data_4E7Y # _entry.id 4E7Y # _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 4E7Y pdb_00004e7y 10.2210/pdb4e7y/pdb NDB NA1692 ? ? RCSB RCSB071282 ? ? WWPDB D_1000071282 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-07-04 2 'Structure model' 1 1 2013-04-24 3 'Structure model' 1 2 2013-06-19 4 'Structure model' 1 3 2017-11-15 5 'Structure model' 1 4 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Non-polymer description' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 4 'Structure model' '_software.version' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.value' 19 5 'Structure model' '_struct_conn.pdbx_dist_value' 20 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4E7Y _pdbx_database_status.recvd_initial_deposition_date 2012-03-19 _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 4DX4 . unspecified PDB 4E87 . unspecified PDB 4E8S . unspecified PDB 4E8X . unspecified PDB 4E95 . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hall, J.P.' 1 'Cardin, C.J.' 2 # _citation.id primary _citation.title ;Crystal Structure of lambda-[Ru(phen)2(dppz)]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes. ; _citation.journal_abbrev 'Nat Chem' _citation.journal_volume 4 _citation.page_first 621 _citation.page_last 628 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1755-4349 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22824893 _citation.pdbx_database_id_DOI 10.1038/nchem.1397 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Niyazi, H.' 1 ? primary 'Hall, J.P.' 2 ? primary ;O'Sullivan, K. ; 3 ? primary 'Winter, G.' 4 ? primary 'Sorensen, T.' 5 ? primary 'Kelly, J.M.' 6 ? primary 'Cardin, C.J.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'" 3045.992 1 ? ? ? ? 2 non-polymer syn 'Lambda-Ru(phen)2(dppz) complex' 743.779 1 ? ? ? ? 3 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 4 water nat water 18.015 53 ? ? ? ? # _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)(DC)(DG)(DG)(DA)(DT)(DC)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGGATCCGG _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 'Lambda-Ru(phen)2(dppz) complex' RKP 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 DC n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DA n 1 6 DT n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 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 'DNA Purchased from ATDBio' # 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 RKP non-polymer . 'Lambda-Ru(phen)2(dppz) complex' ? 'C42 H26 N8 Ru' 743.779 # 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 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DG 10 10 10 DG DG 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 RKP 1 101 1 RKP RKP A . C 3 BA 1 102 1 BA BA A . D 4 HOH 1 201 1 HOH HOH A . D 4 HOH 2 202 2 HOH HOH A . D 4 HOH 3 203 3 HOH HOH A . D 4 HOH 4 204 4 HOH HOH A . D 4 HOH 5 205 5 HOH HOH A . D 4 HOH 6 206 6 HOH HOH A . D 4 HOH 7 207 7 HOH HOH A . D 4 HOH 8 208 8 HOH HOH A . D 4 HOH 9 209 9 HOH HOH A . D 4 HOH 10 210 10 HOH HOH A . D 4 HOH 11 211 11 HOH HOH A . D 4 HOH 12 212 12 HOH HOH A . D 4 HOH 13 213 13 HOH HOH A . D 4 HOH 14 214 14 HOH HOH A . D 4 HOH 15 215 15 HOH HOH A . D 4 HOH 16 216 17 HOH HOH A . D 4 HOH 17 217 18 HOH HOH A . D 4 HOH 18 218 19 HOH HOH A . D 4 HOH 19 219 20 HOH HOH A . D 4 HOH 20 220 21 HOH HOH A . D 4 HOH 21 221 22 HOH