data_4U8A # _entry.id 4U8A # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 4U8A pdb_00004u8a 10.2210/pdb4u8a/pdb WWPDB D_1000202983 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 4U8B PDB . unspecified 4U8C PDB . # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4U8A _pdbx_database_status.recvd_initial_deposition_date 2014-08-01 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhu, W.' 1 'Oldfield, E.' 2 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Med.Chem. _citation.journal_id_ASTM JMCMAR _citation.journal_id_CSD 0151 _citation.journal_id_ISSN 0022-2623 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 58 _citation.language ? _citation.page_first 1215 _citation.page_last 1227 _citation.title 'Antibacterial drug leads: DNA and enzyme multitargeting.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jm501449u _citation.pdbx_database_id_PubMed 25574764 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhu, W.' 1 ? primary 'Wang, Y.' 2 ? primary 'Li, K.' 3 ? primary 'Gao, J.' 4 ? primary 'Huang, C.H.' 5 ? primary 'Chen, C.C.' 6 ? primary 'Ko, T.P.' 7 ? primary 'Zhang, Y.' 8 ? primary 'Guo, R.T.' 9 ? primary 'Oldfield, E.' 10 ? # _cell.length_a 25.175 _cell.length_b 40.144 _cell.length_c 65.633 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 4U8A _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U8A _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*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 "N,N'-bis[3-(1,4,5,6-tetrahydropyrimidin-2-yl)phenyl]biphenyl-4,4'-dicarboxamide" 556.657 1 ? ? ? ? 4 water nat water 18.015 30 ? ? ? ? # _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_ _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 # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 12 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4U8A _struct_ref.pdbx_db_accession 4U8A _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4U8A A 1 ? 12 ? 4U8A 1 ? 12 ? 1 12 2 1 4U8A B 1 ? 12 ? 4U8A 13 ? 24 ? 13 24 # 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 3EZ non-polymer . "N,N'-bis[3-(1,4,5,6-tetrahydropyrimidin-2-yl)phenyl]biphenyl-4,4'-dicarboxamide" ? 'C34 H32 N6 O2' 556.657 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 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 4U8A _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.26 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 45.65 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method EVAPORATION _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.9 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '40 mM sodium cacodylate, pH 6.9, 50 mM Mg(OAc)2, 6 mM spermine-4HCl, 40% MPD' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2013-02-28 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'diamond(111)' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97857 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 21-ID-G' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97857 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-G _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 4U8A _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.480 _reflns.d_resolution_low 50.000 _reflns.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.number_all ? _reflns.number_obs 11466 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 98.300 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 13.800 _reflns.pdbx_Rmerge_I_obs 0.050 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 44.540 _reflns.pdbx_netI_over_sigmaI 14.300 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.097 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 158484 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.480 1.510 ? 