1_555 ? ? ? ? ? ? ? 3.330 ? ? metalc15 metalc ? ? B DC 6 OP1 ? ? ? 1_555 D BA . BA ? ? B DC 6 B BA 8 1_555 ? ? ? ? ? ? ? 2.717 ? ? metalc16 metalc ? ? D BA . BA ? ? ? 1_555 F HOH . O ? ? B BA 8 B HOH 130 1_555 ? ? ? ? ? ? ? 2.701 ? ? metalc17 metalc ? ? D BA . BA ? ? ? 1_555 F HOH . O ? ? B BA 8 B HOH 131 1_555 ? ? ? ? ? ? ? 2.452 ? ? hydrog1 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 1 A DC 6 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 5 N2 ? ? A DC 2 A DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog3 hydrog ? ? B DC 2 O2 ? ? ? 1_555 B DG 5 N2 ? ? B DC 2 B DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? # 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 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 105 ? 1_555 123.4 ? 2 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 60.8 ? 3 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 75.3 ? 4 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 117 ? 1_555 70.3 ? 5 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 117 ? 1_555 143.6 ? 6 O ? E HOH . ? A HOH 106 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 117 ? 1_555 130.7 ? 7 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 120 ? 1_555 116.4 ? 8 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 120 ? 1_555 115.5 ? 9 O ? E HOH . ? A HOH 106 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 120 ? 1_555 119.2 ? 10 O ? E HOH . ? A HOH 117 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 120 ? 1_555 77.0 ? 11 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 121 ? 1_555 142.1 ? 12 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 121 ? 1_555 90.7 ? 13 O ? E HOH . ? A HOH 106 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 121 ? 1_555 154.8 ? 14 O ? E HOH . ? A HOH 117 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 121 ? 1_555 72.1 ? 15 O ? E HOH . ? A HOH 120 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 121 ? 1_555 48.5 ? 16 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 122 ? 1_555 134.6 ? 17 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 122 ? 1_555 55.5 ? 18 O ? E HOH . ? A HOH 106 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 122 ? 1_555 128.4 ? 19 O ? E HOH . ? A HOH 117 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 122 ? 1_555 90.2 ? 20 O ? E HOH . ? A HOH 120 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 122 ? 1_555 97.2 ? 21 O ? E HOH . ? A HOH 121 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 122 ? 1_555 49.7 ? 22 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 113.7 ? 23 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 79.6 ? 24 O ? E HOH . ? A HOH 106 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 70.8 ? 25 O ? E HOH . ? A HOH 117 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 129.0 ? 26 O ? E HOH . ? A HOH 120 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 55.1 ? 27 O ? E HOH . ? A HOH 121 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 86.3 ? 28 O ? E HOH . ? A HOH 122 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 110.4 ? 29 O4 ? A DT 4 ? A DT 4 ? 8_456 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 70.5 ? 30 O ? E HOH . ? A HOH 105 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 139.1 ? 31 O ? E HOH . ? A HOH 106 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 82.7 ? 32 O ? E HOH . ? A HOH 117 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 75.7 ? 33 O ? E HOH . ? A HOH 120 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 49.0 ? 34 O ? E HOH . ? A HOH 121 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 95.5 ? 35 O ? E HOH . ? A HOH 122 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 145.2 ? 36 O ? E HOH . ? A HOH 132 ? 1_555 BA ? C BA . ? A BA 8 ? 1_555 O2 ? B DT 4 ? B DT 4 ? 6_555 60.6 ? 37 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 "O3'" ? B DG 1 ? B DG 1 ? 1_555 120.3 ? 38 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 2 ? B DC 2 ? 1_555 76.0 ? 39 "O3'" ? B DG 1 ? B DG 1 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 2 ? B DC 2 ? 1_555 47.5 ? 40 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 O4 ? B DT 4 ? B DT 4 ? 8_455 74.5 ? 41 "O3'" ? B DG 1 ? B DG 1 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O4 ? B DT 4 ? B DT 4 ? 