data_1ZPH # _entry.id 1ZPH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1ZPH pdb_00001zph 10.2210/pdb1zph/pdb NDB DD0071 ? ? RCSB RCSB032989 ? ? WWPDB D_1000032989 ? ? # 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 2005-10-11 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 5 'Structure model' 1 4 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site 7 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_struct_conn.pdbx_dist_value' 11 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 15 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 16 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1ZPH _pdbx_database_status.recvd_initial_deposition_date 2005-05-16 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1ZPI _pdbx_database_related.details 'Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN 8224 complexed with CGCGAATTCGCG' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Adams, A.' 1 'Leong, C.' 2 'Denny, W.A.' 3 'Guss, J.M.' 4 # _citation.id primary _citation.title ;Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)(2) at 1.6 and 1.8 Angstrom resolution. ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 61 _citation.page_first 1348 _citation.page_last 1353 _citation.year 2005 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16204886 _citation.pdbx_database_id_DOI 10.1107/S0907444905022997 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Adams, A.' 1 ? primary 'Leong, C.' 2 ? primary 'Denny, W.A.' 3 ? primary 'Guss, J.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 "5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'" 3663.392 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn '1,6-DIMETHYL-4-(4-(4-(1-METHYLPYRIDINIUM-4-YLAMINO)PHENYLCARBAMOYL)PHENYLAMINO)QUINOLINIUM' 493.727 1 ? ? ? ? 4 water nat water 18.015 33 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 '1,6-DIMETHYL-4-(4-(4-(1-METHYLPYRIDINIUM-4-YLAMINO)PHENYLCARBAMOYL)PHENYLAMINO)QUINOLINIUM' SN8 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SN8 non-polymer . '1,6-DIMETHYL-4-(4-(4-(1-METHYLPYRIDINIUM-4-YLAMINO)PHENYLCARBAMOYL)PHENYLAMINO)QUINOLINIUM' SN8315 'C30 H47 N5 O' 493.727 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG 1 25 25 MG MG A . D 3 SN8 1 1 1 SN8 DRG B . E 4 HOH 1 26 26 HOH HOH A . E 4 HOH 2 27 27 HOH HOH A . E 4 HOH 3 30 30 HOH HOH A . E 4 HOH 4 31 31 HOH HOH A . E 4 HOH 5 32 32 HOH HOH A . E 4 HOH 6 33 33 HOH HOH A . E 4 HOH 7 35 35 HOH HOH A . E 4 HOH 8 36 36 HOH HOH A . E 4 HOH 9 37 37 HOH HOH A . E 4 HOH 10 38 38 HOH HOH A . E 4 HOH 11 40 40 HOH HOH A . E 4 HOH 12 41 41 HOH HOH A . E 4 HOH 13 42 42 HOH HOH A . E 4 HOH 14 43 43 HOH HOH A . E 4 HOH 15 44 44 HOH HOH A . E 4 HOH 16 45 45 HOH HOH A . E 4 HOH 17 46 46 HOH HOH A . E 4 HOH 18 47 47 HOH HOH A . E 4 HOH 19 48 48 HOH HOH A . E 4 HOH 20 52 52 HOH HOH A . E 4 HOH 21 53 53 HOH HOH A . E 4 HOH 22 54 54 HOH HOH A . E 4 HOH 23 55 55 HOH HOH A . E 4 HOH 24 56 56 HOH HOH A . E 4 HOH 25 58 58 HOH HOH A . E 4 HOH 26 59 59 HOH HOH A . F 4 HOH 1 29 29 HOH HOH B . F 4 HOH 2 34 34 HOH HOH B . F 4 HOH 3 39 39 HOH HOH B . F 4 HOH 4 49 49 HOH HOH B . F 4 HOH 5 50 50 HOH HOH B . F 4 HOH 6 51 51 HOH HOH B . F 4 HOH 7 57 57 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 1ZPH _cell.length_a 24.873 _cell.length_b 39.907 _cell.length_c 65.707 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZPH _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1ZPH _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.13 _exptl_crystal.density_percent_sol 42.32 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 285 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'cacodylate, spermine, magnesium chloride, MPD, pH 7.0, VAPOR DIFFUSION, temperature 285K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 cacodylate ? ? ? 