data_3QF8 # _entry.id 3QF8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 3QF8 pdb_00003qf8 10.2210/pdb3qf8/pdb NDB NA0938 ? ? RCSB RCSB063569 ? ? WWPDB D_1000063569 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-10-19 2 'Structure model' 1 1 2013-06-26 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2024-03-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Refinement description' 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 3 'Structure model' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 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 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 3 'Structure model' '_software.version' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.value' 19 4 'Structure model' '_struct_conn.pdbx_dist_value' 20 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 32 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 33 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3QF8 _pdbx_database_status.recvd_initial_deposition_date 2011-01-21 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cardin, C.J.' 1 'Hall, J.P.' 2 # _citation.id primary _citation.title ;Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand. ; _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 108 _citation.page_first 17610 _citation.page_last 17614 _citation.year 2011 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21969542 _citation.pdbx_database_id_DOI 10.1073/pnas.1108685108 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hall, J.P.' 1 ? primary ;O'Sullivan, K. ; 2 ? primary 'Naseer, A.' 3 ? primary 'Smith, J.A.' 4 ? primary 'Kelly, J.M.' 5 ? primary 'Cardin, C.J.' 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(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'" 3045.992 1 ? ? ? ? 2 non-polymer syn 'Ru(tap)2(dppz) complex' 747.732 1 ? ? ? ? 3 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 4 water nat water 18.015 87 ? ? ? ? # _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 '(DT)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TCGGCGCCGA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'Ru(tap)2(dppz) complex' RKL 3 'BARIUM ION' BA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DA 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 RKL non-polymer . 'Ru(tap)2(dppz) complex' ? 'C38 H22 N12 Ru 2' 747.732 # 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 DT 1 1 1 DT T A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DA 10 10 10 DA A A . 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 B 2 RKL 1 11 1 RKL RKL A . C 3 BA 1 12 1 BA HA A . D 4 HOH 1 13 13 HOH HOH A . D 4 HOH 2 14 14 HOH HOH A . D 4 HOH 3 15 15 HOH HOH A . D 4 HOH 4 16 16 HOH HOH A . D 4 HOH 5 17 1 HOH HOH A . D 4 HOH 6 18 2 HOH HOH A . D 4 HOH 7 19 19 HOH HOH A . D 4 HOH 8 20 20 HOH HOH A . D 4 HOH 9 21 21 HOH HOH A . D 4 HOH 10 22 22 HOH HOH A . D 4 HOH 11 23 23 HOH HOH A . D 4 HOH 12 24 24 HOH HOH A . D 4 HOH 13 25 25 HOH HOH A . D 4 HOH 14 26 26 HOH HOH A . D 4 HOH 15 27 3 HOH HOH A . D 4 HOH 16 28 28 HOH HOH A . D 4 HOH 17 29 29 HOH HOH A . D 4 HOH 18 30 30 HOH HOH A . D 4 HOH 19 31 31 HOH HOH A . D 4 HOH 20 32 32 HOH HOH A . D 4 HOH 21 33 33 HOH HOH A . D 4 HOH 22 34 34 HOH HOH A . D 4 HOH 23 35 4 HOH HOH A . D 4 HOH 24 36 36 HOH HOH A . D 4 HOH 25 37 5 HOH HOH A . D 4 HOH 26 38 38 HOH HOH A . D 4 HOH 27 39 39 HOH HOH A . D 4 HOH 28 40 40 HOH HOH A . D 4 HOH 29 41 6 HOH HOH A . D 4 HOH 30 42 42 HOH HOH A . D 4 HOH 31 43 43 HOH HOH A . D 4 HOH 32 44 44 HOH HOH A . D 4 HOH 33 45 45 HOH HOH A . D 4 HOH 34 46 8 HOH HOH A . D 4 HOH 35 47 47 HOH HOH A . D 4 HOH 36 48 9 HOH HOH A . D 4 HOH 37 49 49 HOH HOH A . D 4 HOH 38 50 50 HOH HOH A . D 4 HOH 39 51 51 HOH HOH A . D 4 HOH 40 52 52 HOH HOH A . D 4 HOH 41 53 53 HOH HOH A . D 4 HOH 42 54 54 HOH HOH A . D 4 HOH 43 55 55 HOH HOH A . D 4 HOH 44 56 56 HOH HOH A . D 4 HOH 45 57 57 HOH HOH A . D 4 HOH 46 58 58 HOH HOH A . D 4 HOH 47 59 10 HOH HOH A . D 4 HOH 48 60 60 HOH HOH A . D 4 HOH 49 61 61 HOH HOH A . D 4 HOH 50 62 62 HOH HOH A . D 4 HOH 51 63 12 HOH HOH A . D 4 HOH 52 64 64 HOH HOH A . D 4 HOH 53 66 66 HOH HOH A . D 4 HOH 54 67 67 HOH HOH A . D 4 HOH 55 68 68 HOH HOH A . D 4 HOH 56 69 69 HOH HOH A . D 4 HOH 57 70 70 HOH HOH A . D 4 HOH 58 72 72 HOH HOH A . D 4 HOH 59 73 73 HOH HOH A . D 4 HOH 60 74 74 HOH HOH A . D 4 HOH 61 75 75 HOH HOH A . D 4 HOH 62 76 76 HOH HOH A . D 4 HOH 63 77 77 HOH HOH A . D 4 HOH 64 78 78 HOH HOH A . D 4 HOH 65 79 79 HOH HOH A . D 4 HOH 66 80 80 HOH HOH A . D 4 HOH 67 81 81 HOH HOH A . D 4 HOH 68 82 82 HOH HOH A . D 4 HOH 69 83 83 HOH HOH A . D 4 HOH 70 84 84 HOH HOH A . D 4 HOH 71 85 85 HOH HOH A . D 4 HOH 72 86 86 HOH HOH A . D 4 HOH 73 88 88 HOH HOH A . D 4 HOH 74 89 89 HOH HOH A . D 4 HOH 75 95 95 HOH HOH A . D 4 HOH 76 108 108 HOH HOH A . D 4 HOH 77 114 114 HOH HOH A . D 4 HOH 78 115 115 HOH HOH A . D 4 HOH 79 122 122 HOH HOH A . D 4 HOH 80 123 123 HOH HOH A . D 4 HOH 81 124 124 HOH HOH A . D 4 HOH 82 125 125 HOH HOH A . D 4 HOH 83 133 133 HOH HOH A . D 4 HOH 84 134 134 HOH HOH A . D 4 HOH 85 136 136 HOH HOH A . D 4 HOH 86 137 137 HOH HOH A . D 4 HOH 87 138 138 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrysalisPro 'data collection' . ? 1 SHELXCD phasing . ? 2 SHELXE 'model building' . ? 3 REFMAC refinement 5.5.0109 ? 4 CrysalisPro 'data reduction' . ? 5 CrysalisPro 'data scaling' . ? 6 # _cell.entry_id 3QF8 _cell.length_a 42.239 _cell.length_b 42.239 _cell.length_c 39.379 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3QF8 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3QF8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.88 _exptl_crystal.density_percent_sol 57.34 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_details ;10% MPD, 40mM Sodium cacodylate, 12mM Spermine hydrochloride, 80mM Sodium chloride, 20mM Barium chloride, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 180 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'OXFORD SAPPHIRE CCD' _diffrn_detector.pdbx_collection_date 2011-01-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'SEALED TUBE' _diffrn_source.type 'OXFORD DIFFRACTION ENHANCE ULTRA' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3QF8 _reflns.observed_criterion_sigma_I 3 _reflns.observed_criterion_sigma_F 3 _reflns.d_resolution_low 29.87 _reflns.d_resolution_high 1.723 _reflns.number_obs 3309 _reflns.number_all 5674 _reflns.percent_possible_obs 44.02 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.72 _reflns_shell.d_res_low 1.88 _reflns_shell.percent_possible_all 38.6 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3QF8 _refine.ls_number_reflns_obs 2497 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 13.963 _refine.ls_d_res_high 1.73 _refine.ls_percent_reflns_obs 86.21 _refine.ls_R_factor_obs 0.18440 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.18214 _refine.ls_R_factor_R_free 0.23313 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.3 _refine.ls_number_reflns_R_free 147 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.940 _refine.correlation_coeff_Fo_to_Fc_free 0.933 _refine.B_iso_mean 21.682 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN DADED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.141 _refine.overall_SU_ML 0.093 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.145 _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 202 _refine_hist.pdbx_number_atoms_ligand 52 _refine_hist.number_atoms_solvent 87 _refine_hist.number_atoms_total 341 _refine_hist.d_res_high 1.73 _refine_hist.d_res_low 13.963 # 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 r_bond_refined_d 0.021 0.021 ? 290 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.722 3.000 ? 456 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.141 0.200 ? 43 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.022 0.020 ? 155 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.925 3.000 ? 290 'X-RAY DIFFRACTION' ? r_scangle_it 3.750 4.500 ? 456 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.734 _refine_ls_shell.d_res_low 1.778 _refine_ls_shell.number_reflns_R_work 45 _refine_ls_shell.R_factor_R_work 0.294 _refine_ls_shell.percent_reflns_obs 16.14 _refine_ls_shell.R_factor_R_free 0.024 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _database_PDB_matrix.entry_id 3QF8 _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 3QF8 _struct.title 'X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA) at medium resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3QF8 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, Intercalation, Kink, Flipped out base, 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 2 ? C N N 3 ? D N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3QF8 _struct_ref.pdbx_db_accession 3QF8 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3QF8 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3QF8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 760 ? 1 MORE -4 ? 1 'SSA (A^2)' 4260 ? # _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 # 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' 8_555 -y,-x,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 19.6895000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DG 3 N7 ? ? ? 1_555 C BA . BA ? ? A DG 3 A BA 12 1_555 ? ? ? ? ? ? ? 3.044 ? ? metalc2 metalc ? ? A DG 4 O6 ? ? ? 1_555 C BA . BA ? ? A DG 4 A BA 12 1_555 ? ? ? ? ? ? ? 2.984 ? ? metalc3 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 12 A HOH 14 1_555 ? ? ? ? ? ? ? 2.980 ? ? metalc4 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 12 A HOH 35 1_555 ? ? ? ? ? ? ? 2.442 ? ? metalc5 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 12 A HOH 42 1_555 ? ? ? ? ? ? ? 2.929 ? ? metalc6 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 12 A HOH 55 1_555 ? ? ? ? ? ? ? 2.870 ? ? metalc7 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 12 A HOH 59 1_555 ? ? ? ? ? ? ? 2.616 ? ? metalc8 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 12 A HOH 138 1_555 ? ? ? ? ? ? ? 