data_2OKS # _entry.id 2OKS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2OKS pdb_00002oks 10.2210/pdb2oks/pdb NDB BD0099 ? ? RCSB RCSB041259 ? ? WWPDB D_1000041259 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1EN8 _pdbx_database_related.details 'An uncrosslinked DNA duplex of identical sequence without an interstrand crosslink.' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2OKS _pdbx_database_status.recvd_initial_deposition_date 2007-01-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Swenson, M.C.' 1 'Paranawithana, S.R.' 2 'Miller, P.S.' 3 'Kielkopf, C.L.' 4 # _citation.id primary _citation.title 'Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 a resolution.' _citation.journal_abbrev Biochemistry _citation.journal_volume 46 _citation.page_first 4545 _citation.page_last 4553 _citation.year 2007 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17375936 _citation.pdbx_database_id_DOI 10.1021/bi700109r # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Swenson, M.C.' 1 ? primary 'Paranawithana, S.R.' 2 ? primary 'Miller, P.S.' 3 ? primary 'Kielkopf, C.L.' 4 ? # _cell.entry_id 2OKS _cell.length_a 31.870 _cell.length_b 24.890 _cell.length_c 34.350 _cell.angle_alpha 90.00 _cell.angle_beta 114.50 _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 2OKS _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'" 3059.031 1 ? ? ? 'N4C-ethyl-N4C crosslinked DNA' 2 non-polymer syn 'CALCIUM ION' 40.078 3 ? ? ? ? 3 water nat water 18.015 75 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DA)(DA)(C34)(DG)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAACGTTGG _entity_poly.pdbx_strand_id A _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 DC n 1 3 DA n 1 4 DA n 1 5 C34 n 1 6 DG n 1 7 DT n 1 8 DT n 1 9 DG n 1 10 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'solid phase synthesis of DNA oligo, crosslink phosphoramidite synthesized separately' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2OKS _struct_ref.pdbx_db_accession 2OKS _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2OKS _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2OKS _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # 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 C34 'DNA linking' n "N4-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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 # _exptl.entry_id 2OKS _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.95 _exptl_crystal.density_percent_sol 37.04 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_details ;The purified crosslinked DNA was dissolved in a buffer containing 22 mM ammonium acetate, 11 mM tris-hydroxymethyl-aminomethane (Tris)-HCl pH 8.0, and 11 mM calcium acetate. Crystals were grown using the sitting drop vapor diffusion method at 277K, in which 3 uL of a reservoir solution containing 27% 2-3 methyl-pentadiol, 115 mM calcium acetate, and 10 mM Tris-HCl pH 8.0 was added to an equal volume of DNA solution, and the mixture was equilibrated against 700 uL of the reservoir solution. Crystals first appeared after two weeks. ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 '2-3 methyl-pentadiol' ? ? ? 1 2 1 'calcium acetate' ? ? ? 1 3 1 Tris-HCl ? ? ? 1 4 1 'ammonium acetate' ? ? ? 1 5 1 H2O ? ? ? 1 6 2 '2-3 methyl-pentadiol' ? ? ? 1 7 2 'calcium acetate' ? ? ? 1 8 2 Tris-HCl ? ? ? 1 9 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 200 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2004-08-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'mirrors, graphite' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.54 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 2OKS _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 40 _reflns.d_resolution_high 1.65 _reflns.number_obs 2924 _reflns.number_all 3043 _reflns.percent_possible_obs 96.1 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.046 _reflns.pdbx_netI_over_sigmaI 38.1 _reflns.B_iso_Wilson_estimate 8.0 _reflns.pdbx_redundancy 4.1 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.71 _reflns_shell.percent_possible_all 79.4 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.047 _reflns_shell.meanI_over_sigI_obs 25.7 _reflns_shell.pdbx_redundancy 2.56 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 239 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2OKS _refine.ls_number_reflns_obs 2924 _refine.ls_number_reflns_all 3043 _refine.pdbx_ls_sigma_I 0.