44.5397 ? ? ? 533 ? 97.100 ? ? ? ? 0.389 ? ? ? ? ? ? ? ? 12.900 ? 0.730 ? ? ? ? 0 1 1 ? ? 1.510 1.530 ? ? ? ? ? 557 ? 98.800 ? ? ? ? 0.302 ? ? ? ? ? ? ? ? 13.500 ? 0.767 ? ? ? ? 0 2 1 ? ? 1.530 1.560 ? ? ? ? ? 575 ? 99.100 ? ? ? ? 0.267 ? ? ? ? ? ? ? ? 13.800 ? 0.757 ? ? ? ? 0 3 1 ? ? 1.560 1.590 ? ? ? ? ? 560 ? 99.600 ? ? ? ? 0.195 ? ? ? ? ? ? ? ? 14.200 ? 0.774 ? ? ? ? 0 4 1 ? ? 1.590 1.630 ? ? ? ? ? 557 ? 99.100 ? ? ? ? 0.140 ? ? ? ? ? ? ? ? 14.400 ? 0.795 ? ? ? ? 0 5 1 ? ? 1.630 1.670 ? ? ? ? ? 579 ? 99.300 ? ? ? ? 0.107 ? ? ? ? ? ? ? ? 14.400 ? 0.856 ? ? ? ? 0 6 1 ? ? 1.670 1.710 ? ? ? ? ? 551 ? 99.500 ? ? ? ? 0.096 ? ? ? ? ? ? ? ? 14.300 ? 0.891 ? ? ? ? 0 7 1 ? ? 1.710 1.750 ? ? ? ? ? 598 ? 99.500 ? ? ? ? 0.094 ? ? ? ? ? ? ? ? 14.400 ? 0.960 ? ? ? ? 0 8 1 ? ? 1.750 1.810 ? ? ? ? ? 573 ? 99.700 ? ? ? ? 0.089 ? ? ? ? ? ? ? ? 14.300 ? 1.109 ? ? ? ? 0 9 1 ? ? 1.810 1.860 ? ? ? ? ? 559 ? 99.600 ? ? ? ? 0.086 ? ? ? ? ? ? ? ? 14.300 ? 1.220 ? ? ? ? 0 10 1 ? ? 1.860 1.930 ? ? ? ? ? 585 ? 99.700 ? ? ? ? 0.084 ? ? ? ? ? ? ? ? 14.200 ? 1.274 ? ? ? ? 0 11 1 ? ? 1.930 2.010 ? ? ? ? ? 576 ? 99.800 ? ? ? ? 0.073 ? ? ? ? ? ? ? ? 14.300 ? 1.246 ? ? ? ? 0 12 1 ? ? 2.010 2.100 ? ? ? ? ? 575 ? 99.800 ? ? ? ? 0.064 ? ? ? ? ? ? ? ? 14.300 ? 1.217 ? ? ? ? 0 13 1 ? ? 2.100 2.210 ? ? ? ? ? 578 ? 100.000 ? ? ? ? 0.059 ? ? ? ? ? ? ? ? 14.300 ? 1.196 ? ? ? ? 0 14 1 ? ? 2.210 2.350 ? ? ? ? ? 593 ? 100.000 ? ? ? ? 0.058 ? ? ? ? ? ? ? ? 14.100 ? 1.346 ? ? ? ? 0 15 1 ? ? 2.350 2.530 ? ? ? ? ? 594 ? 100.000 ? ? ? ? 0.053 ? ? ? ? ? ? ? ? 14.000 ? 1.336 ? ? ? ? 0 16 1 ? ? 2.530 2.790 ? ? ? ? ? 593 ? 100.000 ? ? ? ? 0.050 ? ? ? ? ? ? ? ? 13.800 ? 1.500 ? ? ? ? 0 17 1 ? ? 2.790 3.190 ? ? ? ? ? 591 ? 98.700 ? ? ? ? 0.044 ? ? ? ? ? ? ? ? 13.500 ? 1.327 ? ? ? ? 0 18 1 ? ? 3.190 4.020 ? ? ? ? ? 555 ? 90.500 ? ? ? ? 0.043 ? ? ? ? ? ? ? ? 12.900 ? 1.270 ? ? ? ? 0 19 1 ? ? 4.020 50.000 ? ? ? ? ? 584 ? 87.400 ? ? ? ? 0.043 ? ? ? ? ? ? ? ? 10.600 ? 1.349 ? ? ? ? 0 20 1 ? ? # _refine.aniso_B[1][1] 0.0000 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] -0.0200 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] 0.0200 _refine.B_iso_max 67.710 _refine.B_iso_mean 27.9350 _refine.B_iso_min 16.900 _refine.correlation_coeff_Fo_to_Fc 0.9380 _refine.correlation_coeff_Fo_to_Fc_free 0.9060 _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 4U8A _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.4800 _refine.ls_d_res_low 17.1200 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 11430 _refine.ls_number_reflns_R_free 548 _refine.ls_number_reflns_R_work 10882 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.2800 _refine.ls_percent_reflns_R_free 4.8000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2689 _refine.ls_R_factor_R_free 0.3221 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2663 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details MASK _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 436D _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.1020 _refine.pdbx_overall_ESU_R_Free 0.1100 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 2.0330 _refine.overall_SU_ML 0.0750 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.4800 _refine_hist.d_res_low 17.1200 _refine_hist.pdbx_number_atoms_ligand 43 _refine_hist.number_atoms_solvent 30 _refine_hist.number_atoms_total 559 _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_ligand 46.52 _refine_hist.pdbx_B_iso_mean_solvent 30.11 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 486 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.015 0.012 591 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 2.838 1.469 900 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 0.102 0.200 72 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.033 0.021 304 ? r_gen_planes_refined ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.48 _refine_ls_shell.d_res_low 1.5180 _refine_ls_shell.number_reflns_all 704 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 32 _refine_ls_shell.number_reflns_R_work 672 _refine_ls_shell.percent_reflns_obs 96.9700 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.4220 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.3480 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? # _struct.entry_id 4U8A _struct.title 'Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1503' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 4U8A _struct_keywords.text ;Antibacterial Agents, Bisamidines, Minor Groove Binders, Models, Molecular, Nucleic Acid Conformation, Oligodeoxyribonucleotides, DNA-ANTIBIOTIC complex ; _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC # 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 ? # 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 101 A HOH 202 1_555 ? ? ? ? ? ? ? 1.967 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 203 1_555 ? ? ? ? ? ? ? 2.114 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 206 3_655 ? ? ? ? ? ? ? 2.059 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 208 3_655 ? ? ? ? ? ? ? 2.075 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 209 3_655 ? ? ? ? ? ? ? 2.075 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 101 B HOH 202 1_555 ? ? ? ? ? ? ? 2.055 ? ? 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_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MG 101 ? 6 'binding site for residue MG A 101' AC2 Software B 3EZ 101 ? 11 'binding site for residue 3EZ B 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 6 HOH E . ? HOH A 202 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH A 203 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 206 . ? 3_655 ? 4 AC1 6 HOH E . ? HOH A 208 . ? 3_655 ? 5 AC1 6 HOH E . ? HOH A 209 . ? 3_655 ? 6 AC1 6 HOH F . ? HOH B 202 . ? 1_555 ? 7 AC2 11 DA A 6 ? DA A 6 . ? 1_555 ? 8 AC2 11 DT A 7 ? DT A 7 . ? 1_555 ? 9 AC2 11 DT A 8 ? DT A 8 . ? 1_555 ? 10 AC2 11 DC A 9 ? DC A 9 . ? 1_555 ? 11 AC2 11 DG B 4 ? DG B 16 . ? 1_555 ? 12 AC2 11 DA B 5 ? DA B 17 . ? 1_555 ? 13 AC2 11 DA B 6 ? DA B 18 . ? 1_555 ? 14 AC2 11 DT B 7 ? DT B 19 . ? 1_555 ? 15 AC2 11 DT B 8 ? DT B 20 . ? 1_555 ? 16 AC2 11 DC B 9 ? DC B 21 . ? 1_555 ? 17 AC2 11 DG B 10 ? DG B 22 . ? 1_555 ? # _atom_sites.entry_id 4U8A _atom_sites.fract_transf_matrix[1][1] 0.039722 _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] 0.024910 _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] 0.015236 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 DG 4 16 16 DG DG B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DC 9 21 21 DC DC B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG 1 101 1 MG MG A . D 3 3EZ 1 101 1 3EZ DRG B . E 4 HOH 1 201 14 HOH HOH A . E 4 HOH 2 202 23 HOH HOH A . E 4 HOH 3 203 8 HOH HOH A . E 4 HOH 4 204 2 HOH HOH A . E 4 HOH 5 205 1 HOH HOH A . E 4 HOH 6 206 10 HOH HOH A . E 4 HOH 7 207 30 HOH HOH A . E 4 HOH 8 208 24 HOH HOH A . E 4 HOH 9 209 25 HOH HOH A . E 4 