HOH A . D 4 HOH 22 222 23 HOH HOH A . D 4 HOH 23 223 24 HOH HOH A . D 4 HOH 24 224 25 HOH HOH A . D 4 HOH 25 225 26 HOH HOH A . D 4 HOH 26 226 27 HOH HOH A . D 4 HOH 27 227 28 HOH HOH A . D 4 HOH 28 228 29 HOH HOH A . D 4 HOH 29 229 30 HOH HOH A . D 4 HOH 30 230 31 HOH HOH A . D 4 HOH 31 231 32 HOH HOH A . D 4 HOH 32 232 33 HOH HOH A . D 4 HOH 33 233 34 HOH HOH A . D 4 HOH 34 234 35 HOH HOH A . D 4 HOH 35 235 36 HOH HOH A . D 4 HOH 36 236 37 HOH HOH A . D 4 HOH 37 237 38 HOH HOH A . D 4 HOH 38 238 39 HOH HOH A . D 4 HOH 39 239 40 HOH HOH A . D 4 HOH 40 240 41 HOH HOH A . D 4 HOH 41 241 42 HOH HOH A . D 4 HOH 42 242 43 HOH HOH A . D 4 HOH 43 243 44 HOH HOH A . D 4 HOH 44 244 45 HOH HOH A . D 4 HOH 45 245 46 HOH HOH A . D 4 HOH 46 246 47 HOH HOH A . D 4 HOH 47 247 48 HOH HOH A . D 4 HOH 48 248 49 HOH HOH A . D 4 HOH 49 249 50 HOH HOH A . D 4 HOH 50 250 51 HOH HOH A . D 4 HOH 51 251 52 HOH HOH A . D 4 HOH 52 252 53 HOH HOH A . D 4 HOH 53 253 54 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal GDA 'data collection' . ? 1 SHELXCD phasing . ? 2 SHELXE 'model building' . ? 3 REFMAC refinement 5.6.0117 ? 4 XDS 'data reduction' . ? 5 SCALA 'data scaling' . ? 6 # _cell.entry_id 4E7Y _cell.length_a 47.720 _cell.length_b 47.720 _cell.length_c 34.660 _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 4E7Y _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 4E7Y _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.24 _exptl_crystal.density_percent_sol 62.02 _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 7.0 _exptl_crystal_grow.pdbx_details ;1ul 2mM DNA Oligomer, 1ul 3mM Lambda-[Ru(phen)2(dppz)]2+, 1ul 1mM Lambda-[Ru(tap)2(dppz-(Me)2]2+, 6ul 10% 1-methyl-2,4-pentanediol, 40mM Sodium cacodylate, 12mM Spermeine tetra-HCl, 80mM Potassium Chloride, 20mM Barium Chloride, equilibrated against 1ml 35% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K ; _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 2012-03-13 _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 'Si(111) dual crystal' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I02' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 4E7Y _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 34.66 _reflns.d_resolution_high 1.70 _reflns.number_obs 4747 _reflns.number_all 4747 _reflns.percent_possible_obs 100 _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 1.70 _reflns_shell.d_res_low 1.75 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4E7Y _refine.ls_number_reflns_obs 4506 _refine.ls_number_reflns_all 4596 _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 33.74 _refine.ls_d_res_high 1.70 _refine.ls_percent_reflns_obs 99.98 _refine.ls_R_factor_obs 0.15683 _refine.ls_R_factor_all 0.1553 _refine.ls_R_factor_R_work 0.1553 _refine.ls_R_factor_R_free 0.18837 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 216 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.970 _refine.correlation_coeff_Fo_to_Fc_free 0.967 _refine.B_iso_mean 26.951 _refine.aniso_B[1][1] -0.85 _refine.aniso_B[2][2] -0.85 _refine.aniso_B[3][3] 1.71 _refine.aniso_B[1][2] -0.00 _refine.aniso_B[1][3] -0.00 _refine.aniso_B[2][3] -0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _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 USED IF PRESENT IN THE INPUT' _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 0.082 _refine.pdbx_overall_ESU_R_Free 0.085 _refine.overall_SU_ML 0.056 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.737 _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 202 _refine_hist.pdbx_number_atoms_ligand 52 _refine_hist.number_atoms_solvent 53 _refine_hist.number_atoms_total 307 _refine_hist.d_res_high 1.70 _refine_hist.d_res_low 33.74 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.024 0.013 ? 