data_3IKI # _entry.id 3IKI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.378 _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 3IKI pdb_00003iki 10.2210/pdb3iki/pdb NDB NA0114 ? ? RCSB RCSB054525 ? ? WWPDB D_1000054525 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3IKI _pdbx_database_status.recvd_initial_deposition_date 2009-08-05 _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.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sheng, J.' 1 'Hassan, A.E.A.' 2 'Zhang, W.' 3 'Gan, J.' 4 'Huang, Z.' 5 # _citation.id primary _citation.title 'Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 40 _citation.page_first 8111 _citation.page_last 8118 _citation.year 2012 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22641848 _citation.pdbx_database_id_DOI 10.1093/nar/gks426 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sheng, J.' 1 ? primary 'Zhang, W.' 2 ? primary 'Hassan, A.E.' 3 ? primary 'Gan, J.' 4 ? primary 'Soares, A.S.' 5 ? primary 'Geng, S.' 6 ? primary 'Ren, Y.' 7 ? primary 'Huang, Z.' 8 ? # _cell.entry_id 3IKI _cell.length_a 42.882 _cell.length_b 42.882 _cell.length_c 23.687 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3IKI _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # 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(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'" 2537.642 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 38 ? ? ? ? # _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 '(DG)(UMS)(DG)(US2)(DA)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GUGUACAC _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 DG n 1 2 UMS n 1 3 DG n 1 4 US2 n 1 5 DA n 1 6 DC n 1 7 DA n 1 8 DC 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 'Synthesized by solid phase synthesis' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3IKI _struct_ref.pdbx_db_accession 3IKI _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GUGUACAC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3IKI _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3IKI _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _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 8 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 US2 'DNA linking' n ;2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate) ; "5-SMe-deoxyuridine-5'-phosphate" 'C10 H15 N2 O8 P S' 354.273 # _exptl.entry_id 3IKI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.67 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;10% v / v MPD, 40 mM Na Cacodylate pH 7.0, 12 mM Spermine tetra-HCl, 40 mM Lithium Chloride, 80 mM Strontium Chloride / 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2008-10-22 _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 'channel-cut Si(111) monochromator' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X12B' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X12B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 3IKI _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.38 _reflns.number_obs 4616 _reflns.number_all 4911 _reflns.percent_possible_obs 94 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 23.02 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.4 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.38 _reflns_shell.d_res_low 1.43 _reflns_shell.percent_possible_all 67.8 _reflns_shell.Rmerge_I_obs 0.245 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.86 _reflns_shell.pdbx_redundancy 5.