3.014 ? ? hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 3 A DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 3 A DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 3 A DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 6 N1 ? ? A DC 5 A DG 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 6 O6 ? ? A DC 5 A DG 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 6 N2 ? ? A DC 5 A DG 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 6 A DC 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 6 A DC 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 6 A DC 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 8_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 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 74.7 ? 2 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 14 ? 1_555 76.9 ? 3 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 14 ? 1_555 128.3 ? 4 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 35 ? 1_555 131.2 ? 5 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 35 ? 1_555 104.8 ? 6 O ? D HOH . ? A HOH 14 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 35 ? 1_555 65.6 ? 7 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 42 ? 1_555 68.6 ? 8 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 42 ? 1_555 132.4 ? 9 O ? D HOH . ? A HOH 14 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 42 ? 1_555 71.1 ? 10 O ? D HOH . ? A HOH 35 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 42 ? 1_555 122.1 ? 11 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 55 ? 1_555 135.3 ? 12 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 55 ? 1_555 63.6 ? 13 O ? D HOH . ? A HOH 14 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 55 ? 1_555 142.5 ? 14 O ? D HOH . ? A HOH 35 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 55 ? 1_555 77.0 ? 15 O ? D HOH . ? A HOH 42 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 55 ? 1_555 131.5 ? 16 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 59 ? 1_555 76.4 ? 17 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 59 ? 1_555 72.8 ? 18 O ? D HOH . ? A HOH 14 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 59 ? 1_555 138.6 ? 19 O ? D HOH . ? A HOH 35 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 59 ? 1_555 151.6 ? 20 O ? D HOH . ? A HOH 42 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 59 ? 1_555 69.9 ? 21 O ? D HOH . ? A HOH 55 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 59 ? 1_555 76.7 ? 22 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 131.0 ? 23 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 127.6 ? 24 O ? D HOH . ? A HOH 14 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 103.7 ? 25 O ? D HOH . ? A HOH 35 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 89.0 ? 26 O ? D HOH . ? A HOH 42 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 65.7 ? 27 O ? D HOH . ? A HOH 55 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 71.2 ? 28 O ? D HOH . ? A HOH 59 ? 1_555 BA ? C BA . ? A BA 12 ? 1_555 O ? D HOH . ? A HOH 138 ? 1_555 72.3 ? # 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 RKL 11 ? 11 'BINDING SITE FOR RESIDUE RKL A 11' AC2 Software A BA 12 ? 8 'BINDING SITE FOR RESIDUE BA A 12' # 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 11 DT A 1 ? DT A 1 . ? 8_555 ? 2 AC1 11 DC A 2 ? DC A 2 . ? 