1 2 1 spermine ? ? ? 1 3 1 'magnesium chloride' ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 cacodylate ? ? ? 1 7 2 'magnesium chloride' ? ? ? 1 8 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2004-08-18 _diffrn_detector.details mirror # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1ZPH _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.8 _reflns.d_resolution_low 50 _reflns.number_all ? _reflns.number_obs 6315 _reflns.percent_possible_obs 97.2 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_Rsym_value 0.092 _reflns.pdbx_netI_over_sigmaI 15.3 _reflns.B_iso_Wilson_estimate 35.3 _reflns.pdbx_redundancy 5.3 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.86 _reflns_shell.percent_possible_all 98.9 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.511 _reflns_shell.meanI_over_sigI_obs 2.6 _reflns_shell.pdbx_redundancy 2.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 617 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1ZPH _refine.ls_number_reflns_obs 5807 _refine.ls_number_reflns_all 9114 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.00 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 97.21 _refine.ls_R_factor_obs 0.2405 _refine.ls_R_factor_all 0.2405 _refine.ls_R_factor_R_work 0.23449 _refine.ls_R_factor_R_free 0.31395 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.5 _refine.ls_number_reflns_R_free 473 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.958 _refine.correlation_coeff_Fo_to_Fc_free 0.931 _refine.B_iso_mean 39.035 _refine.aniso_B[1][1] 3.62 _refine.aniso_B[2][2] -1.35 _refine.aniso_B[3][3] -2.27 _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 'BABINET MODEL WITH 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 ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'ndb entry BD0007' _refine.pdbx_method_to_determine_struct Refinement _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 0.172 _refine.pdbx_overall_ESU_R_Free 0.181 _refine.overall_SU_ML 0.149 _refine.overall_SU_B 4.880 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 486 _refine_hist.pdbx_number_atoms_ligand 37 _refine_hist.number_atoms_solvent 33 _refine_hist.number_atoms_total 556 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 34.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.016 0.021 ? 584 'X-RAY DIFFRACTION' ? r_bond_other_d 0.005 0.020 ? 259 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.627 2.998 ? 892 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.221 3.015 ? 610 '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 0.077 0.200 ? 94 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.014 0.020 ? 296 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 3 'X-RAY DIFFRACTION' ? r_nbd_refined 0.190 0.200 ? 65 'X-RAY DIFFRACTION' ? r_nbd_other 0.224 0.200 ? 317 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.245 0.200 ? 242 'X-RAY DIFFRACTION' ? r_nbtor_other 0.094 0.200 ? 155 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.178 0.200 ? 28 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.142 0.200 ? 5 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.068 0.200 ? 3 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.147 0.200 ? 14 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.120 0.200 ? 9 '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 8.888 2.000 ? 869 'X-RAY DIFFRACTION' ? r_scangle_it 9.685 3.000 ? 