data_4GQJ # _entry.id 4GQJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4GQJ pdb_00004gqj 10.2210/pdb4gqj/pdb NDB NA2051 ? ? RCSB RCSB074512 ? ? WWPDB D_1000074512 ? ? # 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 2014-03-05 2 'Structure model' 1 1 2024-02-28 3 'Structure model' 1 2 2024-03-13 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Source and taxonomy' 5 3 'Structure model' 'Structure summary' # 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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' struct_site 5 3 'Structure model' entity 6 3 'Structure model' pdbx_entity_src_syn # 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 2 'Structure model' '_struct_site.pdbx_auth_seq_id' 6 3 'Structure model' '_entity.details' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4GQJ _pdbx_database_status.recvd_initial_deposition_date 2012-08-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.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 3s80 'mononuclear Ru-dppz bound to DNA' unspecified PDB 3qrn 'mononuclear Ru-dppz bound to DNA' unspecified PDB 4e1u 'mononuclear Ru-dppz bound to DNA' unspecified PDB 3u38 'mononuclear Ru-dppz bound to DNA' unspecified PDB 4e7y 'mononuclear Ru-dppz bound to DNA' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Boer, D.R.' 1 'Coll, M.' 2 # _citation.id primary _citation.title ;Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. ; _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 53 _citation.page_first 1949 _citation.page_last 1952 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1433-7851 _citation.journal_id_CSD 9999 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24449275 _citation.pdbx_database_id_DOI 10.1002/anie.201308070 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Boer, D.R.' 1 ? primary 'Wu, L.' 2 ? primary 'Lincoln, P.' 3 ? primary 'Coll, M.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') ; 1809.217 2 ? ? ? ? 2 non-polymer syn ;(mu-11,11'-bidipyrido[3,2-a:2',3'-c]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~4'~,N~5'~)[tetrakis(1,10-phenanthroline-kappa~2~N~1~,N~10~)]diruthenium ; 1485.543 1 ? ? ? 'Synthesized by citation authors' 3 water nat water 18.015 16 ? ? ? 'Synthesized by citation authors' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _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 ;(mu-11,11'-bidipyrido[3,2-a:2',3'-c]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~4'~,N~5'~)[tetrakis(1,10-phenanthroline-kappa~2~N~1~,N~10~)]diruthenium ; RR2 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DT n 1 4 DA n 1 5 DC n 1 6 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Acquired from biomers (Germany)' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 RR2 non-polymer . ;(mu-11,11'-bidipyrido[3,2-a:2',3'-c]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~4'~,N~5'~)[tetrakis(1,10-phenanthroline-kappa~2~N~1~,N~10~)]diruthenium ; ? 