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 992530.75 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.89 _refine.ls_d_res_high 1.65 _refine.ls_percent_reflns_obs 96.1 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.182 _refine.ls_R_factor_R_free 0.208 _refine.ls_R_factor_R_free_error 0.016 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.5 _refine.ls_number_reflns_R_free 162 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 12.8 _refine.aniso_B[1][1] -0.86 _refine.aniso_B[2][2] 0.62 _refine.aniso_B[3][3] 0.24 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.75 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.353499 _refine.solvent_model_param_bsol 25.6312 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 1EN8' _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model 'isotropic individual' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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_analyze.entry_id 2OKS _refine_analyze.Luzzati_coordinate_error_obs 0.18 _refine_analyze.Luzzati_sigma_a_obs 0.15 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.18 _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 203 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 75 _refine_hist.number_atoms_total 281 _refine_hist.d_res_high 1.65 _refine_hist.d_res_low 18.89 # 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 c_bond_d 0.012 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 21.3 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.14 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.34 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 1.89 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.65 _refine_ls_shell.d_res_low 1.75 _refine_ls_shell.number_reflns_R_work 403 _refine_ls_shell.R_factor_R_work 0.24 _refine_ls_shell.percent_reflns_obs 85.7 _refine_ls_shell.R_factor_R_free 0.229 _refine_ls_shell.R_factor_R_free_error 0.044 _refine_ls_shell.percent_reflns_R_free 6.3 _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 xlink2.param xlink2.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' 3 ion.param ion.top 'X-RAY DIFFRACTION' # _struct.entry_id 2OKS _struct.title 'X-ray Structure of a DNA Repair Substrate Containing an Alkyl Interstrand Crosslink at 1.65 Resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2OKS _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'INTERSTRAND CROSSLINK, DNA, DNA DAMAGE' # 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 2 ? D N N 2 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a double-stranded DNA generated by the crystallographic two-fold axis' # 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 covale1 covale both ? A DA 4 "O3'" ? ? ? 1_555 A C34 5 P ? ? A DA 4 A C34 5 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale none ? A C34 5 C7 ? ? ? 1_555 A C34 5 C7 ? ? A C34 5 A C34 5 2_656 ? ? ? ? ? ? ? 1.569 ? ? covale3 covale both ? A C34 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A C34 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.631 ? ? metalc1 metalc ? ? A DG 6 OP2 ? ? ? 4_646 D CA . CA ? ? A DG 6 A CA 103 1_555 ? ? ? ? ? ? ? 2.443 ? ? metalc2 metalc ? ? A DT 7 OP1 ? ? ? 1_555 D CA . CA ? ? A DT 7 A CA 103 1_555 ? ? ? ? ? ? ? 2.440 ? ? metalc3 metalc ? ? A DG 9 N7 ? ? ? 1_555 C CA . CA ? ? A DG 9 A CA 102 1_555 ? ? ? ? ? ? ? 2.666 ? ? metalc4 metalc ? ? A DG 10 O6 ? ? ? 1_555 C CA . CA ? ? A DG 10 A CA 102 1_555 ? ? ? ? ? ? ? 2.954 ? ? metalc5 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 201 4_555 ? ? ? ? ? ? ? 2.191 ? ? metalc6 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 201 3_555 ? ? ? ? ? ? ? 2.703 ? ? metalc7 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 202 1_555 ? ? ? ? ? ? ? 2.472 ? ? metalc8 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 203 1_555 ? ? ? ? ? ? ? 2.509 ? ? metalc9 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 204 1_555 ? ? ? ? ? ? ? 2.212 ? ? metalc10 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 204 2_655 ? ? ? ? ? ? ? 2.950 ? ? metalc11 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 209 1_555 ? ? ? ? ? ? ? 