8_555 ? 3 AC1 11 DG A 3 ? DG A 3 . ? 8_555 ? 4 AC1 11 DG A 3 ? DG A 3 . ? 6_545 ? 5 AC1 11 DG A 4 ? DG A 4 . ? 6_545 ? 6 AC1 11 DC A 7 ? DC A 7 . ? 3_544 ? 7 AC1 11 DC A 8 ? DC A 8 . ? 3_544 ? 8 AC1 11 DG A 9 ? DG A 9 . ? 1_555 ? 9 AC1 11 DA A 10 ? DA A 10 . ? 3_544 ? 10 AC1 11 HOH D . ? HOH A 77 . ? 4_555 ? 11 AC1 11 HOH D . ? HOH A 82 . ? 3_544 ? 12 AC2 8 DG A 3 ? DG A 3 . ? 1_555 ? 13 AC2 8 DG A 4 ? DG A 4 . ? 1_555 ? 14 AC2 8 HOH D . ? HOH A 14 . ? 1_555 ? 15 AC2 8 HOH D . ? HOH A 35 . ? 1_555 ? 16 AC2 8 HOH D . ? HOH A 42 . ? 1_555 ? 17 AC2 8 HOH D . ? HOH A 55 . ? 1_555 ? 18 AC2 8 HOH D . ? HOH A 59 . ? 1_555 ? 19 AC2 8 HOH D . ? HOH A 138 . ? 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 "O3'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.381 1.419 -0.038 0.006 N 2 1 N3 A DG 3 ? ? C4 A DG 3 ? ? 1.398 1.350 0.048 0.007 N 3 1 "O3'" A DG 4 ? ? "C3'" A DG 4 ? ? 1.359 1.419 -0.060 0.006 N 4 1 C6 A DG 4 ? ? N1 A DG 4 ? ? 1.435 1.391 0.044 0.007 N 5 1 "O3'" A DC 5 ? ? "C3'" A DC 5 ? ? 1.376 1.419 -0.043 0.006 N 6 1 N3 A DG 9 ? ? C4 A DG 9 ? ? 1.395 1.350 0.045 0.007 N 7 1 C2 A DG 9 ? ? N2 A DG 9 ? ? 1.273 1.341 -0.068 0.010 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 DT 1 ? ? "C4'" A DT 1 ? ? "C3'" A DT 1 ? ? 100.51 104.50 -3.99 0.40 N 2 1 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 103.61 108.00 -4.39 0.70 N 3 1 C5 A DT 1 ? ? C4 A DT 1 ? ? O4 A DT 1 ? ? 120.58 124.90 -4.32 0.70 N 4 1 C4 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 122.80 119.00 3.80 0.60 N 5 1 C4 A DG 4 ? ? C5 A DG 4 ? ? N7 A DG 4 ? ? 105.95 110.80 -4.85 0.40 N 6 1 C5 A DG 4 ? ? N7 A DG 4 ? ? C8 A DG 4 ? ? 107.55 104.30 3.25 0.50 N 7 1 C6 A DG 4 ? ? C5 A DG 4 ? ? N7 A DG 4 ? ? 136.01 130.40 5.61 0.60 N 8 1 N1 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 113.85 119.90 -6.05 0.60 N 9 1 C5 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 133.28 128.60 4.68 0.60 N 10 1 "O5'" A DC 5 ? ? P A DC 5 ? ? OP2 A DC 5 ? ? 100.03 105.70 -5.67 0.90 N 11 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? "C2'" A DC 5 ? ? 109.91 106.80 3.11 0.50 N 12 1 C4 A DC 5 ? ? C5 A DC 5 ? ? C6 A DC 5 ? ? 121.05 117.40 3.65 0.50 N 13 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.36 108.30 2.06 0.30 N 14 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 114.38 119.90 -5.52 0.60 N 15 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? "C2'" A DC 7 ? ? 109.97 106.80 3.17 0.50 N 16 1 C6 A DG 9 ? ? N1 A DG 9 ? ? C2 A DG 9 ? ? 120.26 125.10 -4.84 0.60 N 17 1 C5 A DG 9 ? ? C6 A DG 9 ? ? N1 A DG 9 ? ? 117.43 111.50 5.93 0.50 N 18 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 115.97 119.90 -3.93 0.60 N 19 1 "O5'" A DA 10 ? ? "C5'" A DA 10 ? ? "C4'" A DA 10 ? ? 98.87 109.40 -10.53 0.80 N 20 1 "C4'" A DA 10 ? ? "C3'" A DA 10 ? ? "C2'" A DA 10 ? ? 97.45 102.20 -4.75 0.70 N 21 1 "C3'" A DA 10 ? ? "C2'" A DA 10 ? ? "C1'" A DA 10 ? ? 96.64 102.40 -5.76 0.80 N 22 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? "C2'" A DA 10 ? ? 