HOH 10 210 13 HOH HOH A . E 4 HOH 11 211 17 HOH HOH A . E 4 HOH 12 212 6 HOH HOH A . E 4 HOH 13 213 11 HOH HOH A . E 4 HOH 14 214 26 HOH HOH A . E 4 HOH 15 215 5 HOH HOH A . E 4 HOH 16 216 12 HOH HOH A . E 4 HOH 17 217 16 HOH HOH A . E 4 HOH 18 218 18 HOH HOH A . E 4 HOH 19 219 19 HOH HOH A . E 4 HOH 20 220 20 HOH HOH A . E 4 HOH 21 221 22 HOH HOH A . E 4 HOH 22 222 27 HOH HOH A . E 4 HOH 23 223 28 HOH HOH A . F 4 HOH 1 201 3 HOH HOH B . F 4 HOH 2 202 21 HOH HOH B . F 4 HOH 3 203 4 HOH HOH B . F 4 HOH 4 204 9 HOH HOH B . F 4 HOH 5 205 7 HOH HOH B . F 4 HOH 6 206 15 HOH HOH B . F 4 HOH 7 207 29 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # 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)' 1560 ? 1 MORE -4 ? 1 'SSA (A^2)' 4380 ? # _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 # 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 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 90.2 ? 2 O ? E HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 206 ? 3_655 93.1 ? 3 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 206 ? 3_655 88.6 ? 4 O ? E HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 208 ? 3_655 173.5 ? 5 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 208 ? 3_655 87.1 ? 6 O ? E HOH . ? A HOH 206 ? 3_655 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 208 ? 3_655 92.8 ? 7 O ? E HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 209 ? 3_655 88.2 ? 8 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 209 ? 3_655 175.6 ? 9 O ? E HOH . ? A HOH 206 ? 3_655 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 209 ? 3_655 87.4 ? 10 O ? E HOH . ? A HOH 208 ? 3_655 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 209 ? 3_655 94.9 ? 11 O ? E HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 202 ? 1_555 88.3 ? 12 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 202 ? 1_555 96.1 ? 13 O ? E HOH . ? A HOH 206 ? 3_655 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 202 ? 1_555 175.1 ? 14 O ? E HOH . ? A HOH 208 ? 3_655 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 202 ? 1_555 86.1 ? 15 O ? E HOH . ? A HOH 209 ? 3_655 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 202 ? 1_555 87.9 ? # 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 2015-02-04 2 'Structure model' 1 1 2015-02-25 3 'Structure model' 1 2 2017-09-13 4 'Structure model' 1 3 2019-12-25 5 'Structure model' 1 4 2023-09-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Author supporting evidence' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other 6 3 'Structure model' 'Source and taxonomy' 7 3 'Structure model' 'Structure summary' 8 4 'Structure model' 'Author supporting evidence' 9 5 'Structure model' 'Data collection' 10 5 'Structure model' 'Database references' 11 5 'Structure model' 'Derived calculations' 12 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 3 'Structure model' citation 2 3 'Structure model' pdbx_audit_support 3 3 'Structure model' pdbx_database_status 4 3 'Structure model' pdbx_entity_src_syn 5 3 'Structure model' pdbx_struct_assembly 6 3 'Structure model' pdbx_struct_assembly_gen 7 3 'Structure model' pdbx_struct_assembly_prop 8 3 'Structure model' pdbx_struct_oper_list 9 3 'Structure model' struct_keywords 10 4 'Structure model' pdbx_audit_support 11 5 'Structure model' chem_comp_atom 12 5 'Structure model' chem_comp_bond 13 5 'Structure model' database_2 14 5 'Structure model' pdbx_initial_refinement_model 15 5 'Structure model' pdbx_struct_conn_angle 16 5 'Structure model' refine_hist 17 