data_4E4O # _entry.id 4E4O # _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 4E4O pdb_00004e4o 10.2210/pdb4e4o/pdb NDB NA1674 ? ? RCSB RCSB071164 ? ? WWPDB D_1000071164 ? ? # 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 2013-03-13 2 'Structure model' 1 1 2024-03-20 3 'Structure model' 1 2 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 3 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' struct_site 5 3 'Structure model' 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4E4O _pdbx_database_status.recvd_initial_deposition_date 2012-03-13 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4E2R _pdbx_database_related.details 'The same oligonucleotide crystallizes in P212121 space group' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mandal, P.K.' 1 'Venkadesh, S.' 2 'Gautham, N.' 3 # _citation.id primary _citation.title 'Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mandal, P.K.' 1 ? primary 'Venkadesh, S.' 2 ? primary 'Gautham, N.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*AP*CP*GP*CP*G)-3') ; 1794.206 2 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*GP*CP*GP*TP*G)-3') ; 1825.216 2 ? ? ? ? 3 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 4 water nat water 18.015 57 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DA)(DC)(DG)(DC)(DG)' CACGCG A,C ? 2 polydeoxyribonucleotide no no '(DC)(DG)(DC)(DG)(DT)(DG)' CGCGTG B,D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 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 DA n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DG n 2 1 DC n 2 2 DG n 2 3 DC n 2 4 DG n 2 5 DT n 2 6 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 BA non-polymer . 'BARIUM ION' ? 'Ba 2' 137.327 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 2 1 DC 1 7 7 DC DC B . n B 2 2 DG 2 8 8 DG DG B . n B 2 3 DC 3 9 9 DC DC B . n B 2 4 DG 4 10 10 DG DG B . n B 2 5 DT 5 11 11 DT DT B . n B 2 6 DG 6 12 12 DG DG B . n C 1 1 DC 1 1 1 DC DC C . n C 1 2 DA 2 2 2 DA DA C . n C 1 3 DC 3 3 3 DC DC C . n C 1 4 DG 4 4 4 DG DG C . n C 1 5 DC 5 5 5 DC DC C . n C 1 6 DG 6 6 6 DG DG C . n D 2 1 DC 1 7 7 DC DC D . n D 2 2 DG 2 8 8 DG DG D . n D 2 3 DC 3 9 9 DC DC D . n D 2 4 DG 4 10 10 DG DG D . n D 2 5 DT 5 11 11 DT DT D . n D 2 6 DG 6 12 12 DG DG D . 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 E 3 BA 1 101 1 BA BA A . F 4 HOH 1 201 3 HOH HOH A . F 4 HOH 2 202 5 HOH HOH A . F 4 HOH 3 203 16 HOH HOH A . F 4 HOH 4 204 17 HOH HOH A . F 4 HOH 5 205 26 HOH HOH A . F 4 HOH 6 206 29 HOH HOH A . F 4 HOH 7 207 37 HOH HOH A . F 4 HOH 8 208 41 HOH HOH A . F 4 HOH 9 209 47 HOH HOH A . F 4 HOH 10 210 48 HOH HOH A . F 4 HOH 11 211 53 HOH HOH A . G 4 HOH 1 101 19 HOH HOH B . G 4 HOH 2 102 1 HOH HOH B . G 4 HOH 3 103 4 HOH HOH B . G 4 HOH 4 104 6 HOH HOH B . G 4 HOH 5 105 9 HOH HOH B . G 4 HOH 6 106 15 HOH HOH B . G 4 HOH 7 107 23 HOH HOH B . G 4 HOH 8 108 24 HOH HOH B . G 4 HOH 9 109 28 HOH HOH B . G 4 HOH 10 110 38 HOH HOH B . G 4 HOH 11 111 44 HOH HOH B . G 4 HOH 12 112 46 HOH HOH B . G 4 HOH 13 113 52 HOH HOH B . G 4 HOH 14 114 56 HOH HOH B . H 4 HOH 1 101 12 HOH HOH C . H 4 HOH 2 102 20 HOH HOH C . H 4 HOH 3 103 21 HOH HOH C . H 4 HOH 4 104 25 HOH HOH C . H 4 HOH 5 105 27 HOH HOH C . H 4 HOH 6 106 30 HOH HOH C . H 4 HOH 7 107 32 HOH HOH C . H 4 HOH 8 108 33 HOH HOH C . H 4 HOH 9 109 35 HOH HOH C . H 4 HOH 10 110 36 HOH HOH C . H 4 HOH 11 111 40 HOH HOH C . H 4 HOH 12 112 43 HOH HOH C . H 4 HOH 13 113 57 HOH HOH C . I 4 HOH 1 101 7 HOH HOH D . I 4 HOH 2 102 2 HOH HOH D . I 4 HOH 3 103 8 HOH HOH D . I 4 HOH 4 104 10 HOH HOH D . I 4 HOH 5 105 11 HOH HOH D . I 4 HOH 6 106 13 HOH HOH D . I 4 HOH 7 107 14 HOH HOH D . I 4 HOH 8 108 18 HOH HOH D . I 4 HOH 9 109 22 HOH HOH D . I 4 HOH 10 110 31 HOH HOH D . I 4 HOH 11 111 34 HOH HOH D . I 4 HOH 12 112 39 HOH HOH D . I 4 HOH 13 113 42 HOH HOH D . I 4 HOH 14 114 45 HOH HOH D . I 4 HOH 15 115 49 HOH HOH D . I 4 HOH 16 116 50 HOH HOH D . I 4 HOH 17 117 51 HOH HOH D . I 4 HOH 18 118 54 HOH HOH D . I 4 HOH 19 119 55 HOH HOH D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 AUTOMAR 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # _cell.entry_id 4E4O _cell.length_a 24.055 _cell.length_b 31.011 _cell.length_c 31.368 _cell.angle_alpha 90.00 _cell.angle_beta 102.