2.769 ? ? metalc12 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 209 2_655 ? ? ? ? ? ? ? 3.098 ? ? metalc13 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 210 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc14 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 211 1_555 ? ? ? ? ? ? ? 2.321 ? ? metalc15 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 212 1_555 ? ? ? ? ? ? ? 3.126 ? ? metalc16 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 213 1_555 ? ? ? ? ? ? ? 2.723 ? ? metalc17 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 103 A HOH 214 1_555 ? ? ? ? ? ? ? 2.391 ? ? metalc18 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 103 A HOH 215 1_555 ? ? ? ? ? ? ? 2.507 ? ? metalc19 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 103 A HOH 216 1_555 ? ? ? ? ? ? ? 2.455 ? ? metalc20 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 103 A HOH 217 1_555 ? ? ? ? ? ? ? 2.461 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 10 N1 ? ? A DC 1 A DG 10 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 10 N2 ? ? A DC 1 A DG 10 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 8 N3 ? ? A DA 3 A DT 8 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 8 O4 ? ? A DA 3 A DT 8 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 7 N3 ? ? A DA 4 A DT 7 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 7 O4 ? ? A DA 4 A DT 7 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C34 5 N3 ? ? ? 1_555 A DG 6 N1 ? ? A C34 5 A DG 6 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C34 5 N4 ? ? ? 1_555 A DG 6 O6 ? ? A C34 5 A DG 6 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C34 5 O2 ? ? ? 1_555 A DG 6 N2 ? ? A C34 5 A DG 6 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A C34 5 N3 ? ? A DG 6 A C34 5 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A C34 5 O2 ? ? A DG 6 A C34 5 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A C34 5 N4 ? ? A DG 6 A C34 5 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 7 A DA 4 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 7 A DA 4 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 8 A DA 3 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 8 A DA 3 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 10 A DC 1 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 10 A DC 1 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 10 A DC 1 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 CA 101 ? 6 'BINDING SITE FOR RESIDUE CA A 101' AC2 Software A CA 102 ? 7 'BINDING SITE FOR RESIDUE CA A 102' AC3 Software A CA 103 ? 6 'BINDING SITE FOR RESIDUE CA A 103' # 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 201 . ? 3_555 ? 2 AC1 6 HOH E . ? HOH A 201 . ? 4_555 ? 3 AC1 6 HOH E . ? HOH A 202 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 203 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH A 204 . ? 2_655 ? 6 AC1 6 HOH E . ? HOH A 204 . ? 1_555 ? 7 AC2 7 DG A 9 ? DG A 9 . ? 1_555 ? 8 AC2 7 DG A 10 ? DG A 10 . ? 1_555 ? 9 AC2 7 HOH E . ? HOH A 209 . ? 2_655 ? 10 AC2 7 HOH E . ? HOH A 209 . ? 1_555 ? 11 AC2 7 HOH E . ? HOH A 210 . ? 1_555 ? 12 AC2 7 HOH E . ? HOH A 211 . ? 1_555 ? 13 AC2 7 HOH E . ? HOH A 213 . ? 1_555 ? 14 AC3 6 DG A 6 ? DG A 6 . ? 4_646 ? 15 AC3 6 DT A 7 ? DT A 7 . ? 1_555 ? 16 AC3 6 HOH E . ? HOH A 214 . ? 1_555 ? 17 AC3 6 HOH E . ? HOH A 215 . ? 1_555 ? 18 AC3 6 HOH E . ? HOH A 216 . ? 1_555 ? 19 AC3 6 HOH E . ? HOH A 217 . ? 1_555 ? # _database_PDB_matrix.entry_id 2OKS _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 # _atom_sites.entry_id 2OKS _atom_sites.fract_transf_matrix[1][1] 0.031377 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.014300 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.040177 _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] 0.031993 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CA 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 CYT A . n A 1 2 DC 2 2 2 DC CYT A . n A 1 3 DA 3 3 3 DA ADE A . n A 1 4 DA 4 4 4 DA ADE A . n A 1 5 C34 5 5 5 C34 CNE A . n A 1 6 DG 6 6 6 DG GUA A . n A 1 7 DT 7 7 7 DT THY A . n A 1 8 DT 8 8 8 DT THY A . n A 1 9 DG 9 9 9 DG GUA A . n A 1 10 DG 10 10 10 DG GUA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CA 1 101 1111 CA CA2 A . C 2 CA 1 102 1131 CA CA2 A . D 2 CA 1 103 1141 CA CA2 A . E 3 HOH 1 201 1112 HOH TIP A . E 