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 324 _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 3IKI _refine.ls_number_reflns_obs 4373 _refine.ls_number_reflns_all 4650 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.32 _refine.ls_d_res_high 1.38 _refine.ls_percent_reflns_obs 94.04 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all 0.17907 _refine.ls_R_factor_R_work 0.17838 _refine.ls_R_factor_R_free 0.19414 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 216 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.957 _refine.correlation_coeff_Fo_to_Fc_free 0.961 _refine.B_iso_mean 12.133 _refine.aniso_B[1][1] 0.12 _refine.aniso_B[2][2] 0.12 _refine.aniso_B[3][3] -0.24 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 1DNS _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.061 _refine.pdbx_overall_ESU_R_Free 0.060 _refine.overall_SU_ML 0.031 _refine.overall_SU_B 1.592 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 3IKI _refine_analyze.Luzzati_coordinate_error_obs 0.061 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.060 _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_Luzzati_d_res_high_obs ? _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 163 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 202 _refine_hist.d_res_high 1.38 _refine_hist.d_res_low 30.32 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.007 0.021 ? 180 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.467 3.000 ? 270 'X-RAY DIFFRACTION' ? r_chiral_restr 0.057 0.200 ? 31 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 83 'X-RAY DIFFRACTION' ? r_nbd_refined 0.371 0.200 ? 66 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.277 0.200 ? 103 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.102 0.200 ? 29 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.180 0.200 ? 26 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.083 0.200 ? 10 'X-RAY DIFFRACTION' ? r_scbond_it 0.825 3.000 ? 261 'X-RAY DIFFRACTION' ? r_scangle_it 1.249 4.500 ? 270 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.380 _refine_ls_shell.d_res_low 1.416 _refine_ls_shell.number_reflns_R_work 216 _refine_ls_shell.R_factor_R_work 0.203 _refine_ls_shell.percent_reflns_obs 65.53 _refine_ls_shell.R_factor_R_free 0.157 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 14 _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' # _struct.entry_id 3IKI _struct.title '5-SMe-dU containing DNA octamer' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3IKI _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;Selenium, Nucleic Acid, 5-SMe-deoxyuridine, 2'-SeMe-deoxyuridine, DNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A UMS 2 P ? ? A DG 1 A UMS 2 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A UMS 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A UMS 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale3 covale both ? A DG 3 "O3'" ? ? ? 