'C84 H50 N16 Ru2' 1485.543 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DT 3 3 3 DT DT B . n B 1 4 DA 4 4 4 DA DA B . n B 1 5 DC 5 5 5 DC DC B . n B 1 6 DG 6 6 6 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 RR2 1 101 1 RR2 RR2 A . D 3 HOH 1 201 2 HOH HOH A . D 3 HOH 2 202 5 HOH HOH A . D 3 HOH 3 203 12 HOH HOH A . D 3 HOH 4 204 13 HOH HOH A . D 3 HOH 5 205 20 HOH HOH A . D 3 HOH 6 206 21 HOH HOH A . D 3 HOH 7 207 22 HOH HOH A . D 3 HOH 8 208 27 HOH HOH A . D 3 HOH 9 209 28 HOH HOH A . D 3 HOH 10 210 29 HOH HOH A . D 3 HOH 11 211 30 HOH HOH A . D 3 HOH 12 212 31 HOH HOH A . E 3 HOH 1 101 1 HOH HOH B . E 3 HOH 2 102 6 HOH HOH B . E 3 HOH 3 103 14 HOH HOH B . E 3 HOH 4 104 18 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B DG 6 ? "C4'" ? B DG 6 "C4'" 2 1 Y 1 B DG 6 ? "O4'" ? B DG 6 "O4'" 3 1 Y 1 B DG 6 ? "C3'" ? B DG 6 "C3'" 4 1 Y 1 B DG 6 ? "O3'" ? B DG 6 "O3'" 5 1 Y 1 B DG 6 ? "C2'" ? B DG 6 "C2'" 6 1 Y 1 B DG 6 ? "C1'" ? B DG 6 "C1'" 7 1 Y 1 B DG 6 ? N9 ? B DG 6 N9 8 1 Y 1 B DG 6 ? C8 ? B DG 6 C8 9 1 Y 1 B DG 6 ? N7 ? B DG 6 N7 10 1 Y 1 B DG 6 ? C5 ? B DG 6 C5 11 1 Y 1 B DG 6 ? C6 ? B DG 6 C6 12 1 Y 1 B DG 6 ? O6 ? B DG 6 O6 13 1 Y 1 B DG 6 ? N1 ? B DG 6 N1 14 1 Y 1 B DG 6 ? C2 ? B DG 6 C2 15 1 Y 1 B DG 6 ? N2 ? B DG 6 N2 16 1 Y 1 B DG 6 ? N3 ? B DG 6 N3 17 1 Y 1 B DG 6 ? C4 ? B DG 6 C4 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MxCuBE 'data collection' . ? 1 SHELXS phasing . ? 2 PHENIX refinement '(phenix.refine: 1.7.1_743)' ? 3 MOSFLM 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # _cell.entry_id 4GQJ _cell.length_a 85.429 _cell.length_b 85.429 _cell.length_c 85.429 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 48 _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 4GQJ _symmetry.space_group_name_H-M 'P 41 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4GQJ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 7.18 _exptl_crystal.density_percent_sol 82.87 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_details ;buffer: 0.2 M KCl 10 mM MgCl2 35% hexanediol 50 mM TRIS.HCl pH 8 drop composition: 0.5 ul 10 mM binuclear Ru compound 0.5 ul 10 mM [ssDNA] 5'-d(CGTACG)-3' 1 ul cryst. buffer 0.5 ul , VAPOR DIFFUSION, SITTING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2009-06-14 _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 'channel-cut Si(111) crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.07205 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.07205 # _reflns.entry_id 4GQJ _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.95 _reflns.number_obs 2419 _reflns.number_all 2419 _reflns.percent_possible_obs 97 _reflns.pdbx_Rmerge_I_obs 0.118 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 10.3 _reflns.B_iso_Wilson_estimate 73.4 _reflns.pdbx_redundancy 4.4 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.95 _reflns_shell.d_res_low 3.11 _reflns_shell.percent_possible_all 99 _reflns_shell.Rmerge_I_obs 0.62 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.1 _reflns_shell.pdbx_redundancy 4.