8_455 101.6 ? 42 OP1 ? B DC 2 ? B DC 2 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O4 ? B DT 4 ? B DT 4 ? 8_455 73.9 ? 43 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 "O3'" ? B DG 5 ? B DG 5 ? 1_555 74.3 ? 44 "O3'" ? B DG 1 ? B DG 1 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 "O3'" ? B DG 5 ? B DG 5 ? 1_555 90.1 ? 45 OP1 ? B DC 2 ? B DC 2 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 "O3'" ? B DG 5 ? B DG 5 ? 1_555 94.0 ? 46 O4 ? B DT 4 ? B DT 4 ? 8_455 BA ? D BA . ? B BA 8 ? 1_555 "O3'" ? B DG 5 ? B DG 5 ? 1_555 148.5 ? 47 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 6 ? B DC 6 ? 1_555 118.9 ? 48 "O3'" ? B DG 1 ? B DG 1 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 6 ? B DC 6 ? 1_555 83.9 ? 49 OP1 ? B DC 2 ? B DC 2 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 6 ? B DC 6 ? 1_555 121.2 ? 50 O4 ? B DT 4 ? B DT 4 ? 8_455 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 6 ? B DC 6 ? 1_555 160.7 ? 51 "O3'" ? B DG 5 ? B DG 5 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 OP1 ? B DC 6 ? B DC 6 ? 1_555 48.6 ? 52 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 130 ? 1_555 156.0 ? 53 "O3'" ? B DG 1 ? B DG 1 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 130 ? 1_555 69.9 ? 54 OP1 ? B DC 2 ? B DC 2 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 130 ? 1_555 103.6 ? 55 O4 ? B DT 4 ? B DT 4 ? 8_455 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 130 ? 1_555 82.3 ? 56 "O3'" ? B DG 5 ? B DG 5 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 130 ? 1_555 129.2 ? 57 OP1 ? B DC 6 ? B DC 6 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 130 ? 1_555 82.2 ? 58 O2 ? A DT 4 ? A DT 4 ? 6_554 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 90.9 ? 59 "O3'" ? B DG 1 ? B DG 1 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 145.4 ? 60 OP1 ? B DC 2 ? B DC 2 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 144.5 ? 61 O4 ? B DT 4 ? B DT 4 ? 8_455 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 70.8 ? 62 "O3'" ? B DG 5 ? B DG 5 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 114.3 ? 63 OP1 ? B DC 6 ? B DC 6 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 94.1 ? 64 O ? F HOH . ? B HOH 130 ? 1_555 BA ? D BA . ? B BA 8 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 75.5 ? # 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 BA 8 ? 7 'BINDING SITE FOR RESIDUE BA A 8' AC2 Software B BA 8 ? 8 'BINDING SITE FOR RESIDUE BA B 8' # 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 7 DT A 4 ? DT A 4 . ? 8_456 ? 2 AC1 7 HOH E . ? HOH A 105 . ? 1_555 ? 3 AC1 7 HOH E . ? HOH A 106 . ? 1_555 ? 4 AC1 7 HOH E . ? HOH A 117 . ? 1_555 ? 5 AC1 7 HOH E . ? HOH A 121 . ? 1_555 ? 6 AC1 7 HOH E . ? HOH A 122 . ? 1_555 ? 7 AC1 7 DT B 4 ? DT B 4 . ? 6_555 ? 8 AC2 8 DT A 4 ? DT A 4 . ? 6_554 ? 9 AC2 8 DG B 1 ? DG B 1 . ? 1_555 ? 10 AC2 8 DC B 2 ? DC B 2 . ? 1_555 ? 11 AC2 8 DT B 4 ? DT B 4 . ? 8_455 ? 12 AC2 8 DG B 5 ? DG B 5 . ? 1_555 ? 13 AC2 8 DC B 6 ? DC B 6 . ? 1_555 ? 14 AC2 8 HOH F . ? HOH B 130 . ? 1_555 ? 15 AC2 8 HOH F . ? HOH B 131 . ? 1_555 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 2 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DC _pdbx_validate_rmsd_bond.auth_seq_id_2 2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.487 _pdbx_validate_rmsd_bond.bond_target_value 1.420 _pdbx_validate_rmsd_bond.bond_deviation 0.067 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.011 _pdbx_validate_rmsd_bond.linker_flag 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 "O5'" A DC 2 ? ? "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? 104.18 109.40 -5.22 0.80 N 2 1 C6 A DC 2 ? ? N1 A DC 2 ? ? C2 A DC 2 ? ? 123.91 120.30 3.61 0.40 N 3 1 N1 A DC 2 ? ? C2 A DC 2 ? ? N3 A DC 2 ? ? 114.47 119.20 -4.73 0.70 N 4 1 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.37 119.90 3.47 0.50 N 5 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 123.36 118.90 4.46 0.60 N 6 1 "O5'" A DA 3 ? ? "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 103.82 109.40 -5.58 0.80 N 7 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 103.13 108.00 -4.87 0.70 N 8 1 N1 A DA 3 ? ? C2 A DA 3 ? ? N3 A DA 3 ? ? 126.22 129.30 -3.08 0.50 N 9 1 C2 A DA 3 ? ? N3 A DA 3 ? ? C4 A DA 3 ? ? 