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 4E4O _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4E4O _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.5809 _exptl_crystal.density_percent_sol 22.1971 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;drop: 1mM of duplex DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM barium dichloride dihydrate, 0.5mM spermine, reservoir: 30% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 'IMAGE PLATE' _diffrn_detector.type 'MAR scanner 345 mm plate' _diffrn_detector.pdbx_collection_date 2010-10-06 _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 graphite _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 'BRUKER AXS MICROSTAR' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 4E4O _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25.0 _reflns.d_resolution_high 1.72 _reflns.number_obs 4873 _reflns.number_all 4897 _reflns.percent_possible_obs 99.5 _reflns.pdbx_Rmerge_I_obs 0.0384 _reflns.pdbx_Rsym_value 0.0357 _reflns.pdbx_netI_over_sigmaI 9.0 _reflns.B_iso_Wilson_estimate 26.9 _reflns.pdbx_redundancy 4.71 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.72 _reflns_shell.d_res_low 1.78 _reflns_shell.percent_possible_all 99.2 _reflns_shell.Rmerge_I_obs 0.2076 _reflns_shell.pdbx_Rsym_value 0.1908 _reflns_shell.meanI_over_sigI_obs 1.9 _reflns_shell.pdbx_redundancy 4.68 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4E4O _refine.ls_number_reflns_obs 4645 _refine.ls_number_reflns_all 4668 _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 23.53 _refine.ls_d_res_high 1.72 _refine.ls_percent_reflns_obs 99.51 _refine.ls_R_factor_obs 0.20373 _refine.ls_R_factor_all 0.23 _refine.ls_R_factor_R_work 0.20126 _refine.ls_R_factor_R_free 0.25709 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 228 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.915 _refine.B_iso_mean 18.700 _refine.aniso_B[1][1] -0.01 _refine.aniso_B[2][2] 0.02 _refine.aniso_B[3][3] -0.02 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.01 _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 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'fiber model of Z-type DNA built using the program InsightII' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.033 _refine.overall_SU_ML 0.082 _refine.overall_SU_B 2.645 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _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_overall_phase_error ? _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 480 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 57 _refine_hist.number_atoms_total 538 _refine_hist.d_res_high 1.72 _refine_hist.d_res_low 23.53 # 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 0.009 0.021 ? 560 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.396 3.000 ? 868 '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 0.223 0.200 ? 98 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.020 ? 252 '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 1.900 3.000 ? 560 'X-RAY DIFFRACTION' ? r_scangle_it 2.532 4.500 ? 862 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.720 _refine_ls_shell.d_res_low 1.764 _refine_ls_shell.number_reflns_R_work 317 _refine_ls_shell.R_factor_R_work 0.256 _refine_ls_shell.percent_reflns_obs 98.54 _refine_ls_shell.R_factor_R_free 0.346 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 21 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _database_PDB_matrix.entry_id 4E4O _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 4E4O _struct.title 'Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4E4O _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Z-type DNA double helices, Barium ions, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 1 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 4E4O 4E4O 1 ? ? ? 