290 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2.520 1.740 ? 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 0.133 0.200 ? 32 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.038 0.020 ? 157 ? '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 ? ? ? ? ? 'X-RAY DIFFRACTION' r_scangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.702 _refine_ls_shell.d_res_low 1.746 _refine_ls_shell.number_reflns_R_work 270 _refine_ls_shell.R_factor_R_work 0.199 _refine_ls_shell.percent_reflns_obs 99.65 _refine_ls_shell.R_factor_R_free 0.205 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 12 _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 4E7Y _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 4E7Y _struct.title 'Lambda-[Ru(phen)2(dppz)]2+ Bound to CCGGATCCGG' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4E7Y _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Intercalation, DNA, Lambda-[Ru(phen)2(dppz)]2+' # 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 4E7Y _struct_ref.pdbx_db_accession 4E7Y _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CCGGATCCGG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4E7Y _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 4E7Y _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)' 900 ? 1 MORE -5 ? 1 'SSA (A^2)' 4400 ? # _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 17.3300000000 # _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 102 1_555 ? ? ? ? ? ? ? 3.007 ? ? metalc2 metalc ? ? A DG 4 O6 ? ? ? 1_555 C BA . BA ? ? A DG 4 A BA 102 1_555 ? ? ? ? ? ? ? 2.921 ? ? metalc3 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 102 A HOH 201 1_555 ? ? ? ? ? ? ? 2.719 ? ? metalc4 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 102 A HOH 202 1_555 ? ? ? ? ? ? ? 2.939 ? ? metalc5 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 102 A HOH 203 1_555 ? ? ? ? ? ? ? 3.081 ? ? metalc6 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 102 A HOH 204 1_555 ? ? ? ? ? ? ? 2.850 ? ? metalc7 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 102 A HOH 208 1_555 ? ? ? ? ? ? ? 2.861 ? ? metalc8 metalc ? ? C BA . BA ? ? ? 1_555 D HOH . O ? ? A BA 102 A HOH 213 1_555 ? ? ? ? ? ? ? 2.838 ? ? hydrog1 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 8_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 3 A DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 3 A DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 3 A DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A DT 6 N3 ? ? A DA 5 A DT 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 6 O4 ? ? A DA 5 A DT 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A DA 5 N1 ? ? A DT 6 A DA 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 6 A DA 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 10 A DC 1 8_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 74.8 ? 2 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 201 ? 1_555 75.4 ? 