114.88 110.60 4.28 0.50 N 10 1 "C3'" A DT 4 ? ? "C2'" A DT 4 ? ? "C1'" A DT 4 ? ? 96.90 102.40 -5.50 0.80 N 11 1 C2 A DT 4 ? ? N3 A DT 4 ? ? C4 A DT 4 ? ? 122.64 127.20 -4.56 0.60 N 12 1 N3 A DT 4 ? ? C4 A DT 4 ? ? C5 A DT 4 ? ? 119.24 115.20 4.04 0.60 N 13 1 C5 A DT 4 ? ? C4 A DT 4 ? ? O4 A DT 4 ? ? 119.72 124.90 -5.18 0.70 N 14 1 C5 A DG 5 ? ? C6 A DG 5 ? ? N1 A DG 5 ? ? 114.70 111.50 3.20 0.50 N 15 1 "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? "C3'" A DT 7 ? ? 109.73 106.00 3.73 0.60 N 16 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 123.58 127.20 -3.62 0.60 N 17 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 124.28 119.00 5.28 0.60 N 18 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 117.93 122.90 -4.97 0.60 N 19 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? "C2'" B DC 2 ? ? 100.52 105.90 -5.38 0.80 N 20 1 C4 B DC 2 ? ? C5 B DC 2 ? ? C6 B DC 2 ? ? 114.09 117.40 -3.31 0.50 N 21 1 "O5'" B DA 3 ? ? "C5'" B DA 3 ? ? "C4'" B DA 3 ? ? 103.99 109.40 -5.41 0.80 N 22 1 C2 B DT 4 ? ? N3 B DT 4 ? ? C4 B DT 4 ? ? 122.75 127.20 -4.45 0.60 N 23 1 N3 B DT 4 ? ? C4 B DT 4 ? ? C5 B DT 4 ? ? 118.96 115.20 3.76 0.60 N 24 1 C5 B DT 4 ? ? C6 B DT 4 ? ? N1 B DT 4 ? ? 120.07 123.70 -3.63 0.60 N 25 1 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 103.49 108.00 -4.51 0.70 N 26 1 "O5'" B DC 6 ? ? "C5'" B DC 6 ? ? "C4'" B DC 6 ? ? 104.19 109.40 -5.21 0.80 N 27 1 N1 B DC 6 ? ? C2 B DC 6 ? ? O2 B DC 6 ? ? 124.97 118.90 6.07 0.60 N 28 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 113.27 108.30 4.97 0.30 N 29 1 C2 B DT 7 ? ? N3 B DT 7 ? ? C4 B DT 7 ? ? 122.31 127.20 -4.89 0.60 N 30 1 N3 B DT 7 ? ? C4 B DT 7 ? ? C5 B DT 7 ? ? 119.71 115.20 4.51 0.60 N # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 107 ? E HOH . 2 1 A HOH 108 ? E HOH . 3 1 B HOH 111 ? F HOH . 4 1 B HOH 142 ? F HOH . # 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 BA BA BA N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 # 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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QYK 'double helix' 1QYK 'hairpin loop' # 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 DG 1 1_555 A DC 6 1_555 -3.130 8.636 -0.425 -3.212 34.095 176.484 1 A_DG1:DC6_A A 1 ? A 6 ? ? ? 1 A DC 2 1_555 A DG 5 1_555 3.148 8.436 -0.166 9.954 34.616 175.146 2 A_DC2:DG5_A A 2 ? A 5 ? ? ? 1 B DC 2 1_555 B DG 5 1_555 -3.057 8.524 0.005 -7.688 34.431 -178.144 3 B_DC2:DG5_B B 2 ? B 5 ? ? ? # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 DG _ndb_struct_na_base_pair_step.i_label_seq_id_1 1 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 A _ndb_struct_na_base_pair_step.j_label_comp_id_1 DC _ndb_struct_na_base_pair_step.j_label_seq_id_1 6 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 DC _ndb_struct_na_base_pair_step.i_label_seq_id_2 2 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 A _ndb_struct_na_base_pair_step.j_label_comp_id_2 DG _ndb_struct_na_base_pair_step.j_label_seq_id_2 5 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift 0.183 _ndb_struct_na_base_pair_step.slide 0.352 _ndb_struct_na_base_pair_step.rise 2.921 _ndb_struct_na_base_pair_step.tilt -2.004 _ndb_struct_na_base_pair_step.roll 6.215 _ndb_struct_na_base_pair_step.twist 28.445 _ndb_struct_na_base_pair_step.x_displacement -0.524 _ndb_struct_na_base_pair_step.y_displacement -0.758 _ndb_struct_na_base_pair_step.helical_rise 2.912 _ndb_struct_na_base_pair_step.inclination 12.442 _ndb_struct_na_base_pair_step.tip 4.011 _ndb_struct_na_base_pair_step.helical_twist 29.170 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_DG1DC2:DG5DC6_AA _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 A _ndb_struct_na_base_pair_step.j_auth_seq_id_1 6 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 A _ndb_struct_na_base_pair_step.j_auth_seq_id_2 5 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # _pdbx_initial_refinement_model.accession_code 184D _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'NDB entry UDG028' # _atom_sites.entry_id 1QYK _atom_sites.fract_transf_matrix[1][1] 0.045424 _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] 0.016797 _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] 0.020979 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol BA C N O P # loop_