892 '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 1.80 _refine_ls_shell.d_res_low 1.848 _refine_ls_shell.number_reflns_R_work 413 _refine_ls_shell.R_factor_R_work 0.297 _refine_ls_shell.percent_reflns_obs 99.13 _refine_ls_shell.R_factor_R_free 0.367 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 41 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1ZPH _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 1ZPH _struct.title 'Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN 8315 complexed with CGCGAATTCGCG' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1ZPH _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, dodecamer, minor groove binding complex, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1ZPH _struct_ref.pdbx_db_accession 1ZPH _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1ZPH A 1 ? 12 ? 1ZPH 1 ? 12 ? 1 12 2 1 1ZPH B 1 ? 12 ? 1ZPH 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 26 1_555 ? ? ? ? ? ? ? 1.998 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 31 1_555 ? ? ? ? ? ? ? 1.826 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 33 1_555 ? ? ? ? ? ? ? 1.944 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 37 1_555 ? ? ? ? ? ? ? 1.871 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 40 1_555 ? ? ? ? ? ? ? 1.752 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 25 B HOH 29 1_555 ? ? ? ? ? ? ? 1.957 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 26 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 31 ? 1_555 92.8 ? 2 O ? E HOH . ? A HOH 26 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 33 ? 1_555 86.7 ? 3 O ? E HOH . ? A HOH 31 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 33 ? 1_555 93.8 ? 4 O ? E HOH . ? A HOH 26 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 37 ? 1_555 179.5 ? 5 O ? E HOH . ? A HOH 31 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 37 ? 1_555 86.7 ? 6 O ? E HOH . ? A HOH 33 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 37 ? 1_555 93.2 ? 7 O ? E HOH . ? A HOH 26 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 40 ? 1_555 83.9 ? 8 O ? E HOH . ? A HOH 31 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 40 ? 1_555 176.2 ? 9 O ? E HOH . ? A HOH 33 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 40 ? 1_555 87.9 ? 10 O ? E HOH . ? A HOH 37 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 40 ? 1_555 96.6 ? 11 O ? E HOH . ? A HOH 26 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 29 ? 1_555 93.4 ? 12 O ? E HOH . ? A HOH 31 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 29 ? 1_555 89.7 ? 13 O ? E HOH . ? A HOH 33 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 29 ? 1_555 176.5 ? 14 O ? E HOH . ? A HOH 37 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 29 ? 1_555 86.7 ? 15 O ? E HOH . ? A HOH 40 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 29 ? 1_555 88.7 ? # 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 B SN8 1 ? 13 'BINDING SITE FOR RESIDUE SN8 B 1' AC2 Software A MG 25 ? 6 'BINDING SITE FOR RESIDUE MG A 25' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 13 DG A 4 ? DG A 4 . ? 1_555 ? 2 AC1 13 DA A 5 ? DA A 5 . ? 1_555 ? 3 AC1 13 DA A 6 ? DA A 6 . ? 1_555 ? 4 AC1 13 DT A 7 ? DT A 7 . ? 1_555 ? 5 AC1 13 DT A 8 ? DT A 8 . ? 1_555 ? 6 AC1 13 DC A 9 ? DC A 9 . ? 1_555 ? 7 AC1 13 DG B 4 ? DG B 16 . ? 1_555 ? 8 AC1 13 DA B 5 ? DA B 17 . ? 1_555 ? 9 AC1 13 DA B 6 ? DA B 18 . ? 1_555 ? 10 AC1 13 DT B 7 ? DT B 19 . ? 1_555 ? 11 AC1 13 DT B 8 ? DT B 20 . ? 1_555 ? 12 AC1 13 DC B 9 ? DC B 21 . ? 1_555 ? 13 AC1 13 DG B 10 ? DG B 22 . ? 1_555 ? 14 AC2 6 HOH E . ? HOH A 26 . ? 1_555 ? 15 AC2 6 HOH E . ? HOH A 31 . ? 1_555 ? 16 AC2 6 HOH E . ? HOH A 33 . ? 1_555 ? 17 AC2 6 HOH E . ? HOH A 37 . ? 1_555 ? 18 AC2 6 HOH E . ? HOH A 40 . ? 1_555 ? 19 AC2 6 HOH F . ? HOH B 29 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DG 10 ? ? "C3'" A DG 10 ? ? 