2 PDB 4E4O 4E4O 2 ? ? ? # 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 4E4O A 1 ? 6 ? 4E4O 1 ? 6 ? 1 6 2 1 4E4O C 1 ? 6 ? 4E4O 1 ? 6 ? 1 6 3 2 4E4O B 1 ? 6 ? 4E4O 7 ? 12 ? 7 12 4 2 4E4O D 1 ? 6 ? 4E4O 7 ? 12 ? 7 12 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 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)' 640 ? 1 MORE -5 ? 1 'SSA (A^2)' 2340 ? 2 'ABSA (A^2)' 820 ? 2 MORE -11 ? 2 'SSA (A^2)' 2390 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,G 2 1 C,D,H,I # _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.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 ? ? E BA . BA ? ? ? 1_555 F HOH . O ? ? A BA 101 A HOH 202 1_555 ? ? ? ? ? ? ? 2.617 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 2 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 2 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? C DC 1 N3 ? ? ? 1_555 D DG 6 N1 ? ? C DC 1 D DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C DC 1 N4 ? ? ? 1_555 D DG 6 O6 ? ? C DC 1 D DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C DC 1 O2 ? ? ? 1_555 D DG 6 N2 ? ? C DC 1 D DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C DA 2 N1 ? ? ? 1_555 D DT 5 N3 ? ? C DA 2 D DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C DA 2 N6 ? ? ? 1_555 D DT 5 O4 ? ? C DA 2 D DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C DC 3 N3 ? ? ? 1_555 D DG 4 N1 ? ? C DC 3 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C DC 3 N4 ? ? ? 1_555 D DG 4 O6 ? ? C DC 3 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C DC 3 O2 ? ? ? 1_555 D DG 4 N2 ? ? C DC 3 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C DG 4 N1 ? ? ? 1_555 D DC 3 N3 ? ? C DG 4 D DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C DG 4 N2 ? ? ? 1_555 D DC 3 O2 ? ? C DG 4 D DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C DG 4 O6 ? ? ? 1_555 D DC 3 N4 ? ? C DG 4 D DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C DC 5 N3 ? ? ? 1_555 D DG 2 N1 ? ? C DC 5 D DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DC 5 N4 ? ? ? 1_555 D DG 2 O6 ? ? C DC 5 D DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DC 5 O2 ? ? ? 1_555 D DG 2 N2 ? ? C DC 5 D DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DG 6 N1 ? ? ? 1_555 D DC 1 N3 ? ? C DG 6 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DG 6 N2 ? ? ? 1_555 D DC 1 O2 ? ? C DG 6 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DG 6 O6 ? ? ? 1_555 D DC 1 N4 ? ? C DG 6 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id BA _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE BA A 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 DA A 2 ? DA A 2 . ? 1_555 ? 2 AC1 5 HOH F . ? HOH A 202 . ? 1_555 ? 3 AC1 5 DG C 4 ? DG C 4 . ? 1_555 ? 4 AC1 5 HOH H . ? HOH C 101 . ? 1_555 ? 5 AC1 5 HOH H . ? HOH C 105 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.26 108.30 1.96 0.30 N 2 1 "C3'" A DA 2 ? ? "O3'" A DA 2 ? ? P A DC 3 ? A 128.11 119.70 8.41 1.20 Y 3 1 "O3'" A DG 4 ? ? P A DC 5 ? B "O5'" A DC 5 ? ? 90.85 104.00 -13.15 1.90 Y 4 1 "O3'" A DG 4 ? ? P A DC 5 ? B OP2 A DC 5 ? B 83.53 105.20 -21.67 2.20 Y 5 1 "O3'" A DG 4 ? ? P A DC 5 ? B OP1 A DC 5 ? B 90.92 105.20 -14.28 2.20 Y 6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.34 108.30 3.04 0.30 N 7 1 C6 B DG 12 ? ? C5 B DG 12 ? ? N7 B DG 12 ? ? 126.61 130.40 -3.79 0.60 N 8 1 "C3'" C DA 2 ? ? "O3'" C DA 2 ? ? P C DC 3 ? B 128.03 119.70 8.33 1.20 Y 9 1 "O4'" C DC 3 ? ? "C1'" C DC 3 ? ? N1 C DC 3 ? ? 111.88 108.30 3.58 0.30 N 10 1 "O4'" D DC 7 ? ? "C1'" D DC 7 ? ? N1 D DC 7 ? ? 110.83 108.30 2.53 0.30 N 11 1 "C3'" D DC 7 ? ? "O3'" D DC 7 ? ? P D DG 8 ? B 136.07 119.70 16.37 1.20 Y 12 1 P D DG 8 ? A "O5'" D DG 8 ? ? "C5'" D DG 8 ? ? 