1_555 A US2 4 P ? ? A DG 3 A US2 4 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale4 covale both ? A US2 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A US2 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.597 ? ? metalc1 metalc ? ? A DG 3 OP2 ? ? ? 1_555 B MG . MG ? ? A DG 3 A MG 11 1_555 ? ? ? ? ? ? ? 2.123 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 11 A HOH 36 1_555 ? ? ? ? ? ? ? 2.612 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 11 A HOH 45 1_555 ? ? ? ? ? ? ? 2.680 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A UMS 2 N3 ? ? ? 1_555 A DA 7 N1 ? ? A UMS 2 A DA 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A UMS 2 O4 ? ? ? 1_555 A DA 7 N6 ? ? A UMS 2 A DA 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A UMS 2 N3 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A UMS 2 O4 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 11 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE MG A 11' # 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 4 UMS A 2 ? UMS A 2 . ? 1_555 ? 2 AC1 4 DG A 3 ? DG A 3 . ? 1_555 ? 3 AC1 4 HOH C . ? HOH A 36 . ? 1_555 ? 4 AC1 4 HOH C . ? HOH A 45 . ? 1_555 ? # _database_PDB_matrix.entry_id 3IKI _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 3IKI _atom_sites.fract_transf_matrix[1][1] 0.023320 _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] 0.023320 _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] 0.042217 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P S SE # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 O "O5'" . DG A 1 1 ? 29.200 19.006 -5.269 1.00 10.16 ? 1 DG A "O5'" 1 ATOM 2 C "C5'" . DG A 1 1 ? 29.102 17.599 -5.012 1.00 8.50 ? 1 DG A "C5'" 1 ATOM 3 C "C4'" . DG A 1 1 ? 30.337 17.073 -4.294 1.00 8.52 ? 1 DG A "C4'" 1 ATOM 4 O "O4'" . DG A 1 1 ? 31.516 17.253 -5.121 1.00 8.26 ? 1 DG A "O4'" 1 ATOM 5 C "C3'" . DG A 1 1 ? 30.689 17.780 -2.994 1.00 8.15 ? 1 DG A "C3'" 1 ATOM 6 O "O3'" . DG A 1 1 ? 29.917 17.237 -1.924 1.00 8.52 ? 1 DG A "O3'" 1 ATOM 7 C "C2'" . DG A 1 1 ? 32.172 17.447 -2.873 1.00 8.35 ? 1 DG A "C2'" 1 ATOM 8 C "C1'" . DG A 1 1 ? 32.630 17.593 -4.320 1.00 8.79 ? 1 DG A "C1'" 1 ATOM 9 N N9 . DG A 1 1 ? 33.046 18.962 -4.621 1.00 8.63 ? 1 DG A N9 1 ATOM 10 C C8 . DG A 1 1 ? 32.299 19.947 -5.227 1.00 9.29 ? 1 DG A C8 1 ATOM 11 N N7 . DG A 1 1 ? 32.930 21.082 -5.340 1.00 9.41 ? 1 DG A N7 1 ATOM 12 C C5 . DG A 1 1 ? 34.171 20.842 -4.765 1.00 8.80 ? 1 DG A C5 1 ATOM 13 C C6 . DG A 1 1 ? 35.285 21.702 -4.603 1.00 8.54 ? 1 DG A C6 1 ATOM 14 O O6 . DG A 1 1 ? 35.392 22.885 -4.953 1.00 9.84 ? 1 DG A O6 1 ATOM 15 N N1 . DG A 1 1 ? 36.351 21.070 -3.970 1.00 9.08 ? 1 DG A N1 1 ATOM 16 C C2 . DG A 1 1 ? 36.342 19.757 -3.553 1.00 9.48 ? 1 DG A C2 1 ATOM 17 N N2 . DG A 1 1 ? 37.462 19.309 -2.967 1.00 10.47 ? 1 DG A N2 1 ATOM 18 N N3 . DG A 1 1 ? 35.307 18.934 -3.701 1.00 9.12 ? 1 DG A N3 1 ATOM 19 C C4 . DG A 1 1 ? 34.257 19.542 -4.310 1.00 8.79 ? 1 DG A C4 1 HETATM 20 P P . UMS A 1 2 ? 29.421 18.150 -0.706 1.00 9.05 ? 2 UMS A P 1 HETATM 21 O OP1 . UMS A 1 2 ? 28.566 17.307 0.151 1.00 10.34 ? 2 UMS A OP1 1 HETATM 22 O OP2 . UMS A 1 2 ? 