1.382 1.419 -0.037 0.006 N 2 1 "O3'" B DC 15 ? ? "C3'" B DC 15 ? ? 1.367 1.419 -0.052 0.006 N 3 1 "O3'" B DA 18 ? ? "C3'" B DA 18 ? ? 1.361 1.419 -0.058 0.006 N 4 1 "O3'" B DG 22 ? ? "C3'" B DG 22 ? ? 1.382 1.419 -0.037 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N3 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 124.24 119.90 4.34 0.60 N 2 1 C5 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 119.34 124.90 -5.56 0.70 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'minor groove binder' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MG MG MG N N 147 SN8 CBG C Y N 148 SN8 CAU C Y N 149 SN8 CAZ C Y N 150 SN8 CAA C N N 151 SN8 CAM C Y N 152 SN8 CAQ C Y N 153 SN8 CBH C Y N 154 SN8 NBJ N N N 155 SN8 CAC C N N 156 SN8 CAT C N N 157 SN8 CAP C N N 158 SN8 CBF C N N 159 SN8 NAX N N N 160 SN8 CBC C N N 161 SN8 CAJ C N N 162 SN8 CAL C N N 163 SN8 CAI C N N 164 SN8 CAK C N N 165 SN8 CBE C N N 166 SN8 CAY C N N 167 SN8 OAD O N N 168 SN8 NAV N N N 169 SN8 CBA C N N 170 SN8 CAF C N N 171 SN8 CAH C N N 172 SN8 CAE C N N 173 SN8 CAG C N N 174 SN8 CBB C N N 175 SN8 NAW N N N 176 SN8 CBD C N N 177 SN8 CAN C N N 178 SN8 CAR C N N 179 SN8 NBI N N N 180 SN8 CAB C N N 181 SN8 CAS C N N 182 SN8 CAO C N N 183 SN8 HAU H N N 184 SN8 HAA1 H N N 185 SN8 HAA2 H N N 186 SN8 HAA3 H N N 187 SN8 HAM H N N 188 SN8 HAQ H N N 189 SN8 HAC1 H N N 190 SN8 HAC2 H N N 191 SN8 HAC3 H N N 192 SN8 HAT H N N 193 SN8 HAT1 H N N 194 SN8 HAP H N N 195 SN8 HAX H N N 196 SN8 HBC H N N 197 SN8 HAJ H N N 198 SN8 HAJ1 H N N 199 SN8 HAL H N N 200 SN8 HAL1 H N N 201 SN8 HAI H N N 202 SN8 HAI1 H N N 203 SN8 HAK H N N 204 SN8 HAK1 H N N 205 SN8 HBE H N N 206 SN8 HAV H N N 207 SN8 HBA H N N 208 SN8 HAF H N N 209 SN8 HAF1 H N N 210 SN8 HAH H N N 211 SN8 HAH1 H N N 212 SN8 HAE H N N 213 SN8 HAE1 H N N 214 SN8 HAG H N N 215 SN8 HAG1 H N N 216 SN8 HBB H N N 217 SN8 HAW H N N 218 SN8 HBD H N N 219 SN8 HAN H N N 220 SN8 HAN1 H N N 221 SN8 HAR H N N 222 SN8 HAR1 H N N 223 SN8 HAB1 H N N 224 SN8 HAB2 H N N 225 SN8 HAB3 H N N 226 SN8 HAS H N N 227 SN8 HAS1 H N N 228 SN8 HAO H N N 229 SN8 HAO1 H N N 230 # 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 SN8 CBG CAU sing Y N 152 SN8 CBG CBH doub Y N 153 SN8 CBG CBF sing N N 154 SN8 CAU CAZ doub Y N 155 SN8 CAU HAU sing N N 156 SN8 CAZ CAA sing N N 157 SN8 CAZ CAM sing Y N 158 SN8 CAA HAA1 sing N N 159 SN8 CAA HAA2 sing N N 160 SN8 CAA HAA3 sing N N 161 SN8 CAM CAQ doub Y N 162 SN8 CAM HAM sing N N 163 SN8 CAQ CBH sing Y N 164 SN8 CAQ HAQ sing N N 165 SN8 CBH NBJ sing N N 166 SN8 NBJ CAC sing N N 167 SN8 NBJ CAT sing N N 168 SN8 CAC HAC1 sing N N 169 SN8 CAC HAC2 sing N N 170 SN8 CAC HAC3 sing N N 171 SN8 CAT CAP sing N N 172 SN8 CAT HAT sing N N 173 SN8 CAT HAT1 sing N N 174 SN8 CAP CBF doub N N 175 SN8 CAP HAP sing N N 176 SN8 CBF NAX sing N N 177 SN8 NAX CBC sing N N 178 SN8 NAX HAX sing N N 179 SN8 CBC CAJ sing N N 180 SN8 CBC CAI sing N N 181 SN8 CBC HBC sing N N 182 SN8 CAJ CAL sing N N 183 SN8 CAJ HAJ sing N N 184 SN8 CAJ HAJ1 sing N N 185 SN8 CAL CBE sing N N 186 SN8 CAL HAL sing N N 187 SN8 CAL HAL1 sing N N 188 SN8 CAI CAK sing N N 189 SN8 CAI HAI sing N N 190 SN8 CAI HAI1 sing N N 191 SN8 CAK CBE sing N N 192 SN8 CAK HAK sing N N 193 SN8 CAK HAK1 sing N N 194 SN8 CBE CAY sing N N 195 SN8 CBE HBE sing N N 196 SN8 CAY OAD doub N N 197 SN8 CAY NAV sing N N 198 SN8 NAV CBA sing N N 199 SN8 NAV HAV sing N N 200 SN8 CBA CAF sing N N 201 SN8 CBA CAE sing N N 202 SN8 CBA HBA sing N N 203 SN8 CAF CAH sing N N 204 SN8 CAF HAF sing N N 205 SN8 CAF HAF1 sing N N 206 SN8 CAH CBB sing N N 207 SN8 CAH HAH sing N N 208 SN8 CAH HAH1 sing N N 209 SN8 CAE CAG sing N N 210 SN8 CAE HAE sing N N 211 SN8 CAE HAE1 sing N N 212 SN8 CAG CBB sing N N 213 SN8 