3 HOH 2 202 1113 HOH TIP A . E 3 HOH 3 203 1114 HOH TIP A . E 3 HOH 4 204 1115 HOH TIP A . E 3 HOH 5 205 1121 HOH TIP A . E 3 HOH 6 206 1122 HOH TIP A . E 3 HOH 7 207 1123 HOH TIP A . E 3 HOH 8 208 1124 HOH TIP A . E 3 HOH 9 209 1132 HOH TIP A . E 3 HOH 10 210 1133 HOH TIP A . E 3 HOH 11 211 1134 HOH TIP A . E 3 HOH 12 212 1135 HOH TIP A . E 3 HOH 13 213 1136 HOH TIP A . E 3 HOH 14 214 1142 HOH TIP A . E 3 HOH 15 215 1143 HOH TIP A . E 3 HOH 16 216 1144 HOH TIP A . E 3 HOH 17 217 1145 HOH TIP A . E 3 HOH 18 218 2001 HOH TIP A . E 3 HOH 19 219 2002 HOH TIP A . E 3 HOH 20 220 2003 HOH TIP A . E 3 HOH 21 221 2004 HOH TIP A . E 3 HOH 22 222 2005 HOH TIP A . E 3 HOH 23 223 2006 HOH TIP A . E 3 HOH 24 224 2007 HOH TIP A . E 3 HOH 25 225 2008 HOH TIP A . E 3 HOH 26 226 2009 HOH TIP A . E 3 HOH 27 227 2010 HOH TIP A . E 3 HOH 28 228 2011 HOH TIP A . E 3 HOH 29 229 2012 HOH TIP A . E 3 HOH 30 230 2013 HOH TIP A . E 3 HOH 31 231 2014 HOH TIP A . E 3 HOH 32 232 2015 HOH TIP A . E 3 HOH 33 233 2016 HOH TIP A . E 3 HOH 34 234 2017 HOH TIP A . E 3 HOH 35 235 2018 HOH TIP A . E 3 HOH 36 236 2019 HOH TIP A . E 3 HOH 37 237 2020 HOH TIP A . E 3 HOH 38 238 2021 HOH TIP A . E 3 HOH 39 239 2022 HOH TIP A . E 3 HOH 40 240 2023 HOH TIP A . E 3 HOH 41 241 2024 HOH TIP A . E 3 HOH 42 242 2025 HOH TIP A . E 3 HOH 43 243 2026 HOH TIP A . E 3 HOH 44 244 2027 HOH TIP A . E 3 HOH 45 245 2028 HOH TIP A . E 3 HOH 46 246 2029 HOH TIP A . E 3 HOH 47 247 2030 HOH TIP A . E 3 HOH 48 248 2031 HOH TIP A . E 3 HOH 49 249 2032 HOH TIP A . E 3 HOH 50 250 2033 HOH TIP A . E 3 HOH 51 251 2034 HOH TIP A . E 3 HOH 52 252 2035 HOH TIP A . E 3 HOH 53 253 2036 HOH TIP A . E 3 HOH 54 254 2037 HOH TIP A . E 3 HOH 55 255 2038 HOH TIP A . E 3 HOH 56 256 2039 HOH TIP A . E 3 HOH 57 257 2040 HOH TIP A . E 3 HOH 58 258 2041 HOH TIP A . E 3 HOH 59 259 2042 HOH TIP A . E 3 HOH 60 260 2043 HOH TIP A . E 3 HOH 61 261 2044 HOH TIP A . E 3 HOH 62 262 2045 HOH TIP A . E 3 HOH 63 263 2046 HOH TIP A . E 3 HOH 64 264 2047 HOH TIP A . E 3 HOH 65 265 2048 HOH TIP A . E 3 HOH 66 266 2049 HOH TIP A . E 3 HOH 67 267 2050 HOH TIP A . E 3 HOH 68 268 2051 HOH TIP A . E 3 HOH 69 269 2052 HOH TIP A . E 3 HOH 70 270 2053 HOH TIP A . E 3 HOH 71 271 2054 HOH TIP A . E 3 HOH 72 272 2055 HOH TIP A . E 3 HOH 73 273 2056 HOH TIP A . E 3 HOH 74 274 2057 HOH TIP A . E 3 HOH 75 275 2058 HOH TIP A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id C34 _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id C34 _pdbx_struct_mod_residue.auth_seq_id 5 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DC _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 17.6252871148 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 31.2571696546 # 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 OP2 ? A DG 6 ? A DG 6 ? 4_646 CA ? D CA . ? A CA 103 ? 1_555 OP1 ? A DT 7 ? A DT 7 ? 1_555 177.5 ? 2 OP2 ? A DG 6 ? A DG 6 ? 4_646 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 214 ? 1_555 91.5 ? 3 OP1 ? A DT 7 ? A DT 7 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 214 ? 1_555 85.9 ? 4 OP2 ? A DG 6 ? A DG 6 ? 4_646 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 215 ? 1_555 88.0 ? 5 OP1 ? A DT 7 ? A DT 7 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 215 ? 1_555 92.4 ? 6 O ? E HOH . ? A HOH 214 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 215 ? 1_555 96.2 ? 7 OP2 ? A DG 6 ? A DG 6 ? 4_646 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 216 ? 1_555 94.7 ? 8 OP1 ? A DT 7 ? A DT 7 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 216 ? 1_555 85.1 ? 9 O ? E HOH . ? A HOH 214 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 216 ? 1_555 88.9 ? 10 O ? E HOH . ? A HOH 215 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 216 ? 1_555 174.2 ? 11 OP2 ? A DG 6 ? A DG 6 ? 4_646 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 217 ? 1_555 99.8 ? 12 OP1 ? A DT 7 ? A DT 7 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 217 ? 1_555 82.7 ? 13 O ? E HOH . ? A HOH 214 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 217 ? 1_555 168.3 ? 14 O ? E HOH . ? A HOH 215 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 217 ? 1_555 87.1 ? 15 O ? E HOH . ? A HOH 216 ? 1_555 CA ? D CA . ? A CA 103 ? 1_555 O ? E HOH . ? A HOH 217 ? 1_555 87.4 ? 