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 343 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4GQJ _refine.ls_number_reflns_obs 2396 _refine.ls_number_reflns_all 2419 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.36 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.205 _refine.ls_d_res_high 2.951 _refine.ls_percent_reflns_obs 95.34 _refine.ls_R_factor_obs 0.1786 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1773 _refine.ls_R_factor_R_free 0.2065 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.34 _refine.ls_number_reflns_R_free 104 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _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] -0.0000 _refine.aniso_B[2][2] 0.0000 _refine.aniso_B[3][3] -0.0000 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.272 _refine.solvent_model_param_bsol 19.848 _refine.pdbx_solvent_vdw_probe_radii 1.00 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.72 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _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 0.29 _refine.pdbx_overall_phase_error 19.82 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_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 223 _refine_hist.pdbx_number_atoms_ligand 102 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 341 _refine_hist.d_res_high 2.951 _refine_hist.d_res_low 38.205 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.007 ? ? 383 ? 'X-RAY DIFFRACTION' f_angle_d 1.390 ? ? 579 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 34.982 ? ? 123 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.085 ? ? 51 ? 'X-RAY DIFFRACTION' f_plane_restr 0.007 ? ? 17 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.9511 _refine_ls_shell.d_res_low ? _refine_ls_shell.number_reflns_R_work 2292 _refine_ls_shell.R_factor_R_work 0.1773 _refine_ls_shell.percent_reflns_obs 95.00 _refine_ls_shell.R_factor_R_free 0.2065 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 104 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4GQJ _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 4GQJ _struct.title ;Complex of a binuclear Ruthenium compound D,D-([mu-(11,11')-bi(dppz)-(1,10-phenanthroline)4-Ru2]4+) bound to d(CGTACG) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4GQJ _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA recognition, DNA binsinf, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4GQJ _struct_ref.pdbx_db_accession 4GQJ _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGTACG _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 4GQJ A 1 ? 6 ? 4GQJ 1 ? 6 ? 1 6 2 1 4GQJ B 1 ? 6 ? 4GQJ 1 ? 6 ? 1 6 # _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 # 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' 13_545 y+3/4,x-3/4,-z+1/4 0.0000000000 1.0000000000 0.0000000000 64.0717500000 1.0000000000 0.0000000000 0.0000000000 -64.0717500000 0.0000000000 0.0000000000 -1.0000000000 21.3572500000 # _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 hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id RR2 _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 15 _struct_site.details 'BINDING SITE FOR RESIDUE RR2 A 101' # 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 15 DC A 1 ? DC A 1 . ? 8_544 ? 2 AC1 15 DG A 2 ? DG A 2 . ? 8_544 ? 3 AC1 15 DT A 3 ? DT A 3 . ? 8_544 ? 4 AC1 15 DT A 3 ? DT A 3 . ? 1_555 ? 5 AC1 15 DA A 4 ? DA A 4 . ? 8_544 ? 6 AC1 15 DA A 4 ? DA A 4 . ? 1_555 ? 7 AC1 15 DC A 5 ? DC A 5 . ? 1_555 ? 8 AC1 15 DG A 6 ? DG A 6 . ? 