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_citation.journal_id_CSD' 2 3 'Structure model' '_pdbx_audit_support.funding_organization' 3 3 'Structure model' '_pdbx_database_status.pdb_format_compatible' 4 3 'Structure model' '_pdbx_entity_src_syn.pdbx_alt_source_flag' 5 3 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 6 3 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 7 3 'Structure model' '_pdbx_struct_assembly_prop.type' 8 3 'Structure model' '_pdbx_struct_assembly_prop.value' 9 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 10 3 'Structure model' '_struct_keywords.text' 11 4 'Structure model' '_pdbx_audit_support.funding_organization' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 19 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 20 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 21 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 22 5 'Structure model' '_pdbx_struct_conn_angle.value' 23 5 'Structure model' '_refine_hist.pdbx_number_atoms_nucleic_acid' 24 5 'Structure model' '_refine_hist.pdbx_number_atoms_protein' 25 5 'Structure model' '_struct_conn.pdbx_dist_value' 26 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 27 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 5 'Structure model' '_struct_conn.ptnr2_symmetry' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.6.0117 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.14 3 # 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 "O5'" A DG 10 ? ? P A DG 10 ? ? OP2 A DG 10 ? ? 96.12 105.70 -9.58 0.90 N 2 1 "O5'" B DG 14 ? ? P B DG 14 ? ? OP1 B DG 14 ? ? 99.90 105.70 -5.80 0.90 N 3 1 "C3'" B DG 16 ? ? "O3'" B DG 16 ? ? P B DA 17 ? ? 129.01 119.70 9.31 1.20 Y # 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 3EZ NBA N N N 1 3EZ CAW C N N 2 3EZ CAS C N N 3 3EZ CAU C N N 4 3EZ NAY N N N 5 3EZ CBG C N N 6 3EZ CBM C Y N 7 3EZ CAQ C Y N 8 3EZ CAG C Y N 9 3EZ CAC C Y N 10 3EZ CAE C Y N 11 3EZ CBI C Y N 12 3EZ NBC N N N 13 3EZ CBE C N N 14 3EZ OAA O N N 15 3EZ CBK C Y N 16 3EZ CAJ C Y N 17 3EZ CAN C Y N 18 3EZ CAI C Y N 19 3EZ CAM C Y N 20 3EZ CBO C Y N 21 3EZ CBP C Y N 22 3EZ CAP C Y N 23 3EZ CAL C Y N 24 3EZ CAO C Y N 25 3EZ CAK C Y N 26 3EZ CBL C Y N 27 3EZ CBF C N N 28 3EZ OAB O N N 29 3EZ NBD N N N 30 3EZ CBJ C Y N 31 3EZ CAR C Y N 32 3EZ CAF C Y N 33 3EZ CAD C Y N 34 3EZ CAH C Y N 35 3EZ CBN C Y N 36 3EZ CBH C N N 37 3EZ NAZ N N N 38 3EZ CAV C N N 39 3EZ CAT C N N 40 3EZ CAX C N N 41 3EZ NBB N N N 42 3EZ H1 H N N 43 3EZ H2 H N N 44 3EZ H3 H N N 45 3EZ H4 H N N 46 3EZ H5 H N N 47 3EZ H6 H N N 48 3EZ H7 H N N 49 3EZ H8 H N N 50 3EZ H9 H N N 51 3EZ H10 H N N 52 3EZ H11 H N N 53 3EZ H12 H N N 54 3EZ H13 H N N 55 3EZ H14 H N N 56 3EZ H15 H N N 57 3EZ H16 H N N 58 3EZ H17 H N N 59 3EZ H18 H N N 60 3EZ H19 H N N 61 3EZ H20 H N N 62 3EZ H21 H N N 63 3EZ H22 H N N 64 3EZ H23 H N N 65 3EZ H24 H N N 66 3EZ H25 H N N 67 3EZ H26 H N N 68 3EZ H27 H N N 69 3EZ H28 H N N 70 3EZ H29 H N N 71 3EZ H30 H N N 72 3EZ H31 H N N 73 3EZ H32 H N N 74 DA OP3 O N N 75 DA P P N N 76 DA OP1 O N N 77 DA OP2 O N N 78 DA "O5'" O N N 79 DA "C5'" C N N 80 DA "C4'" C N R 81 DA "O4'" O N N 82 DA "C3'" C N S 83 DA "O3'" O N N 84 DA "C2'" C N N 85 DA "C1'" C N R 86 DA N9 N Y N 87 DA C8 C Y N 88 DA N7 N Y N 89 DA C5 C Y N 90 DA C6 C Y N 91 DA N6 N N N 92 DA N1 N Y N 93 DA C2 C Y N 94 DA N3 N Y N 95 DA C4 C Y N 96 DA HOP3 H N N 97 DA HOP2 H N N 98 DA "H5'" H N N 99 DA "H5''" H N N 100 DA "H4'" H N N 101 DA "H3'" H N N 102 DA "HO3'" H N N 103 DA "H2'" H N N 104 DA "H2''" H N N 105 DA "H1'" H N N 106 DA