16 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O6 ? A DG 10 ? A DG 10 ? 1_555 72.0 ? 17 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 209 ? 1_555 126.3 ? 18 O6 ? A DG 10 ? A DG 10 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 209 ? 1_555 54.8 ? 19 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 209 ? 2_655 116.1 ? 20 O6 ? A DG 10 ? A DG 10 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 209 ? 2_655 53.0 ? 21 O ? E HOH . ? A HOH 209 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 209 ? 2_655 21.8 ? 22 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 210 ? 1_555 80.3 ? 23 O6 ? A DG 10 ? A DG 10 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 210 ? 1_555 149.3 ? 24 O ? E HOH . ? A HOH 209 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 210 ? 1_555 147.4 ? 25 O ? E HOH . ? A HOH 209 ? 2_655 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 210 ? 1_555 135.8 ? 26 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 211 ? 1_555 160.2 ? 27 O6 ? A DG 10 ? A DG 10 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 211 ? 1_555 105.9 ? 28 O ? E HOH . ? A HOH 209 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 211 ? 1_555 57.6 ? 29 O ? E HOH . ? A HOH 209 ? 2_655 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 211 ? 1_555 74.0 ? 30 O ? E HOH . ? A HOH 210 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 211 ? 1_555 104.6 ? 31 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 212 ? 1_555 83.3 ? 32 O6 ? A DG 10 ? A DG 10 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 212 ? 1_555 92.1 ? 33 O ? E HOH . ? A HOH 209 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 212 ? 1_555 103.7 ? 34 O ? E HOH . ? A HOH 209 ? 2_655 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 212 ? 1_555 124.0 ? 35 O ? E HOH . ? A HOH 210 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 212 ? 1_555 97.4 ? 36 O ? E HOH . ? A HOH 211 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 212 ? 1_555 77.0 ? 37 N7 ? A DG 9 ? A DG 9 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 88.4 ? 38 O6 ? A DG 10 ? A DG 10 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 79.9 ? 39 O ? E HOH . ? A HOH 209 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 76.8 ? 40 O ? E HOH . ? A HOH 209 ? 2_655 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 55.4 ? 41 O ? E HOH . ? A HOH 210 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 86.7 ? 42 O ? E HOH . ? A HOH 211 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 110.9 ? 43 O ? E HOH . ? A HOH 212 ? 1_555 CA ? C CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 213 ? 1_555 170.0 ? 44 O ? E HOH . ? A HOH 201 ? 4_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 201 ? 3_555 81.7 ? 45 O ? E HOH . ? A HOH 201 ? 4_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 202 ? 1_555 80.4 ? 46 O ? E HOH . ? A HOH 201 ? 3_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 202 ? 1_555 131.9 ? 47 O ? E HOH . ? A HOH 201 ? 4_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 157.5 ? 48 O ? E HOH . ? A HOH 201 ? 3_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 100.2 ? 49 O ? E HOH . ? A HOH 202 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 81.9 ? 50 O ? E HOH . ? A HOH 201 ? 4_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 100.2 ? 51 O ? E HOH . ? A HOH 201 ? 3_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 144.8 ? 52 O ? E HOH . ? A HOH 202 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 82.4 ? 53 O ? E HOH . ? A HOH 203 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 91.1 ? 54 O ? E HOH . ? A HOH 201 ? 4_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 2_655 130.9 ? 55 O ? E HOH . ? A HOH 201 ? 3_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 2_655 73.2 ? 56 O ? E HOH . ? A HOH 202 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 2_655 146.2 ? 57 O ? E HOH . ? A HOH 203 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 2_655 70.0 ? 58 O ? E HOH . ? A HOH 204 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 204 ? 