100.01 105.90 -5.89 0.80 N # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 134 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 10.9142 _pdbx_refine_tls.origin_y -9.1098 _pdbx_refine_tls.origin_z 6.8128 _pdbx_refine_tls.T[1][1] 0.0147 _pdbx_refine_tls.T[2][2] 0.0402 _pdbx_refine_tls.T[3][3] 0.0141 _pdbx_refine_tls.T[1][2] -0.0105 _pdbx_refine_tls.T[1][3] 0.0004 _pdbx_refine_tls.T[2][3] -0.0058 _pdbx_refine_tls.L[1][1] 1.1842 _pdbx_refine_tls.L[2][2] 3.3631 _pdbx_refine_tls.L[3][3] 1.9843 _pdbx_refine_tls.L[1][2] 1.0165 _pdbx_refine_tls.L[1][3] -0.7409 _pdbx_refine_tls.L[2][3] -1.5239 _pdbx_refine_tls.S[1][1] 0.0082 _pdbx_refine_tls.S[1][2] 0.1169 _pdbx_refine_tls.S[1][3] 0.0279 _pdbx_refine_tls.S[2][1] -0.0693 _pdbx_refine_tls.S[2][2] 0.0821 _pdbx_refine_tls.S[2][3] -0.0184 _pdbx_refine_tls.S[3][1] 0.0025 _pdbx_refine_tls.S[3][2] -0.0483 _pdbx_refine_tls.S[3][3] -0.0903 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 10 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # 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 RKL RU RU N N 148 RKL C1 C Y N 149 RKL N1 N Y N 150 RKL C2 C Y N 151 RKL N2 N Y N 152 RKL C3 C Y N 153 RKL N3 N Y N 154 RKL C4 C Y N 155 RKL N4 N Y N 156 RKL C5 C Y N 157 RKL N5 N Y N 158 RKL C6 C Y N 159 RKL N6 N Y N 160 RKL C7 C Y N 161 RKL N7 N Y N 162 RKL C8 C Y N 163 RKL N8 N Y N 164 RKL C9 C Y N 165 RKL N9 N Y N 166 RKL C10 C Y N 167 RKL N10 N Y N 168 RKL C11 C Y N 169 RKL N11 N Y N 170 RKL C12 C Y N 171 RKL N12 N Y N 172 RKL C13 C Y N 173 RKL C14 C Y N 174 RKL C15 C Y N 175 RKL C16 C Y N 176 RKL C17 C Y N 177 RKL C18 C Y N 178 RKL C19 C Y N 179 RKL C20 C Y N 180 RKL C21 C Y N 181 RKL C22 C Y N 182 RKL C23 C Y N 183 RKL C24 C Y N 184 RKL C25 C Y N 185 RKL C26 C Y N 186 RKL C27 C Y N 187 RKL C28 C Y N 188 RKL C29 C Y N 189 RKL C30 C Y N 190 RKL C31 C Y N 191 RKL C32 C Y N 192 RKL C33 C Y N 193 RKL C34 C Y N 194 RKL C35 C Y N 195 RKL C36 C Y N 196 RKL C37 C Y N 197 RKL C38 C Y N 198 RKL H2 H N N 199 RKL H3 H N N 200 RKL H4 H N N 201 RKL H9 H N N 202 RKL H11 H N N 203 RKL H12 H N N 204 RKL H14 H N N 205 RKL H16 H N N 206 RKL H17 H N N 207 RKL H18 H N N 208 RKL H20 H N N 209 RKL H21 H N N 210 RKL H23 H N N 211 RKL H24 H N N 212 RKL H27 H N N 213 RKL H28 H N N 214 RKL H30 H N N 215 RKL H31 H N N 216 RKL H33 H N N 217 RKL H34 H N N 218 RKL H37 H N N 219 RKL H38 H N N 220 # 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 RKL RU N1 sing N N 152 RKL RU N2 sing N N 153 RKL RU N5 sing N N 154 RKL RU N8 sing N N 155 RKL RU N9 sing N N 156 RKL RU N12 sing N N 157 RKL C1 N2 doub Y N 158 RKL C1 C5 sing Y N 159 RKL C1 C10 sing Y N 160 RKL N1 C10 doub Y N 161 RKL N1 C12 sing Y N 162 RKL C2 N2 sing Y N 163 RKL C2 C3 doub Y N 164 RKL C2 H2 sing N N 165 RKL C3 C4 sing Y N 166 RKL C3 H3 sing N N 167 RKL N3 C6 doub Y N 168 RKL N3 C15 sing Y N 169 RKL C4 C5 doub Y N 170 RKL C4 H4 sing N N 171 RKL N4 C7 doub Y N 172 RKL N4 C13 sing Y N 173 RKL C5 C6 sing Y N 174 RKL N5 C19 doub Y N 175 RKL N5 C20 sing Y N 176 RKL C6 C7 sing Y N 177 RKL N6 C21 sing Y N 178 RKL N6 C22 doub Y N 179 RKL C7 C8 sing Y N 180 RKL N7 C25 doub Y N 181 RKL N7 C27 sing Y N 182 RKL C8 C9 doub Y N 183 RKL C8 C10 sing Y N 184 RKL N8 C26 doub Y N 185 RKL N8 C28 sing Y N 186 RKL C9 C11 sing Y N 187 RKL C9 H9 sing N N 188 RKL N9 C29 doub Y N 189 RKL N9 C30 sing Y N 190 RKL N10 C31 sing Y N 191 RKL N10 C32 doub Y N 192 RKL C11 C12 doub Y N 193 RKL C11 H11 sing N N 194 RKL N11 C35 doub Y N 195 RKL N11 C37 sing Y N 196 RKL C12 H12 sing N N 197 RKL N12 C36 doub Y N 198 RKL N12 C38 sing Y N 199 RKL C13 C14 sing Y N 200 RKL C13 C15 doub Y N 201 RKL C14 C18 doub Y N 202 RKL C14 H14 sing N N 203 RKL C15 C16 sing Y N 204 RKL C16 C17 doub