28.924 19.445 -1.225 1.00 10.47 ? 2 UMS A OP2 1 HETATM 23 O "O5'" . UMS A 1 2 ? 30.757 18.496 0.103 1.00 8.89 ? 2 UMS A "O5'" 1 HETATM 24 C "C5'" . UMS A 1 2 ? 31.441 17.472 0.807 1.00 8.83 ? 2 UMS A "C5'" 1 HETATM 25 C "C4'" . UMS A 1 2 ? 32.791 17.955 1.276 1.00 9.12 ? 2 UMS A "C4'" 1 HETATM 26 O "O4'" . UMS A 1 2 ? 33.581 18.369 0.134 1.00 8.82 ? 2 UMS A "O4'" 1 HETATM 27 C "C3'" . UMS A 1 2 ? 32.756 19.173 2.179 1.00 10.51 ? 2 UMS A "C3'" 1 HETATM 28 O "O3'" . UMS A 1 2 ? 32.423 18.731 3.481 1.00 12.79 ? 2 UMS A "O3'" 1 HETATM 29 C "C2'" . UMS A 1 2 ? 34.192 19.676 2.028 1.00 9.97 ? 2 UMS A "C2'" 1 HETATM 30 SE "SE2'" . UMS A 1 2 ? 35.473 18.592 3.062 0.80 11.05 ? 2 UMS A "SE2'" 1 HETATM 31 C "C1'" . UMS A 1 2 ? 34.417 19.438 0.533 1.00 8.91 ? 2 UMS A "C1'" 1 HETATM 32 C "CA'" . UMS A 1 2 ? 37.126 19.644 2.969 1.00 11.95 ? 2 UMS A "CA'" 1 HETATM 33 N N1 . UMS A 1 2 ? 34.107 20.625 -0.339 1.00 9.25 ? 2 UMS A N1 1 HETATM 34 C C2 . UMS A 1 2 ? 35.086 21.588 -0.498 1.00 9.47 ? 2 UMS A C2 1 HETATM 35 O O2 . UMS A 1 2 ? 36.173 21.525 0.045 1.00 10.23 ? 2 UMS A O2 1 HETATM 36 N N3 . UMS A 1 2 ? 34.746 22.642 -1.310 1.00 9.45 ? 2 UMS A N3 1 HETATM 37 C C4 . UMS A 1 2 ? 33.543 22.828 -1.974 1.00 9.06 ? 2 UMS A C4 1 HETATM 38 O O4 . UMS A 1 2 ? 33.389 23.829 -2.666 1.00 9.46 ? 2 UMS A O4 1 HETATM 39 C C5 . UMS A 1 2 ? 32.565 21.787 -1.765 1.00 9.55 ? 2 UMS A C5 1 HETATM 40 C C6 . UMS A 1 2 ? 32.877 20.746 -0.974 1.00 9.05 ? 2 UMS A C6 1 ATOM 41 P P . DG A 1 3 ? 31.679 19.652 4.556 1.00 15.71 ? 3 DG A P 1 ATOM 42 O OP1 . DG A 1 3 ? 31.260 18.752 5.651 1.00 17.09 ? 3 DG A OP1 1 ATOM 43 O OP2 . DG A 1 3 ? 30.721 20.539 3.869 1.00 16.48 ? 3 DG A OP2 1 ATOM 44 O "O5'" . DG A 1 3 ? 32.908 20.543 5.059 1.00 15.23 ? 3 DG A "O5'" 1 ATOM 45 C "C5'" . DG A 1 3 ? 32.843 21.945 5.006 1.00 13.73 ? 3 DG A "C5'" 1 ATOM 46 C "C4'" . DG A 1 3 ? 34.257 22.474 4.941 1.00 13.22 ? 3 DG A "C4'" 1 ATOM 47 O "O4'" . DG A 1 3 ? 34.749 22.336 3.591 1.00 12.36 ? 3 DG A "O4'" 1 ATOM 48 C "C3'" . DG A 1 3 ? 34.357 23.950 5.234 1.00 12.39 ? 3 DG A "C3'" 1 ATOM 49 O "O3'" . DG A 1 3 ? 34.459 24.186 6.669 1.00 9.15 ? 3 DG A "O3'" 1 ATOM 50 C "C2'" . DG A 1 3 ? 35.586 24.360 4.437 1.00 11.58 ? 3 DG A "C2'" 1 ATOM 51 C "C1'" . DG A 1 3 ? 35.429 23.505 3.188 1.00 10.43 ? 3 DG A "C1'" 1 ATOM 52 N N9 . DG A 1 3 ? 34.648 24.135 2.126 1.00 10.22 ? 3 DG A N9 1 ATOM 53 C C8 . DG A 1 3 ? 33.428 23.744 1.627 1.00 9.97 ? 3 DG A C8 1 ATOM 54 N N7 . DG A 1 3 ? 32.986 24.510 0.667 1.00 9.92 ? 3 DG A N7 1 ATOM 55 C C5 . DG A 1 3 ? 33.985 25.467 0.517 1.00 9.40 ? 3 DG A C5 1 ATOM 56 C C6 . DG A 1 3 ? 34.076 26.571 -0.367 1.00 8.93 ? 3 DG A C6 1 ATOM 57 O O6 . DG A 1 3 ? 33.263 26.922 -1.229 1.00 9.41 ? 3 DG A O6 1 ATOM 58 N N1 . DG A 1 3 ? 35.255 27.297 -0.184 1.00 9.13 ? 3 DG A N1 1 ATOM 59 C C2 . DG A 1 3 ? 36.230 27.001 0.742 1.00 9.39 ? 3 DG A C2 1 ATOM 60 N N2 . DG A 1 3 ? 37.307 27.803 0.793 1.00 9.27 ? 3 DG A N2 1 ATOM 61 N N3 . DG A 1 3 ? 36.160 25.968 1.570 1.00 9.25 ? 3 DG A N3 1 ATOM 62 C C4 . DG A 1 3 ? 35.013 25.252 1.407 1.00 9.74 ? 3 DG A C4 1 HETATM 63 P P . US2 A 1 4 ? 34.000 25.547 7.366 1.00 9.16 ? 4 US2 A P 1 HETATM 64 N N1 . US2 A 1 4 ? 