2_655 79.8 ? # 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 2007-02-13 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-07-30 5 'Structure model' 1 4 2017-01-11 6 'Structure model' 1 5 2023-08-30 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Non-polymer description' 4 4 'Structure model' 'Structure summary' 5 5 'Structure model' Other 6 6 'Structure model' 'Data collection' 7 6 'Structure model' 'Database references' 8 6 'Structure model' 'Derived calculations' 9 6 '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 6 'Structure model' chem_comp_atom 2 6 'Structure model' chem_comp_bond 3 6 'Structure model' database_2 4 6 'Structure model' pdbx_initial_refinement_model 5 6 'Structure model' pdbx_struct_conn_angle 6 6 'Structure model' struct_conn 7 6 'Structure model' struct_conn_type 8 6 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 6 'Structure model' '_database_2.pdbx_DOI' 2 6 'Structure model' '_database_2.pdbx_database_accession' 3 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 10 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 17 6 'Structure model' '_pdbx_struct_conn_angle.value' 18 6 'Structure model' '_struct_conn.conn_type_id' 19 6 'Structure model' '_struct_conn.id' 20 6 'Structure model' '_struct_conn.pdbx_dist_value' 21 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 22 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 23 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 24 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 25 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 26 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 27 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 28 6 'Structure model' '_struct_conn.ptnr1_symmetry' 29 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 30 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 31 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 32 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 33 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 34 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 35 6 'Structure model' '_struct_conn.ptnr2_symmetry' 36 6 'Structure model' '_struct_conn_type.id' 37 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 38 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 39 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 CBASS 'data collection' . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 CNS phasing . ? 5 # _pdbx_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN THIS IS A N4C-ETHYL-N4C CROSSLINKED DNA. ONLY HALF OF THE ETHYL LINKER IS PRESENT IN THE COORDINATES SINCE IT IS LOCATED ON THE TWO-FOLD AXES. ; # 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 C34 P P N N 1 C34 OP1 O N N 2 C34 OP2 O N N 3 C34 OP3 O N N 4 C34 "O5'" O N N 5 C34 "C5'" C N N 6 C34 "C4'" C N R 7 C34 "O4'" O N N 8 C34 "C1'" C N R 9 C34 N1 N N N 10 C34 C6 C N N 11 C34 C2 C N N 12 C34 O2 O N N 13 C34 N3 N N N 14 C34 C4 C N N 15 C34 N4 N N N 16 C34 C7 C N N 17 C34 C5 C N N 18 C34 "C2'" C N N 19 C34 "C3'" C N S 20 C34 "O3'" O N N 21 C34 HOP2 H N N 22 C34 HOP3 H N N 23 C34 "H5'" H N N 24 C34 "H5''" H N N 25 C34 "H4'" H N N 26 C34 "H1'" H N N 27 C34 H6 H N N 28 C34 H4 H N N 29 C34 H7C1 H N N 30 C34 H7C2 H N N 31 C34 H7C3 H N N 32 C34 H5 H N N 33 C34 "H2'" H N N 34 C34 "H2''" H N N 35 C34 "H3'" H N N 36 C34 "HO3'" H N N 37 CA CA CA N N 38 DA OP3 O N N 39 DA P P N N 40 DA OP1 O N N 41 DA OP2 O N N 42 DA "O5'" O N N 43 DA "C5'" C N N 44 DA "C4'" C N R 45 DA "O4'" O N N 46 DA "C3'" C N S 47 DA "O3'" O N N 48 DA "C2'" C N N 49 DA "C1'" C N R 50 DA N9 N Y N 51 DA C8 C Y N 52 DA N7 N Y N 53 DA C5 C Y N 54 DA C6 C Y N 55 DA N6 N N N 56 DA N1 N Y N 57 DA C2 C Y N 58 DA N3 N Y N 59 DA C4 C Y N 60 DA HOP3 H N N 61 DA HOP2 H N N 62 DA "H5'" H N N 63 DA "H5''" H N N 64 DA "H4'" H N N 65 DA "H3'" H N N 66 DA "HO3'" H N N 67 DA "H2'" H N N 68 DA "H2''" H N N 69 DA "H1'" H N N 70 DA H8 H N N 71 DA H61 H N N 72 DA H62 H N N 73 DA H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DG OP3 O N N 109 DG P P N N 110 DG OP1 O N N 111 DG OP2 O N N 112 DG "O5'" O N N 113 DG "C5'" C N N 114 DG "C4'" C N R 115 DG "O4'" O N N 116 DG "C3'" C N S 117 DG "O3'" O N N 118 DG "C2'" C N N 119 DG "C1'" C N R 120 DG N9 N Y N 121 DG C8 C Y N 122 DG N7 N Y N 123 DG C5 C Y N 124 DG C6 C N N 125 DG O6 O N N 126 DG N1 N N N 127 DG C2 C N N 128 DG N2 N N N 129 DG N3 N N N 130 DG C4 C Y N 131 DG HOP3 H N N 132 DG HOP2 H N N 133 DG "H5'" H N N 134 DG "H5''" H N N 135 DG "H4'" H N N 136 DG "H3'" H N N 137 DG "HO3'" H N N 138 DG "H2'" H