1_555 ? 9 AC1 15 DG A 6 ? DG A 6 . ? 13_545 ? 10 AC1 15 DC B 1 ? DC B 1 . ? 13_545 ? 11 AC1 15 DG B 2 ? DG B 2 . ? 1_555 ? 12 AC1 15 DT B 3 ? DT B 3 . ? 13_545 ? 13 AC1 15 DA B 4 ? DA B 4 . ? 1_555 ? 14 AC1 15 DC B 5 ? DC B 5 . ? 1_555 ? 15 AC1 15 DC B 5 ? DC B 5 . ? 8_544 ? # 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 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.82 108.30 2.52 0.30 N 2 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 102.76 108.00 -5.24 0.70 N 3 1 "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? "C1'" A DC 5 ? ? 97.15 102.40 -5.25 0.80 N 4 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.91 108.30 2.61 0.30 N 5 1 "O4'" B DC 1 ? ? "C4'" B DC 1 ? ? "C3'" B DC 1 ? ? 101.70 104.50 -2.80 0.40 N 6 1 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 112.53 108.30 4.23 0.30 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 RR2 CA1 C Y N 147 RR2 CA2 C Y N 148 RR2 CA3 C Y N 149 RR2 NA1 N Y N 150 RR2 CA4 C Y N 151 RR2 CA5 C Y N 152 RR2 CA6 C Y N 153 RR2 CA7 C Y N 154 RR2 CA8 C Y N 155 RR2 NA2 N Y N 156 RR2 CA9 C Y N 157 RR2 CA0 C Y N 158 RR2 CAA C Y N 159 RR2 CAB C Y N 160 RR2 CB1 C Y N 161 RR2 CB2 C Y N 162 RR2 CB3 C Y N 163 RR2 NB1 N Y N 164 RR2 CB4 C Y N 165 RR2 CB5 C Y N 166 RR2 CB6 C Y N 167 RR2 CB7 C Y N 168 RR2 CB8 C Y N 169 RR2 NB2 N Y N 170 RR2 CB9 C Y N 171 RR2 CB0 C Y N 172 RR2 CBA C Y N 173 RR2 CBB C Y N 174 RR2 CC1 C Y N 175 RR2 CC2 C Y N 176 RR2 CC3 C Y N 177 RR2 NC1 N Y N 178 RR2 CC4 C Y N 179 RR2 CC5 C Y N 180 RR2 CC6 C Y N 181 RR2 CC7 C Y N 182 RR2 CC8 C Y N 183 RR2 NC2 N Y N 184 RR2 CC9 C Y N 185 RR2 CC0 C Y N 186 RR2 CCA C Y N 187 RR2 CCB C Y N 188 RR2 CD1 C Y N 189 RR2 CD2 C Y N 190 RR2 CD3 C Y N 191 RR2 ND1 N Y N 192 RR2 CD4 C Y N 193 RR2 CD5 C Y N 194 RR2 CD6 C Y N 195 RR2 CD7 C Y N 196 RR2 CD8 C Y N 197 RR2 ND2 N Y N 198 RR2 CD9 C Y N 199 RR2 CD0 C Y N 200 RR2 CDA C Y N 201 RR2 CDB C Y N 202 RR2 RU1 RU N N 203 RR2 RU2 RU N N 204 RR2 C11 C Y N 205 RR2 C10 C Y N 206 RR2 C12 C Y N 207 RR2 C13 C Y N 208 RR2 C9B C Y N 209 RR2 C9A C Y N 210 RR2 N9 N Y N 211 RR2 N14 N Y N 212 RR2 C8C C Y N 213 RR2 C8D C Y N 214 RR2 C4A C Y N 215 RR2 N4 N Y N 216 RR2 C3 C Y N 217 RR2 C2 C Y N 218 RR2 C1 C Y N 219 RR2 C8B C Y N 220 RR2 C8A C Y N 221 RR2 C4B C Y N 222 RR2 C8 C Y N 223 RR2 C7 C Y N 224 RR2 C6 C Y N 225 RR2 N5 N Y N 226 RR2 C31 C Y N 227 RR2 C30 C Y N 228 RR2 C32 C Y N 229 RR2 C33 C Y N 230 RR2 C9D C Y N 231 RR2 C9C C Y N 232 RR2 N29 N Y N 233 RR2 N N Y N 234 RR2 C8G C Y N 235 RR2 C8H C Y N 236 RR2 C4C C Y N 237 RR2 N24 N Y N 238 RR2 C23 C Y N 239 RR2 C22 C Y N 240 RR2 C21 C Y N 241 RR2 C8F C Y N 242 RR2 C8E C Y N 243 RR2 C4D C Y N 244 RR2 C28 C Y N 245 RR2 C27 C Y N 246 RR2 C26 C Y N 247 RR2 N25 N Y N 248 RR2 H1 H N N 249 RR2 H2 H N N 250 RR2 H3 H N N 251 RR2 H4 H N N 252 RR2 H5 H N N 253 RR2 H6 H N N 254 RR2 H7 H N N 255 RR2 H8 H N N 256 RR2 H9 H N N 257 RR2 H10 H N N 258 RR2 H11 H N N 259 RR2 H12 H N N 260 RR2 H13 H N N 261 RR2 H14 H N N 262 RR2 H15 H N N 263 RR2 H16 H N N 264 RR2 H17 H N N 265 RR2 H18 H N N 266 RR2 H19 H N N 267 RR2 H20 H N N 268 RR2 H21 H N N 269 RR2 H22 H N N 270 RR2 H23 H N N 271 RR2 H24 H N N 272 RR2 H25 H N N 273 RR2 H26 H