133.02 120.90 12.12 1.60 N 13 1 P D DG 8 ? B "O5'" D DG 8 ? ? "C5'" D DG 8 ? ? 109.02 120.90 -11.88 1.60 N 14 1 "C3'" D DG 10 ? ? "O3'" D DG 10 ? ? P D DT 11 ? A 127.50 119.70 7.80 1.20 Y 15 1 N3 D DT 11 ? ? C2 D DT 11 ? ? O2 D DT 11 ? ? 117.91 122.30 -4.39 0.60 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal BA BA BA N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 4E4O _ndb_struct_conf_na.feature 'z-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 6 1_555 -0.303 -0.333 0.193 -1.859 6.352 2.543 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DA 2 1_555 B DT 5 1_555 0.001 -0.181 0.081 -2.640 -5.132 -0.579 2 A_DA2:DT11_B A 2 ? B 11 ? 20 1 1 A DC 3 1_555 B DG 4 1_555 -0.281 -0.177 0.067 10.024 -3.156 0.150 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.422 -0.087 0.204 -8.618 0.318 0.925 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 -0.346 -0.070 0.367 0.358 8.432 0.128 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.482 -0.168 0.102 -5.134 5.109 1.580 6 A_DG6:DC7_B A 6 ? B 7 ? 19 1 1 C DC 1 1_555 D DG 6 1_555 -0.392 -0.321 0.035 5.235 4.931 2.977 7 C_DC1:DG12_D C 1 ? D 12 ? 19 1 1 C DA 2 1_555 D DT 5 1_555 0.105 -0.166 -0.136 -8.349 -3.317 2.951 8 C_DA2:DT11_D C 2 ? D 11 ? 20 1 1 C DC 3 1_555 D DG 4 1_555 -0.178 -0.230 0.055 6.625 0.812 2.060 9 C_DC3:DG10_D C 3 ? D 10 ? 19 1 1 C DG 4 1_555 D DC 3 1_555 0.226 -0.116 0.134 -2.024 4.403 -0.466 10 C_DG4:DC9_D C 4 ? D 9 ? 19 1 1 C DC 5 1_555 D DG 2 1_555 -0.248 -0.117 0.163 4.267 1.879 -0.510 11 C_DC5:DG8_D C 5 ? D 8 ? 19 1 1 C DG 6 1_555 D DC 1 1_555 0.310 -0.109 0.035 -3.786 3.283 -0.355 12 C_DG6:DC7_D C 6 ? D 7 ? 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 6 1_555 A DA 2 1_555 B DT 5 1_555 -0.537 5.111 3.503 -2.038 -2.476 -10.584 -21.851 -6.636 4.395 13.033 -10.727 -11.058 1 AA_DC1DA2:DT11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DA 2 1_555 B DT 5 1_555 A DC 3 1_555 B DG 4 1_555 -0.020 -1.299 3.192 -1.726 -2.996 -42.436 2.081 -0.195 3.094 4.131 -2.380 -42.571 2 AA_DA2DC3:DG10DT11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 0.186 5.533 4.051 0.107 0.067 -9.098 -35.068 1.472 4.007 -0.423 0.673 -9.098 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B DG 2 1_555 0.483 -1.060 3.194 0.105 -3.222 -48.758 1.519 0.592 3.121 3.898 0.128 -48.858 4 AA_DG4DC5:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.183 5.507 3.794 -0.222 5.227 -11.437 -30.062 -1.043 1.167 -24.609 -1.045 -12.573 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 C DC 1 1_555 D DG 6 1_555 C DA 2 1_555 D DT 5 1_555 -0.243 5.564 3.775 -1.976 -2.336 -4.932 -35.336 -19.012 5.364 24.297 -20.560 -5.803 6 CC_DC1DA2:DT11DG12_DD C 1 ? D 12 ? C 2 ? D 11 ? 1 C DA 2 1_555 D DT 5 1_555 C DC 3 1_555 D DG 4 1_555 0.441 -0.914 3.110 -1.362 -1.703 -52.752 1.133 0.412 3.091 1.916 -1.532 -52.793 7 CC_DA2DC3:DG10DT11_DD C 2 ? D 11 ? C 3 ? D 10 ? 1 C DC 3 1_555 D DG 4 1_555 C DG 4 1_555 D DC 3 1_555 -0.021 5.527 3.775 1.821 -0.062 -11.888 -26.287 2.630 3.763 0.298 8.725 -12.026 8 CC_DC3DG4:DC9DG10_DD C 3 ? D 10 ? C 4 ? D 9 ? 1 C DG 4 1_555 D DC 3 1_555 C DC 5 1_555 D DG 2 1_555 -0.206 -1.032 3.234 -0.979 -4.759 -48.943 1.588 -0.319 3.122 5.728 -1.178 -49.169 9 CC_DG4DC5:DG8DC9_DD C 4 ? D 9 ? C 5 ? D 8 ? 1 C DC 5 1_555 D DG 2 1_555 C DG 6 1_555 D DC 1 1_555 0.186 5.466 3.769 0.705 1.316 -10.590 -31.584 2.208 3.049 -7.083 3.795 -10.694 10 CC_DC5DG6:DC7DG8_DD C 5 ? D 8 ? C 6 ? D 7 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name InsightII _pdbx_initial_refinement_model.details 'fiber model of Z-type DNA built using the program InsightII' # _atom_sites.entry_id 4E4O _atom_sites.fract_transf_matrix[1][1] 0.041571 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008839 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032247 _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] 0.032592 _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 # loop_