N N 139 DG "H2''" H N N 140 DG "H1'" H N N 141 DG H8 H N N 142 DG H1 H N N 143 DG H21 H N N 144 DG H22 H N N 145 DT OP3 O N N 146 DT P P N N 147 DT OP1 O N N 148 DT OP2 O N N 149 DT "O5'" O N N 150 DT "C5'" C N N 151 DT "C4'" C N R 152 DT "O4'" O N N 153 DT "C3'" C N S 154 DT "O3'" O N N 155 DT "C2'" C N N 156 DT "C1'" C N R 157 DT N1 N N N 158 DT C2 C N N 159 DT O2 O N N 160 DT N3 N N N 161 DT C4 C N N 162 DT O4 O N N 163 DT C5 C N N 164 DT C7 C N N 165 DT C6 C N N 166 DT HOP3 H N N 167 DT HOP2 H N N 168 DT "H5'" H N N 169 DT "H5''" H N N 170 DT "H4'" H N N 171 DT "H3'" H N N 172 DT "HO3'" H N N 173 DT "H2'" H N N 174 DT "H2''" H N N 175 DT "H1'" H N N 176 DT H3 H N N 177 DT H71 H N N 178 DT H72 H N N 179 DT H73 H N N 180 DT H6 H N N 181 HOH O O N N 182 HOH H1 H N N 183 HOH H2 H N N 184 # 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 C34 P OP1 doub N N 1 C34 P OP2 sing N N 2 C34 P OP3 sing N N 3 C34 P "O5'" sing N N 4 C34 OP2 HOP2 sing N N 5 C34 OP3 HOP3 sing N N 6 C34 "O5'" "C5'" sing N N 7 C34 "C5'" "C4'" sing N N 8 C34 "C5'" "H5'" sing N N 9 C34 "C5'" "H5''" sing N N 10 C34 "C4'" "O4'" sing N N 11 C34 "C4'" "C3'" sing N N 12 C34 "C4'" "H4'" sing N N 13 C34 "O4'" "C1'" sing N N 14 C34 "C1'" N1 sing N N 15 C34 "C1'" "C2'" sing N N 16 C34 "C1'" "H1'" sing N N 17 C34 N1 C6 sing N N 18 C34 N1 C2 sing N N 19 C34 C6 C5 doub N N 20 C34 C6 H6 sing N N 21 C34 C2 O2 doub N N 22 C34 C2 N3 sing N N 23 C34 N3 C4 doub N N 24 C34 C4 N4 sing N N 25 C34 C4 C5 sing N N 26 C34 N4 C7 sing N N 27 C34 N4 H4 sing N N 28 C34 C7 H7C1 sing N N 29 C34 C7 H7C2 sing N N 30 C34 C7 H7C3 sing N N 31 C34 C5 H5 sing N N 32 C34 "C2'" "C3'" sing N N 33 C34 "C2'" "H2'" sing N N 34 C34 "C2'" "H2''" sing N N 35 C34 "C3'" "O3'" sing N N 36 C34 "C3'" "H3'" sing N N 37 C34 "O3'" "HO3'" sing N N 38 DA OP3 P sing N N 39 DA OP3 HOP3 sing N N 40 DA P OP1 doub N N 41 DA P OP2 sing N N 42 DA P "O5'" sing N N 43 DA OP2 HOP2 sing N N 44 DA "O5'" "C5'" sing N N 45 DA "C5'" "C4'" sing N N 46 DA "C5'" "H5'" sing N N 47 DA "C5'" "H5''" sing N N 48 DA "C4'" "O4'" sing N N 49 DA "C4'" "C3'" sing N N 50 DA "C4'" "H4'" sing N N 51 DA "O4'" "C1'" sing N N 52 DA "C3'" "O3'" sing N N 53 DA "C3'" "C2'" sing N N 54 DA "C3'" "H3'" sing N N 55 DA "O3'" "HO3'" sing N N 56 DA "C2'" "C1'" sing N N 57 DA "C2'" "H2'" sing N N 58 DA "C2'" "H2''" sing N N 59 DA "C1'" N9 sing N N 60 DA "C1'" "H1'" sing N N 61 DA N9 C8 sing Y N 62 DA N9 C4 sing Y N 63 DA C8 N7 doub Y N 64 DA C8 H8 sing N N 65 DA N7 C5 sing Y N 66 DA C5 C6 sing Y N 67 DA C5 C4 doub Y N 68 DA C6 N6 sing N N 69 DA C6 N1 doub Y N 70 DA N6 H61 sing N N 71 DA N6 H62 sing N N 72 DA N1 C2 sing Y N 73 DA C2 N3 doub Y N 74 DA C2 H2 sing N N 75 DA N3 C4 sing Y N 76 DC OP3 P sing N N 77 DC OP3 HOP3 sing N N 78 DC P OP1 doub N N 79 DC P OP2 sing N N 80 DC P "O5'" sing N N 81 DC OP2 HOP2 sing N N 82 DC "O5'" "C5'" sing N N 83 DC "C5'" "C4'" sing N N 84 DC "C5'" "H5'" sing N N 85 DC "C5'" "H5''" sing N N 86 DC "C4'" "O4'" sing N N 87 DC "C4'" "C3'" sing N N 88 DC "C4'" "H4'" sing N N 89 DC "O4'" "C1'" sing N N 90 DC "C3'" "O3'" sing N N 91 DC "C3'" "C2'" sing N N 92 DC "C3'" "H3'" sing N N 93 DC "O3'" "HO3'" sing N N 94 DC "C2'" "C1'" sing N N 95 DC "C2'" "H2'" sing N N 96 DC "C2'" "H2''" sing N N 97 DC "C1'" N1 sing N N 98 DC "C1'" "H1'" sing N N 99 DC N1 C2 sing N N 100 DC N1 C6 sing N N 101 DC C2 O2 doub N N 102 DC C2 N3 sing N N 103 DC N3 C4 doub N N 104 DC C4 N4 sing N N 105 DC C4 C5 sing N N 106 DC N4 H41 sing N N 107 DC N4 H42 sing N N 108 DC C5 C6 doub N N 109 DC C5 H5 sing N N 110 DC C6 H6 sing N N 111 DG OP3 P sing N N 112 DG OP3 HOP3 sing N N 113 DG P OP1 doub N N 114 DG P OP2 sing N N 115 DG P "O5'" sing N N 116 DG OP2 HOP2 sing N N 117 DG "O5'" "C5'" sing N N 118 DG "C5'" "C4'" sing N N 119 DG "C5'" "H5'" sing N N 120 DG "C5'" "H5''" sing N N 121 DG "C4'" "O4'" sing N N 122 DG "C4'" "C3'" sing N N 123 DG "C4'" "H4'" sing N N 124 DG "O4'" "C1'" sing N N 125 DG "C3'" "O3'" sing N N 126 DG "C3'" "C2'" sing N N 127 DG "C3'" "H3'" sing N N 128 DG "O3'" "HO3'" sing N N 129 DG "C2'" "C1'" sing N N 130 DG "C2'" "H2'" sing N N 131 DG "C2'" "H2''" sing N N 132 DG "C1'" N9 sing N N 133 DG "C1'" "H1'" sing N N 134 DG N9 C8 sing Y N 135 DG N9 C4 sing Y N 136 DG C8 N7 doub Y N 137 DG C8 H8 sing N N 138 DG N7 C5 sing Y N 139 DG C5 C6 