N N 274 RR2 H27 H N N 275 RR2 H28 H N N 276 RR2 H29 H N N 277 RR2 H30 H N N 278 RR2 H31 H N N 279 RR2 H32 H N N 280 RR2 H33 H N N 281 RR2 H34 H N N 282 RR2 H35 H N N 283 RR2 H36 H N N 284 RR2 H37 H N N 285 RR2 H38 H N N 286 RR2 H39 H N N 287 RR2 H40 H N N 288 RR2 H41 H N N 289 RR2 H42 H N N 290 RR2 H43 H N N 291 RR2 H44 H N N 292 RR2 H45 H N N 293 RR2 H46 H N N 294 RR2 H47 H N N 295 RR2 H48 H N N 296 RR2 H49 H N N 297 RR2 H50 H N N 298 # 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 RR2 CA1 NA1 doub Y N 152 RR2 CA1 H1 sing N N 153 RR2 CA2 CA1 sing Y N 154 RR2 CA2 H2 sing N N 155 RR2 CA3 CA2 doub Y N 156 RR2 CA3 CA5 sing Y N 157 RR2 CA3 H3 sing N N 158 RR2 NA1 RU1 sing N N 159 RR2 CA4 NA1 sing Y N 160 RR2 CA4 CA8 doub Y N 161 RR2 CA5 CA4 sing Y N 162 RR2 CA6 CA5 doub Y N 163 RR2 CA6 CA7 sing Y N 164 RR2 CA6 H4 sing N N 165 RR2 CA7 CA9 doub Y N 166 RR2 CA7 H5 sing N N 167 RR2 CA8 NA2 sing Y N 168 RR2 NA2 CAB doub Y N 169 RR2 CA9 CA8 sing Y N 170 RR2 CA9 CA0 sing Y N 171 RR2 CA0 CAA doub Y N 172 RR2 CA0 H6 sing N N 173 RR2 CAA CAB sing Y N 174 RR2 CAA H7 sing N N 175 RR2 CAB H8 sing N N 176 RR2 CB1 NB1 doub Y N 177 RR2 CB1 CB2 sing Y N 178 RR2 CB1 H9 sing N N 179 RR2 CB2 CB3 doub Y N 180 RR2 CB2 H10 sing N N 181 RR2 CB3 CB5 sing Y N 182 RR2 CB3 H11 sing N N 183 RR2 NB1 CB4 sing Y N 184 RR2 CB4 CB8 doub Y N 185 RR2 CB4 CB5 sing Y N 186 RR2 CB5 CB6 doub Y N 187 RR2 CB6 CB7 sing Y N 188 RR2 CB6 H12 sing N N 189 RR2 CB7 H13 sing N N 190 RR2 CB8 CB9 sing Y N 191 RR2 NB2 CBB doub Y N 192 RR2 NB2 CB8 sing Y N 193 RR2 CB9 CB0 sing Y N 194 RR2 CB9 CB7 doub Y N 195 RR2 CB0 H14 sing N N 196 RR2 CBA CB0 doub Y N 197 RR2 CBA H15 sing N N 198 RR2 CBB CBA sing Y N 199 RR2 CBB H16 sing N N 200 RR2 CC1 NC1 doub Y N 201 RR2 CC1 H17 sing N N 202 RR2 CC2 CC3 doub Y N 203 RR2 CC2 CC1 sing Y N 204 RR2 CC2 H18 sing N N 205 RR2 CC3 CC5 sing Y N 206 RR2 CC3 H19 sing N N 207 RR2 NC1 CC4 sing Y N 208 RR2 NC1 RU2 sing N N 209 RR2 CC4 CC8 doub Y N 210 RR2 CC5 CC6 doub Y N 211 RR2 CC5 CC4 sing Y N 212 RR2 CC6 CC7 sing Y N 213 RR2 CC6 H20 sing N N 214 RR2 CC7 CC9 doub Y N 215 RR2 CC7 H21 sing N N 216 RR2 CC8 CC9 sing Y N 217 RR2 CC8 NC2 sing Y N 218 RR2 NC2 CCB doub Y N 219 RR2 CC9 CC0 sing Y N 220 RR2 CC0 CCA doub Y N 221 RR2 CC0 H22 sing N N 222 RR2 CCA H23 sing N N 223 RR2 CCB CCA sing Y N 224 RR2 CCB H24 sing N N 225 RR2 CD1 ND1 doub Y N 226 RR2 CD1 H25 sing N N 227 RR2 CD2 CD1 sing Y N 228 RR2 CD2 H26 sing N N 229 RR2 CD3 CD2 doub Y N 230 RR2 CD3 CD5 sing Y N 231 RR2 CD3 H27 sing N N 232 RR2 ND1 RU2 sing N N 233 RR2 CD4 ND1 sing Y N 234 RR2 CD4 CD8 doub Y N 235 RR2 CD5 CD4 sing Y N 236 RR2 CD6 CD5 doub Y N 237 RR2 CD6 CD7 sing Y N 238 RR2 CD6 H28 sing N N 239 RR2 CD7 CD9 doub Y N 240 RR2 CD7 H29 sing N N 241 RR2 CD8 ND2 sing Y N 242 RR2 ND2 CDB doub Y N 243 RR2 CD9 CD8 sing Y N 244 RR2 CD9 CD0 sing Y N 245 RR2 CD0 CDA doub Y N 246 RR2 CD0 H30 sing N N 247 RR2 CDA CDB sing Y N 248 RR2 CDA H31 sing N N 249 RR2 CDB H32 sing N N 250 RR2 RU1 NA2 sing N N 251 RR2 RU1 NB1 sing N N 252 RR2 RU1 NB2 sing N N 253 RR2 RU2 ND2 sing N N 254 RR2 RU2 N4 sing N N 255 RR2 RU2 NC2 sing N N 256 RR2 RU2 N5 sing N N 257 RR2 C11 C31 sing N N 258 RR2 C10 