H8 H N N 107 DA H61 H N N 108 DA H62 H N N 109 DA H2 H N N 110 DC OP3 O N N 111 DC P P N N 112 DC OP1 O N N 113 DC OP2 O N N 114 DC "O5'" O N N 115 DC "C5'" C N N 116 DC "C4'" C N R 117 DC "O4'" O N N 118 DC "C3'" C N S 119 DC "O3'" O N N 120 DC "C2'" C N N 121 DC "C1'" C N R 122 DC N1 N N N 123 DC C2 C N N 124 DC O2 O N N 125 DC N3 N N N 126 DC C4 C N N 127 DC N4 N N N 128 DC C5 C N N 129 DC C6 C N N 130 DC HOP3 H N N 131 DC HOP2 H N N 132 DC "H5'" H N N 133 DC "H5''" H N N 134 DC "H4'" H N N 135 DC "H3'" H N N 136 DC "HO3'" H N N 137 DC "H2'" H N N 138 DC "H2''" H N N 139 DC "H1'" H N N 140 DC H41 H N N 141 DC H42 H N N 142 DC H5 H N N 143 DC H6 H N N 144 DG OP3 O N N 145 DG P P N N 146 DG OP1 O N N 147 DG OP2 O N N 148 DG "O5'" O N N 149 DG "C5'" C N N 150 DG "C4'" C N R 151 DG "O4'" O N N 152 DG "C3'" C N S 153 DG "O3'" O N N 154 DG "C2'" C N N 155 DG "C1'" C N R 156 DG N9 N Y N 157 DG C8 C Y N 158 DG N7 N Y N 159 DG C5 C Y N 160 DG C6 C N N 161 DG O6 O N N 162 DG N1 N N N 163 DG C2 C N N 164 DG N2 N N N 165 DG N3 N N N 166 DG C4 C Y N 167 DG HOP3 H N N 168 DG HOP2 H N N 169 DG "H5'" H N N 170 DG "H5''" H N N 171 DG "H4'" H N N 172 DG "H3'" H N N 173 DG "HO3'" H N N 174 DG "H2'" H N N 175 DG "H2''" H N N 176 DG "H1'" H N N 177 DG H8 H N N 178 DG H1 H N N 179 DG H21 H N N 180 DG H22 H N N 181 DT OP3 O N N 182 DT P P N N 183 DT OP1 O N N 184 DT OP2 O N N 185 DT "O5'" O N N 186 DT "C5'" C N N 187 DT "C4'" C N R 188 DT "O4'" O N N 189 DT "C3'" C N S 190 DT "O3'" O N N 191 DT "C2'" C N N 192 DT "C1'" C N R 193 DT N1 N N N 194 DT C2 C N N 195 DT O2 O N N 196 DT N3 N N N 197 DT C4 C N N 198 DT O4 O N N 199 DT C5 C N N 200 DT C7 C N N 201 DT C6 C N N 202 DT HOP3 H N N 203 DT HOP2 H N N 204 DT "H5'" H N N 205 DT "H5''" H N N 206 DT "H4'" H N N 207 DT "H3'" H N N 208 DT "HO3'" H N N 209 DT "H2'" H N N 210 DT "H2''" H N N 211 DT "H1'" H N N 212 DT H3 H N N 213 DT H71 H N N 214 DT H72 H N N 215 DT H73 H N N 216 DT H6 H N N 217 HOH O O N N 218 HOH H1 H N N 219 HOH H2 H N N 220 MG MG MG N N 221 # 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 3EZ CAS CAU sing N N 1 3EZ CAS CAW sing N N 2 3EZ CAU NAY sing N N 3 3EZ CAW NBA sing N N 4 3EZ NBA CBG sing N N 5 3EZ NAY CBG doub N N 6 3EZ CBG CBM sing N N 7 3EZ CBM CAG doub Y N 8 3EZ CBM CAQ sing Y N 9 3EZ CAG CAC sing Y N 10 3EZ CAQ CBI doub Y N 11 3EZ CAC CAE doub Y N 12 3EZ CBI CAE sing Y N 13 3EZ CBI NBC sing N N 14 3EZ NBC CBE sing N N 15 3EZ OAA CBE doub N N 16 3EZ CBE CBK sing N N 17 3EZ CBK CAJ doub Y N 18 3EZ CBK CAI sing Y N 19 3EZ CAJ CAN sing Y N 20 3EZ CAI CAM doub Y N 21 3EZ CAN CBO doub Y N 22 3EZ CAM CBO sing Y N 23 3EZ CBO CBP sing N N 24 3EZ CBP CAO doub Y N 25 3EZ CBP CAP sing Y N 26 3EZ CAO CAK sing Y N 27 3EZ CAP CAL doub Y N 28 3EZ CAK CBL doub Y N 29 3EZ CAL CBL sing Y N 30 3EZ CBL CBF sing N N 31 3EZ CBF OAB doub N N 32 3EZ CBF NBD sing N N 33 3EZ NBD CBJ sing N N 34 3EZ CBJ CAF doub Y N 35 3EZ CBJ CAR sing Y N 36 3EZ CAF CAD sing Y N 37 3EZ CAR CBN doub Y N 38 3EZ CAD CAH doub Y N 39 3EZ CBN CAH sing Y N 40 3EZ CBN CBH sing N N 41 3EZ CBH NAZ doub N N 42 3EZ CBH NBB sing N N 43 3EZ NAZ CAV sing N N 44 3EZ NBB CAX sing N N 45 3EZ CAV CAT sing N N 46 3EZ CAX CAT sing N N 47 3EZ NBA H1 sing N N 48 3EZ CAW H2 sing N N 49 3EZ CAW H3 sing N N 50 3EZ CAS H4 sing N N 51 3EZ CAS H5 sing N N 52 3EZ CAU H6 sing N N 53 3EZ CAU H7 sing N N 54 3EZ CAQ H8 sing N N 55 3EZ CAG H9 sing N N 56 3EZ CAC H10 sing N N 57 3EZ CAE H11 sing N N 58 3EZ NBC H12 sing N N 59 3EZ CAJ H13 sing N N 60 3EZ CAN H14 sing N N 61 3EZ CAI H15 sing N N 62 