Y N 205 RKL C16 H16 sing N N 206 RKL C17 C18 sing Y N 207 RKL C17 H17 sing N N 208 RKL C18 H18 sing N N 209 RKL C19 C22 sing Y N 210 RKL C19 C26 sing Y N 211 RKL C20 C21 doub Y N 212 RKL C20 H20 sing N N 213 RKL C21 H21 sing N N 214 RKL C22 C23 sing Y N 215 RKL C23 C24 doub Y N 216 RKL C23 H23 sing N N 217 RKL C24 C25 sing Y N 218 RKL C24 H24 sing N N 219 RKL C25 C26 sing Y N 220 RKL C27 C28 doub Y N 221 RKL C27 H27 sing N N 222 RKL C28 H28 sing N N 223 RKL C29 C32 sing Y N 224 RKL C29 C36 sing Y N 225 RKL C30 C31 doub Y N 226 RKL C30 H30 sing N N 227 RKL C31 H31 sing N N 228 RKL C32 C33 sing Y N 229 RKL C33 C34 doub Y N 230 RKL C33 H33 sing N N 231 RKL C34 C35 sing Y N 232 RKL C34 H34 sing N N 233 RKL C35 C36 sing Y N 234 RKL C37 C38 doub Y N 235 RKL C37 H37 sing N N 236 RKL C38 H38 sing N N 237 # _ndb_struct_conf_na.entry_id 3QF8 _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 2 1_555 A DG 9 8_555 0.045 0.074 0.372 -16.660 11.282 -0.539 1 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 8_555 -0.386 0.022 0.408 24.970 -2.117 -1.517 2 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 8_555 -0.275 -0.080 -0.323 -10.492 -0.297 -1.509 3 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DC 5 1_555 A DG 6 8_555 0.221 -0.064 0.116 -5.357 -7.924 -1.749 4 A_DC5:DG6_A A 5 ? A 6 ? 19 1 1 A DG 6 1_555 A DC 5 8_555 -0.221 -0.064 0.116 5.357 -7.924 -1.749 5 A_DG6:DC5_A A 6 ? A 5 ? 19 1 1 A DC 7 1_555 A DG 4 8_555 0.275 -0.080 -0.323 10.492 -0.297 -1.509 6 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DC 8 1_555 A DG 3 8_555 0.386 0.022 0.408 -24.970 -2.117 -1.517 7 A_DC8:DG3_A A 8 ? A 3 ? 19 1 1 A DG 9 1_555 A DC 2 8_555 -0.045 0.074 0.372 16.660 11.282 -0.539 8 A_DG9:DC2_A A 9 ? A 2 ? 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 2 1_555 A DG 9 8_555 A DG 3 1_555 A DC 8 8_555 -0.510 1.618 2.438 1.038 3.260 20.039 3.435 1.811 2.635 9.281 -2.956 20.326 1 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 3 1_555 A DC 8 8_555 A DG 4 1_555 A DC 7 8_555 -0.252 0.797 5.277 0.644 53.291 15.546 -5.181 0.344 2.296 74.910 -0.905 55.356 2 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 8_555 A DC 5 1_555 A DG 6 8_555 -1.023 0.256 3.212 -5.842 -1.576 37.482 0.596 0.824 3.316 -2.433 9.019 37.950 3 AA_DG4DC5:DG6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DC 5 1_555 A DG 6 8_555 A DG 6 1_555 A DC 5 8_555 0.000 0.895 3.297 0.000 17.608 29.208 -1.535 0.000 3.296 31.561 0.000 34.006 4 AA_DC5DG6:DC5DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A DC 5 8_555 A DC 7 1_555 A DG 4 8_555 1.023 0.256 3.212 5.842 -1.576 37.482 0.596 -0.824 3.316 -2.433 -9.019 37.950 5 AA_DG6DC7:DG4DC5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 8_555 A DC 8 1_555 A DG 3 8_555 0.252 0.797 5.277 -0.644 53.291 15.546 -5.181 -0.344 2.296 74.910 0.905 55.356 6 AA_DC7DC8:DG3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DC 8 1_555 A DG 3 8_555 A DG 9 1_555 A DC 2 8_555 0.510 1.618 2.438 -1.038 3.260 20.039 3.435 -1.811 2.635 9.281 2.956 20.326 7 AA_DC8DG9:DC2DG3_AA A 8 ? A 3 ? A 9 ? A 2 ? # _atom_sites.entry_id 3QF8 _atom_sites.fract_transf_matrix[1][1] 0.023675 _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] 0.023675 _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] 0.025394 _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 BA C N O P RU # loop_