3 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 201 ? 1_555 69.6 ? 4 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 202 ? 1_555 76.8 ? 5 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 202 ? 1_555 126.2 ? 6 O ? D HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 202 ? 1_555 141.9 ? 7 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 130.3 ? 8 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 89.7 ? 9 O ? D HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 142.5 ? 10 O ? D HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 75.5 ? 11 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 144.2 ? 12 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 139.0 ? 13 O ? D HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 102.5 ? 14 O ? D HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 85.6 ? 15 O ? D HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 72.6 ? 16 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 138.0 ? 17 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 69.2 ? 18 O ? D HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 72.5 ? 19 O ? D HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 143.1 ? 20 O ? D HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 71.0 ? 21 O ? D HOH . ? A HOH 204 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 70.1 ? 22 N7 ? A DG 3 ? A DG 3 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 74.7 ? 23 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 140.9 ? 24 O ? D HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 79.4 ? 25 O ? D HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 68.6 ? 26 O ? D HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 129.0 ? 27 O ? D HOH . ? A HOH 204 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 69.8 ? 28 O ? D HOH . ? A HOH 208 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 123.7 ? # 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 RKP 101 ? 10 'BINDING SITE FOR RESIDUE RKP A 101' AC2 Software A BA 102 ? 8 'BINDING SITE FOR RESIDUE BA A 102' # 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 10 DC A 1 ? DC A 1 . ? 8_555 ? 2 AC1 10 DC A 2 ? DC A 2 . ? 8_555 ? 3 AC1 10 DG A 3 ? DG A 3 . ? 8_555 ? 4 AC1 10 DG A 3 ? DG A 3 . ? 6_555 ? 5 AC1 10 DG A 4 ? DG A 4 . ? 6_555 ? 6 AC1 10 DC A 7 ? DC A 7 . ? 3_554 ? 7 AC1 10 DC A 8 ? DC A 8 . ? 3_554 ? 8 AC1 10 DG A 9 ? DG A 9 . ? 1_555 ? 9 AC1 10 DG A 10 ? DG A 10 . ? 1_555 ? 10 AC1 10 HOH D . ? HOH A 240 . ? 8_555 ? 11 AC2 8 DG A 3 ? DG A 3 . ? 1_555 ? 12 AC2 8 DG A 4 ? DG A 4 . ? 1_555 ? 13 AC2 8 HOH D . ? HOH A 201 . ? 1_555 ? 14 AC2 8 HOH D . ? HOH A 202 . ? 1_555 ? 15 AC2 8 HOH D . ? HOH A 203 . ? 1_555 ? 16 AC2 8 HOH D . ? HOH A 204 . ? 1_555 ? 17 AC2 8 HOH D . ? HOH A 208 . ? 1_555 ? 18 AC2 8 HOH D . ? HOH A 213 . ? 1_555 ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 245 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 245 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 8_555 _pdbx_validate_symm_contact.dist 2.11 # 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 "O3'" A DC 1 ? ? P A DC 2 ? ? "O5'" A DC 2 ? ? 90.60 104.00 -13.40 1.90 Y 2 1 "O3'" A DC 1 ? ? P A DC 2 ? ? OP2 A DC 2 ? ? 118.73 110.50 8.23 1.10 Y 3 1 "O3'" A DT 6 ? ? P A DC 7 ? ? OP2 A DC 7 ? ? 