C11 sing Y N 259 RR2 C10 H33 sing N N 260 RR2 C12 C11 doub Y N 261 RR2 C12 H34 sing N N 262 RR2 C13 C12 sing Y N 263 RR2 C13 H35 sing N N 264 RR2 C9B C13 doub Y N 265 RR2 C9B C9A sing Y N 266 RR2 C9A C10 doub Y N 267 RR2 N9 C9A sing Y N 268 RR2 N14 C9B sing Y N 269 RR2 C8C N14 doub Y N 270 RR2 C8C C8B sing Y N 271 RR2 C8D C8C sing Y N 272 RR2 C4A C8D sing Y N 273 RR2 C4A C4B sing Y N 274 RR2 N4 C4A doub Y N 275 RR2 C3 C2 doub Y N 276 RR2 C3 N4 sing Y N 277 RR2 C3 H36 sing N N 278 RR2 C2 C1 sing Y N 279 RR2 C2 H37 sing N N 280 RR2 C1 C8D doub Y N 281 RR2 C1 H38 sing N N 282 RR2 C8B N9 doub Y N 283 RR2 C8A C8B sing Y N 284 RR2 C8A C8 doub Y N 285 RR2 C4B C8A sing Y N 286 RR2 C8 H39 sing N N 287 RR2 C7 C8 sing Y N 288 RR2 C7 H40 sing N N 289 RR2 C6 C7 doub Y N 290 RR2 C6 H41 sing N N 291 RR2 N5 C4B doub Y N 292 RR2 N5 C6 sing Y N 293 RR2 C31 C32 doub Y N 294 RR2 C31 C30 sing Y N 295 RR2 C30 C9C doub Y N 296 RR2 C30 H42 sing N N 297 RR2 C32 C33 sing Y N 298 RR2 C32 H43 sing N N 299 RR2 C33 C9D doub Y N 300 RR2 C33 H44 sing N N 301 RR2 C9D N sing Y N 302 RR2 C9C C9D sing Y N 303 RR2 C9C N29 sing Y N 304 RR2 N29 C8F doub Y N 305 RR2 N C8G doub Y N 306 RR2 C8G C8H sing Y N 307 RR2 C8H C21 doub Y N 308 RR2 C8H C4C sing Y N 309 RR2 C4C N24 doub Y N 310 RR2 N24 C23 sing Y N 311 RR2 N24 RU1 sing N N 312 RR2 C23 H45 sing N N 313 RR2 C22 C23 doub Y N 314 RR2 C22 H46 sing N N 315 RR2 C21 C22 sing Y N 316 RR2 C21 H47 sing N N 317 RR2 C8F C8G sing Y N 318 RR2 C8F C8E sing Y N 319 RR2 C8E C4D sing Y N 320 RR2 C4D C4C sing Y N 321 RR2 C4D N25 doub Y N 322 RR2 C28 C8E doub Y N 323 RR2 C28 C27 sing Y N 324 RR2 C28 H48 sing N N 325 RR2 C27 C26 doub Y N 326 RR2 C26 N25 sing Y N 327 RR2 N25 RU1 sing N N 328 RR2 C27 H49 sing N N 329 RR2 C26 H50 sing N N 330 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4GQJ 'double helix' 4GQJ 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 2 1_555 B DC 5 1_555 0.133 0.052 -0.676 -16.754 16.736 1.718 1 A_DG2:DC5_B A 2 ? B 5 ? 19 1 1 A DT 3 1_555 B DA 4 1_555 -0.018 -0.031 -0.226 7.213 8.564 2.185 2 A_DT3:DA4_B A 3 ? B 4 ? 20 1 1 A DC 5 1_555 B DG 2 1_555 -0.010 -0.137 -0.237 0.161 20.340 -0.325 3 A_DC5:DG2_B A 5 ? B 2 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.196 0.100 0.442 33.760 7.144 -0.517 4 A_DG6:DC1_B A 6 ? B 1 ? 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 DG 2 1_555 B DC 5 1_555 A DT 3 1_555 B DA 4 1_555 -0.411 -0.046 2.793 -2.856 4.808 21.452 -1.688 0.138 2.747 12.642 7.510 22.160 1 AA_DG2DT3:DA4DC5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A DT 3 1_555 B DA 4 1_555 A DC 5 1_555 B DG 2 1_555 -0.247 2.501 6.754 -9.058 4.825 59.989 1.983 -0.673 6.888 4.788 8.988 60.780 2 AA_DT3DC5:DG2DA4_BB A 3 ? B 4 ? A 5 ? B 2 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.462 0.722 2.806 -3.737 -4.751 32.528 1.952 0.274 2.712 -8.391 6.600 33.070 3 AA_DC5DG6:DC1DG2_BB A 5 ? B 2 ? A 6 ? B 1 ? # _atom_sites.entry_id 4GQJ _atom_sites.fract_transf_matrix[1][1] 0.011706 _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] 0.011706 _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] 0.011706 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P RU # loop_