3EZ CAM H16 sing N N 63 3EZ CAP H17 sing N N 64 3EZ CAL H18 sing N N 65 3EZ CAO H19 sing N N 66 3EZ CAK H20 sing N N 67 3EZ NBD H21 sing N N 68 3EZ CAR H22 sing N N 69 3EZ CAF H23 sing N N 70 3EZ CAD H24 sing N N 71 3EZ CAH H25 sing N N 72 3EZ CAV H26 sing N N 73 3EZ CAV H27 sing N N 74 3EZ CAT H28 sing N N 75 3EZ CAT H29 sing N N 76 3EZ CAX H30 sing N N 77 3EZ CAX H31 sing N N 78 3EZ NBB H32 sing N N 79 DA OP3 P sing N N 80 DA OP3 HOP3 sing N N 81 DA P OP1 doub N N 82 DA P OP2 sing N N 83 DA P "O5'" sing N N 84 DA OP2 HOP2 sing N N 85 DA "O5'" "C5'" sing N N 86 DA "C5'" "C4'" sing N N 87 DA "C5'" "H5'" sing N N 88 DA "C5'" "H5''" sing N N 89 DA "C4'" "O4'" sing N N 90 DA "C4'" "C3'" sing N N 91 DA "C4'" "H4'" sing N N 92 DA "O4'" "C1'" sing N N 93 DA "C3'" "O3'" sing N N 94 DA "C3'" "C2'" sing N N 95 DA "C3'" "H3'" sing N N 96 DA "O3'" "HO3'" sing N N 97 DA "C2'" "C1'" sing N N 98 DA "C2'" "H2'" sing N N 99 DA "C2'" "H2''" sing N N 100 DA "C1'" N9 sing N N 101 DA "C1'" "H1'" sing N N 102 DA N9 C8 sing Y N 103 DA N9 C4 sing Y N 104 DA C8 N7 doub Y N 105 DA C8 H8 sing N N 106 DA N7 C5 sing Y N 107 DA C5 C6 sing Y N 108 DA C5 C4 doub Y N 109 DA C6 N6 sing N N 110 DA C6 N1 doub Y N 111 DA N6 H61 sing N N 112 DA N6 H62 sing N N 113 DA N1 C2 sing Y N 114 DA C2 N3 doub Y N 115 DA C2 H2 sing N N 116 DA N3 C4 sing Y N 117 DC OP3 P sing N N 118 DC OP3 HOP3 sing N N 119 DC P OP1 doub N N 120 DC P OP2 sing N N 121 DC P "O5'" sing N N 122 DC OP2 HOP2 sing N N 123 DC "O5'" "C5'" sing N N 124 DC "C5'" "C4'" sing N N 125 DC "C5'" "H5'" sing N N 126 DC "C5'" "H5''" sing N N 127 DC "C4'" "O4'" sing N N 128 DC "C4'" "C3'" sing N N 129 DC "C4'" "H4'" sing N N 130 DC "O4'" "C1'" sing N N 131 DC "C3'" "O3'" sing N N 132 DC "C3'" "C2'" sing N N 133 DC "C3'" "H3'" sing N N 134 DC "O3'" "HO3'" sing N N 135 DC "C2'" "C1'" sing N N 136 DC "C2'" "H2'" sing N N 137 DC "C2'" "H2''" sing N N 138 DC "C1'" N1 sing N N 139 DC "C1'" "H1'" sing N N 140 DC N1 C2 sing N N 141 DC N1 C6 sing N N 142 DC C2 O2 doub N N 143 DC C2 N3 sing N N 144 DC N3 C4 doub N N 145 DC C4 N4 sing N N 146 DC C4 C5 sing N N 147 DC N4 H41 sing N N 148 DC N4 H42 sing N N 149 DC C5 C6 doub N N 150 DC C5 H5 sing N N 151 DC C6 H6 sing N N 152 DG OP3 P sing N N 153 DG OP3 HOP3 sing N N 154 DG P OP1 doub N N 155 DG P OP2 sing N N 156 DG P "O5'" sing N N 157 DG OP2 HOP2 sing N N 158 DG "O5'" "C5'" sing N N 159 DG "C5'" "C4'" sing N N 160 DG "C5'" "H5'" sing N N 161 DG "C5'" "H5''" sing N N 162 DG "C4'" "O4'" sing N N 163 DG "C4'" "C3'" sing N N 164 DG "C4'" "H4'" sing N N 165 DG "O4'" "C1'" sing N N 166 DG "C3'" "O3'" sing N N 167 DG "C3'" "C2'" sing N N 168 DG "C3'" "H3'" sing N N 169 DG "O3'" "HO3'" sing N N 170 DG "C2'" "C1'" sing N N 171 DG "C2'" "H2'" sing N N 172 DG "C2'" "H2''" sing N N 173 DG "C1'" N9 sing N N 174 DG "C1'" "H1'" sing N N 175 DG N9 C8 sing Y N 176 DG N9 C4 sing Y N 177 DG C8 N7 doub Y N 178 DG C8 H8 sing N N 179 DG N7 C5 sing Y N 180 DG C5 C6 sing N N 181 DG C5 C4 doub Y N 182 DG C6 O6 doub N N 183 DG C6 N1 sing N N 184 DG N1 C2 sing N N 185 DG N1 H1 sing N N 186 DG C2 N2 sing N N 187 DG C2 N3 doub N N 188 DG N2 H21 sing N N 189 DG N2 H22 sing N N 190 DG N3 C4 sing N N 191 DT OP3 P sing N N 192 DT OP3 HOP3 sing N N 193 DT P OP1 doub N N 194 DT P OP2 sing N N 195 DT P "O5'" sing N N 196 DT OP2 HOP2 sing N N 197 DT "O5'" "C5'" sing N N 198 DT "C5'" "C4'" sing N N 199 DT "C5'" "H5'" sing N N 200 DT "C5'" "H5''" sing N N 201 DT "C4'" "O4'" sing N N 202 DT "C4'" "C3'" sing N N 203 DT "C4'" "H4'" sing N N 204 DT "O4'" "C1'" sing N