CAG HAG sing N N 214 SN8 CAG HAG1 sing N N 215 SN8 CBB NAW sing N N 216 SN8 CBB HBB sing N N 217 SN8 NAW CBD sing N N 218 SN8 NAW HAW sing N N 219 SN8 CBD CAN sing N N 220 SN8 CBD CAO sing N N 221 SN8 CBD HBD sing N N 222 SN8 CAN CAR sing N N 223 SN8 CAN HAN sing N N 224 SN8 CAN HAN1 sing N N 225 SN8 CAR NBI sing N N 226 SN8 CAR HAR sing N N 227 SN8 CAR HAR1 sing N N 228 SN8 NBI CAB sing N N 229 SN8 NBI CAS sing N N 230 SN8 CAB HAB1 sing N N 231 SN8 CAB HAB2 sing N N 232 SN8 CAB HAB3 sing N N 233 SN8 CAS CAO sing N N 234 SN8 CAS HAS sing N N 235 SN8 CAS HAS1 sing N N 236 SN8 CAO HAO sing N N 237 SN8 CAO HAO1 sing N N 238 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1ZPH 'double helix' 1ZPH '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 B DG 12 1_555 0.410 -0.275 -0.002 3.632 -14.891 -1.363 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.406 -0.173 0.233 1.858 -12.895 -3.491 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.134 -0.142 0.186 -3.050 -6.747 -3.035 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.363 -0.071 -0.158 8.564 -8.895 -2.027 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.200 -0.035 -0.260 4.536 -15.195 4.913 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.330 -0.120 -0.001 1.043 -17.685 4.060 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.243 -0.144 -0.013 -3.323 -18.670 5.186 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.032 -0.075 0.128 -6.149 -13.734 2.453 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.229 -0.176 0.015 -7.612 -12.942 0.629 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.024 -0.166 0.210 10.181 -5.455 2.448 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 -0.039 -0.168 0.662 1.443 -19.964 -2.495 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.574 -0.136 -0.525 5.363 21.655 -3.987 12 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.169 0.177 3.295 -1.519 8.118 32.577 -1.045 0.040 3.249 14.189 2.656 33.580 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.670 0.552 3.480 1.906 -6.775 40.042 1.590 -0.742 3.373 -9.803 -2.758 40.631 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.295 0.811 3.108 3.910 12.830 26.625 -1.116 1.395 3.092 25.877 -7.886 29.758 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 0.214 0.188 3.374 0.397 2.378 41.190 0.002 -0.259 3.381 3.377 -0.564 41.258 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.012 -0.121 3.302 -2.472 3.954 33.936 -0.832 -0.372 3.260 6.735 4.210 34.246 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.168 -0.648 3.219 1.067 0.659 30.206 -1.373 -0.110 3.208 1.264 -2.046 30.231 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 0.108 -0.158 3.311 0.796 2.927 35.578 -0.685 -0.060 3.290 4.780 -1.300 35.703 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.329 0.270 3.329 0.985 -3.879 43.387 0.743 0.540 3.287 -5.233 -1.329 43.563 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.549 1.224 3.089 -1.627 7.064 26.760 0.869 -1.535 3.261 14.918 3.437 27.707 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.112 0.601 3.687 -6.677 -10.163 40.776 2.000 0.766 3.576 -14.210 9.336 42.476 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 1.052 0.732 3.559 9.183 -11.929 35.966 2.689 -0.355 3.323 -18.360 -14.134 38.893 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_initial_refinement_model.accession_code 436D _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'ndb entry BD0007' # _atom_sites.entry_id 1ZPH _atom_sites.fract_transf_matrix[1][1] 0.040204 _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] 0.025058 _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] 0.015219 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P # loop_