sing N N 140 DG C5 C4 doub Y N 141 DG C6 O6 doub N N 142 DG C6 N1 sing N N 143 DG N1 C2 sing N N 144 DG N1 H1 sing N N 145 DG C2 N2 sing N N 146 DG C2 N3 doub N N 147 DG N2 H21 sing N N 148 DG N2 H22 sing N N 149 DG N3 C4 sing N N 150 DT OP3 P sing N N 151 DT OP3 HOP3 sing N N 152 DT P OP1 doub N N 153 DT P OP2 sing N N 154 DT P "O5'" sing N N 155 DT OP2 HOP2 sing N N 156 DT "O5'" "C5'" sing N N 157 DT "C5'" "C4'" sing N N 158 DT "C5'" "H5'" sing N N 159 DT "C5'" "H5''" sing N N 160 DT "C4'" "O4'" sing N N 161 DT "C4'" "C3'" sing N N 162 DT "C4'" "H4'" sing N N 163 DT "O4'" "C1'" sing N N 164 DT "C3'" "O3'" sing N N 165 DT "C3'" "C2'" sing N N 166 DT "C3'" "H3'" sing N N 167 DT "O3'" "HO3'" sing N N 168 DT "C2'" "C1'" sing N N 169 DT "C2'" "H2'" sing N N 170 DT "C2'" "H2''" sing N N 171 DT "C1'" N1 sing N N 172 DT "C1'" "H1'" sing N N 173 DT N1 C2 sing N N 174 DT N1 C6 sing N N 175 DT C2 O2 doub N N 176 DT C2 N3 sing N N 177 DT N3 C4 sing N N 178 DT N3 H3 sing N N 179 DT C4 O4 doub N N 180 DT C4 C5 sing N N 181 DT C5 C7 sing N N 182 DT C5 C6 doub N N 183 DT C7 H71 sing N N 184 DT C7 H72 sing N N 185 DT C7 H73 sing N N 186 DT C6 H6 sing N N 187 HOH O H1 sing N N 188 HOH O H2 sing N N 189 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2OKS 'double helix' 2OKS 'b-form double helix' 2OKS 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 A DG 10 2_656 0.318 -0.047 0.131 -7.206 -11.632 -0.936 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 2_656 0.376 -0.167 0.252 1.746 -11.703 0.087 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 2_656 -0.050 -0.173 0.312 -1.291 -11.347 4.067 3 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DA 4 1_555 A DT 7 2_656 0.231 -0.069 0.223 -0.183 -18.113 4.930 4 A_DA4:DT7_A A 4 ? A 7 ? 20 1 1 A C34 5 1_555 A DG 6 2_656 0.223 -0.057 0.138 -4.211 -20.346 0.007 5 A_C345:DG6_A A 5 ? A 6 ? 19 1 1 A DG 6 1_555 A C34 5 2_656 -0.223 -0.057 0.138 4.211 -20.346 0.007 6 A_DG6:C345_A A 6 ? A 5 ? 19 1 1 A DT 7 1_555 A DA 4 2_656 -0.231 -0.069 0.223 0.183 -18.113 4.930 7 A_DT7:DA4_A A 7 ? A 4 ? 20 1 1 A DT 8 1_555 A DA 3 2_656 0.050 -0.173 0.312 1.291 -11.347 4.067 8 A_DT8:DA3_A A 8 ? A 3 ? 20 1 1 A DG 9 1_555 A DC 2 2_656 -0.376 -0.167 0.252 -1.746 -11.703 0.087 9 A_DG9:DC2_A A 9 ? A 2 ? 19 1 1 A DG 10 1_555 A DC 1 2_656 -0.318 -0.047 0.131 7.206 -11.632 -0.936 10 A_DG10:DC1_A A 10 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 A DG 10 2_656 A DC 2 1_555 A DG 9 2_656 -0.516 0.787 3.123 2.086 11.183 28.024 -0.755 1.414 3.153 21.981 -4.100 30.202 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 2_656 A DA 3 1_555 A DT 8 2_656 0.363 2.852 3.381 -0.053 -10.862 50.139 4.008 -0.423 2.748 -12.647 0.062 51.228 2 AA_DC2DA3:DT8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DA 3 1_555 A DT 8 2_656 A DA 4 1_555 A DT 7 2_656 0.279 0.341 3.372 0.837 8.392 32.446 -0.854 -0.340 3.359 14.710 -1.467 33.495 3 AA_DA3DA4:DT7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DA 4 1_555 A DT 7 2_656 A C34 5 1_555 A DG 6 2_656 0.526 -0.484 3.336 1.406 -2.997 29.072 -0.288 -0.727 3.388 -5.946 -2.790 29.256 4 AA_DA4C345:DG6DT7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A C34 5 1_555 A DG 6 2_656 A DG 6 1_555 A C34 5 2_656 0.000 0.523 3.289 0.000 14.286 39.548 -0.811 0.000 3.280 20.326 0.000 41.952 5 AA_C345DG6:C345DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A C34 5 2_656 A DT 7 1_555 A DA 4 2_656 -0.526 -0.484 3.336 -1.406 -2.997 29.072 -0.288 0.727 3.388 -5.946 2.790 29.256 6 AA_DG6DT7:DA4C345_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DT 7 1_555 A DA 4 2_656 A DT 8 1_555 A DA 3 2_656 -0.279 0.341 3.372 -0.837 8.392 32.446 -0.854 0.340 3.359 14.710 1.467 33.495 7 AA_DT7DT8:DA3DA4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DT 8 1_555 A DA 3 2_656 A DG 9 1_555 A DC 2 2_656 -0.363 2.852 3.381 0.053 -10.862 50.139 4.008 0.423 2.748 -12.647 -0.062 51.228 8 AA_DT8DG9:DC2DA3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DG 9 1_555 A DC 2 2_656 A DG 10 1_555 A DC 1 2_656 0.516 0.787 3.123 -2.086 11.183 28.024 -0.755 -1.414 3.153 21.981 4.100 30.202 9 AA_DG9DG10:DC1DC2_AA A 9 ? A 2 ? A 10 ? A 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 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 1EN8 _pdbx_initial_refinement_model.details 'PDB ENTRY 1EN8' #