N 205 DT "C3'" "O3'" sing N N 206 DT "C3'" "C2'" sing N N 207 DT "C3'" "H3'" sing N N 208 DT "O3'" "HO3'" sing N N 209 DT "C2'" "C1'" sing N N 210 DT "C2'" "H2'" sing N N 211 DT "C2'" "H2''" sing N N 212 DT "C1'" N1 sing N N 213 DT "C1'" "H1'" sing N N 214 DT N1 C2 sing N N 215 DT N1 C6 sing N N 216 DT C2 O2 doub N N 217 DT C2 N3 sing N N 218 DT N3 C4 sing N N 219 DT N3 H3 sing N N 220 DT C4 O4 doub N N 221 DT C4 C5 sing N N 222 DT C5 C7 sing N N 223 DT C5 C6 doub N N 224 DT C7 H71 sing N N 225 DT C7 H72 sing N N 226 DT C7 H73 sing N N 227 DT C6 H6 sing N N 228 HOH O H1 sing N N 229 HOH O H2 sing N N 230 # _ndb_struct_conf_na.entry_id 4U8A _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.336 -0.136 0.043 4.483 -15.138 0.574 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.269 -0.208 0.364 5.940 -11.888 -2.489 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.153 -0.113 0.135 -1.420 -5.774 0.624 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.229 -0.076 -0.014 11.649 -10.455 0.200 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.079 0.005 -0.121 6.133 -17.550 2.206 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.067 -0.072 0.096 1.706 -16.228 4.357 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.041 -0.155 0.077 0.188 -17.514 3.809 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.126 -0.185 -0.064 -1.060 -12.642 1.639 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.179 -0.141 -0.029 -10.116 -10.658 -0.605 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.048 -0.136 0.184 5.674 -8.488 1.558 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.090 -0.178 0.239 3.622 -16.198 -3.131 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.138 -0.283 0.167 4.418 -6.074 -5.388 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 -0.148 0.040 3.246 -3.212 8.334 32.909 -1.254 -0.257 3.162 14.383 5.544 34.067 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 0.658 0.631 3.531 2.803 -7.252 41.969 1.649 -0.603 3.416 -10.022 -3.873 42.651 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 -0.273 0.800 3.090 2.087 9.952 26.359 -0.649 1.039 3.147 20.863 -4.376 28.220 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 -0.166 0.020 3.389 0.427 3.691 38.915 -0.430 0.301 3.375 5.525 -0.640 39.085 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 0.044 -0.379 3.283 -2.355 1.467 35.129 -0.844 -0.422 3.256 2.426 3.894 35.235 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 0.078 -0.601 3.235 0.645 -0.188 32.339 -1.046 -0.027 3.239 -0.338 -1.159 32.346 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 -0.084 -0.337 3.241 1.515 -1.176 35.163 -0.384 0.362 3.243 -1.946 -2.506 35.213 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 -0.010 -0.141 3.484 1.797 -1.797 40.804 0.008 0.225 3.484 -2.574 -2.575 40.879 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 0.560 0.908 3.058 -2.388 6.559 27.542 0.402 -1.670 3.128 13.503 4.916 28.396 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 -1.199 0.595 3.399 -4.149 -8.962 41.389 1.765 1.216 3.306 -12.467 5.772 42.501 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 0.039 0.462 3.273 -0.204 5.840 36.206 -0.075 -0.091 3.305 9.322 0.325 36.659 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number GM065307 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 "N,N'-bis[3-(1,4,5,6-tetrahydropyrimidin-2-yl)phenyl]biphenyl-4,4'-dicarboxamide" 3EZ 4 water HOH # _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.accession_code 436D _pdbx_initial_refinement_model.details ? #