117.75 110.50 7.25 1.10 Y # _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 225 _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 . # 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 RKP RU RU N N 148 RKP C1 C Y N 149 RKP N1 N Y N 150 RKP C2 C Y N 151 RKP N2 N Y N 152 RKP C3 C Y N 153 RKP N3 N Y N 154 RKP C4 C Y N 155 RKP N4 N Y N 156 RKP C5 C Y N 157 RKP N5 N Y N 158 RKP C6 C Y N 159 RKP C7 C Y N 160 RKP C8 C Y N 161 RKP N8 N Y N 162 RKP C9 C Y N 163 RKP N9 N Y N 164 RKP C10 C Y N 165 RKP C11 C Y N 166 RKP C12 C Y N 167 RKP N12 N Y N 168 RKP C13 C Y N 169 RKP C14 C Y N 170 RKP C15 C Y N 171 RKP C16 C Y N 172 RKP C17 C Y N 173 RKP C18 C Y N 174 RKP C19 C Y N 175 RKP C20 C Y N 176 RKP C21 C Y N 177 RKP C22 C Y N 178 RKP C23 C Y N 179 RKP C24 C Y N 180 RKP C25 C Y N 181 RKP C26 C Y N 182 RKP C27 C Y N 183 RKP C28 C Y N 184 RKP C29 C Y N 185 RKP C30 C Y N 186 RKP C31 C Y N 187 RKP C32 C Y N 188 RKP C33 C Y N 189 RKP C34 C Y N 190 RKP C35 C Y N 191 RKP C36 C Y N 192 RKP C37 C Y N 193 RKP C38 C Y N 194 RKP C41 C Y N 195 RKP C42 C Y N 196 RKP C43 C Y N 197 RKP C44 C Y N 198 RKP H2 H N N 199 RKP H3 H N N 200 RKP H4 H N N 201 RKP H9 H N N 202 RKP H11 H N N 203 RKP H12 H N N 204 RKP H14 H N N 205 RKP H16 H N N 206 RKP H17 H N N 207 RKP H18 H N N 208 RKP H20 H N N 209 RKP H21 H N N 210 RKP H23 H N N 211 RKP H24 H N N 212 RKP H27 H N N 213 RKP H28 H N N 214 RKP H30 H N N 215 RKP H31 H N N 216 RKP H33 H N N 217 RKP H34 H N N 218 RKP H37 H N N 219 RKP H38 H N N 220 RKP H41 H N N 221 RKP H42 H N N 222 RKP H43 H N N 223 RKP H44 H N N 224 # 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 RKP C1 N2 sing Y N 152 RKP C1 C5 doub Y N 153 RKP C1 C10 sing Y N 154 RKP N1 C10 sing Y N 155 RKP N1 C12 doub Y N 156 RKP C2 N2 doub Y N 157 RKP C2 C3 sing Y N 158 RKP C3 C4 doub Y N 159 RKP N3 C6 sing Y N 160 RKP N3 C15 doub Y N 161 RKP C4 C5 sing Y N 162 RKP N4 C7 sing Y N 163 RKP N4 C13 doub Y N 164 RKP C5 C6 sing Y N 165 RKP N5 C19 sing Y N 166 RKP N5 C20 doub Y N 167 RKP C6 C7 doub Y N 168 RKP C7 C8 sing Y N 169 RKP C8 C9 sing Y N 170 RKP C8 C10 doub Y N 171 RKP N8 C26 sing Y N 172 RKP N8 C28 doub Y N 173 RKP C9 C11 doub Y N 174 RKP N9 C29 sing Y N 175 RKP N9 C30 doub Y N 176 RKP C11 C12 sing Y N 177 RKP N12 C36 sing Y N 178 RKP N12 C38 doub Y N 179 RKP C13 C14 sing Y N 180 RKP C13 C15 sing Y N 181 RKP C14 C18 doub Y N 182 RKP C15 C16 sing Y N 183 RKP C16 C17 doub Y N 184 RKP C17 C18 sing Y N 185 RKP C19 C22 doub Y N 186 RKP C19 C26 sing Y N 187 RKP C20 C21 sing Y N 188 RKP C21 C41 doub Y N 189 RKP C22 C23 sing Y N 190 RKP C22 C41 sing Y N 191 RKP C23 C24 doub Y N 192 RKP C24 C25 sing Y N 193 RKP C25 C26 doub Y N 194 RKP C25 C42 sing Y N 195 RKP C27 C28 sing Y N 196 RKP C27 C42 doub Y N 197 RKP C29 C32 doub Y N 198 RKP C29 C36 sing Y N 199 RKP C30 C31 sing Y N 200 RKP C31 C43 doub Y N 201 RKP C32 C33 sing Y N 202 RKP C32 C43 sing Y N 203 RKP C33 C34 doub Y N 204 RKP C34 C35 sing Y N 205 RKP C35 C36 doub Y N 206 RKP C35 C44 sing Y N 207 RKP C37 C38 sing Y N 208 RKP C37 C44 doub Y N 209 RKP C2 H2 sing N N 210 RKP C3 H3 sing N N 211 RKP C4 H4 sing N N 212 RKP C9 H9 sing N N 213 RKP C11 H11 sing N N 214 RKP C12 H12 sing N N 215 RKP C14 H14 sing N N 216 RKP C16 H16 sing N N 217 RKP C17 H17 sing N N 218 RKP C18 H18 sing N N 219 RKP C20 H20 sing N N 220 RKP C21 H21 sing N N 221 RKP C23 H23 sing N N 222 RKP C24 H24 sing N N 223 RKP C27 H27 sing N N 224 RKP C28 H28 sing N N 225 RKP C30 H30 sing N N 226 RKP C31 H31 sing N N 227 RKP C33 H33 sing N N 228 RKP C34 H34 sing N N 229 RKP C37 H37 sing N N 230 RKP C38 H38 sing N N 231 RKP C41 H41 sing N N 232 RKP C42 H42 sing N N 233 RKP C43 H43 sing N N 234 RKP C44 H44 sing N N 235 RKP RU N1 sing N N 236 RKP RU N2 sing N N 237 RKP RU N5 sing N N 238 RKP RU N8 sing N N 239 RKP RU N9 sing N N 240 RKP RU N12 sing N N 241 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4E7Y 'double helix' 4E7Y 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 A DG 10 8_555 -3.783 5.170 -0.151 -2.150 -8.831 -128.061 1 A_DC1:DG10_A A 1 ? A 10 ? ? 3 1 A DC 2 1_555 A DG 9 8_555 0.235 -0.133 0.106 -8.023 3.306 1.277 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 8_555 -0.248 -0.039 0.188 22.823 -5.629 -0.414 3 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 8_555 -0.242 -0.056 -0.211 -15.191 -0.547 -0.488 4 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DA 5 1_555 A DT 6 8_555 0.063 -0.143 0.064 -3.613 -6.008 2.761 5 A_DA5:DT6_A A 5 ? A 6 ? 20 1 1 A DT 6 1_555 A DA 5 8_555 -0.063 -0.143 0.064 3.613 -6.008 2.761 6 A_DT6:DA5_A A 6 ? A 5 ? 20 1 1 A DC 7 1_555 A DG 4 8_555 0.242 -0.056 -0.211 15.191 -0.547 -0.488 7 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DC 8 1_555 A DG 3 8_555 0.248 -0.039 0.188 -22.822 -5.629 -0.414 8 A_DC8:DG3_A A 8 ? A 3 ? 19 1 1 A DG 9 1_555 A DC 2 8_555 -0.235 -0.133 0.106 8.023 3.306 1.277 9 A_DG9:DC2_A A 9 ? A 2 ? 19 1 1 A DG 10 1_555 A DC 1 8_555 3.783 -5.170 0.151 2.150 8.831 128.061 10 A_DG10:DC1_A A 10 ? A 1 ? ? 3 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 A DG 10 8_555 A DC 2 1_555 A DG 9 8_555 0.618 1.034 7.069 -2.268 3.151 -8.396 -21.104 -6.740 6.218 -20.165 -14.510 -9.249 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 8_555 A DG 3 1_555 A DC 8 8_555 -0.321 1.552 2.776 1.028 3.289 21.305 2.984 1.219 2.960 8.821 -2.758 21.578 2 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 -0.221 0.958 5.357 -1.763 55.236 11.237 -5.345 0.031 2.055 79.366 2.533 56.307 3 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 8_555 A DA 5 1_555 A DT 6 8_555 -1.161 0.664 3.123 -8.681 8.039 34.178 -0.091 0.618 3.376 13.197 14.252 36.110 4 AA_DG4DA5:DT6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DA 5 1_555 A DT 6 8_555 A DT 6 1_555 A DA 5 8_555 0.000 -0.511 3.125 0.000 4.850 26.593 -2.255 0.000 2.986 10.433 0.000 27.024 5 AA_DA5DT6:DA5DT6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DT 6 1_555 A DA 5 8_555 A DC 7 1_555 A DG 4 8_555 1.161 0.664 3.123 8.681 8.039 34.178 -0.091 -0.618 3.376 13.197 -14.252 36.110 6 AA_DT6DC7:DG4DA5_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 0.221 0.958 5.357 1.763 55.236 11.237 -5.345 -0.031 2.055 79.366 -2.533 56.307 7 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 0.321 1.552 2.776 -1.028 3.289 21.305 2.984 -1.219 2.960 8.821 2.758 21.578 8 AA_DC8DG9:DC2DG3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DG 9 1_555 A DC 2 8_555 A DG 10 1_555 A DC 1 8_555 -0.040 -7.085 1.105 -175.645 12.893 108.525 -3.564 -0.257 0.618 6.473 88.187 177.733 9 AA_DG9DG10:DC1DC2_AA A 9 ? A 2 ? A 10 ? A 1 ? # _atom_sites.entry_id 4E7Y _atom_sites.fract_transf_matrix[1][1] 0.020956 _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] 0.020956 _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] 0.028852 _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_