35.349 29.061 3.421 1.00 5.92 ? 4 US2 A N1 1 HETATM 65 C C6 . US2 A 1 4 ? 34.393 28.074 3.644 1.00 5.69 ? 4 US2 A C6 1 HETATM 66 C C2 . US2 A 1 4 ? 35.177 30.017 2.439 1.00 4.71 ? 4 US2 A C2 1 HETATM 67 O O2 . US2 A 1 4 ? 35.968 30.918 2.207 1.00 4.70 ? 4 US2 A O2 1 HETATM 68 N N3 . US2 A 1 4 ? 34.017 29.894 1.719 1.00 5.07 ? 4 US2 A N3 1 HETATM 69 C C4 . US2 A 1 4 ? 33.024 28.938 1.884 1.00 5.05 ? 4 US2 A C4 1 HETATM 70 O O4 . US2 A 1 4 ? 32.024 28.926 1.172 1.00 5.04 ? 4 US2 A O4 1 HETATM 71 C C5 . US2 A 1 4 ? 33.257 27.957 2.936 1.00 5.87 ? 4 US2 A C5 1 HETATM 72 S S5 . US2 A 1 4 ? 32.100 26.680 3.276 1.00 6.82 ? 4 US2 A S5 1 HETATM 73 C C5A . US2 A 1 4 ? 30.857 27.447 4.289 1.00 9.62 ? 4 US2 A C5A 1 HETATM 74 C "C1'" . US2 A 1 4 ? 36.597 29.111 4.259 1.00 5.73 ? 4 US2 A "C1'" 1 HETATM 75 O "O4'" . US2 A 1 4 ? 36.828 27.841 4.861 1.00 7.43 ? 4 US2 A "O4'" 1 HETATM 76 C "C4'" . US2 A 1 4 ? 36.862 28.001 6.302 1.00 6.32 ? 4 US2 A "C4'" 1 HETATM 77 C "C3'" . US2 A 1 4 ? 36.066 29.277 6.546 1.00 5.74 ? 4 US2 A "C3'" 1 HETATM 78 O "O3'" . US2 A 1 4 ? 36.420 29.819 7.805 1.00 5.91 ? 4 US2 A "O3'" 1 HETATM 79 C "C2'" . US2 A 1 4 ? 36.527 30.143 5.380 1.00 6.02 ? 4 US2 A "C2'" 1 HETATM 80 C "C5'" . US2 A 1 4 ? 36.305 26.760 6.964 1.00 7.21 ? 4 US2 A "C5'" 1 HETATM 81 O "O5'" . US2 A 1 4 ? 34.908 26.665 6.673 1.00 7.56 ? 4 US2 A "O5'" 1 HETATM 82 O O1P . US2 A 1 4 ? 32.584 25.785 7.061 1.00 8.52 ? 4 US2 A O1P 1 HETATM 83 O O2P . US2 A 1 4 ? 34.409 25.429 8.789 1.00 11.42 ? 4 US2 A O2P 1 ATOM 84 P P . DA A 1 5 ? 35.464 30.875 8.528 1.00 6.43 ? 5 DA A P 1 ATOM 85 O OP1 . DA A 1 5 ? 35.871 30.926 9.984 1.00 11.11 ? 5 DA A OP1 1 ATOM 86 O OP2 . DA A 1 5 ? 34.015 30.623 8.221 1.00 11.96 ? 5 DA A OP2 1 ATOM 87 O "O5'" . DA A 1 5 ? 35.911 32.253 7.849 1.00 8.28 ? 5 DA A "O5'" 1 ATOM 88 C "C5'" . DA A 1 5 ? 35.012 33.322 7.615 1.00 8.06 ? 5 DA A "C5'" 1 ATOM 89 C "C4'" . DA A 1 5 ? 35.548 34.164 6.476 1.00 7.41 ? 5 DA A "C4'" 1 ATOM 90 O "O4'" . DA A 1 5 ? 35.696 33.336 5.293 1.00 7.13 ? 5 DA A "O4'" 1 ATOM 91 C "C3'" . DA A 1 5 ? 34.652 35.320 6.061 1.00 7.28 ? 5 DA A "C3'" 1 ATOM 92 O "O3'" . DA A 1 5 ? 34.988 36.456 6.830 1.00 7.95 ? 5 DA A "O3'" 1 ATOM 93 C "C2'" . DA A 1 5 ? 35.028 35.501 4.599 1.00 7.02 ? 5 DA A "C2'" 1 ATOM 94 C "C1'" . DA A 1 5 ? 35.185 34.047 4.179 1.00 6.99 ? 5 DA A "C1'" 1 ATOM 95 N N9 . DA A 1 5 ? 33.962 33.373 3.730 1.00 6.98 ? 5 DA A N9 1 ATOM 96 C C8 . DA A 1 5 ? 33.331 32.310 4.324 1.00 6.83 ? 5 DA A C8 1 ATOM 97 N N7 . DA A 1 5 ? 32.272 31.890 3.684 1.00 6.48 ? 5 DA A N7 1 ATOM 98 C C5 . DA A 1 5 ? 32.207 32.728 2.581 1.00 6.74 ? 5 DA A C5 1 ATOM 99 C C6 . DA A 1 5 ? 31.308 32.799 1.496 1.00 6.78 ? 5 DA A C6 1 ATOM 100 N N6 . DA A 1 5 ? 30.269 31.973 1.356 1.00 7.73 ? 5 DA A N6 1 ATOM 101 N N1 . DA A 1 5 ? 31.527 33.754 0.563 1.00 6.47 ? 5 DA A N1 1 ATOM 102 C C2 . DA A 1 5 ? 32.568 34.588 0.708 1.00 6.79 ? 5 DA A C2 1 ATOM 103 N N3 . DA A 1 5 ? 33.482 34.609 1.683 1.00 7.00 ? 5 DA A N3 1 ATOM 104 C C4 . DA A 1 5 ? 33.243 33.648 2.590 1.00 6.90 ? 5 DA A C4 1 ATOM 105 P P . DC A 1 6 ? 33.841 37.463 7.312 1.00 8.67 ? 6 DC A P 1 ATOM 106 O OP1 . DC A 1 6 ? 34.510 38.533 8.086 1.00 10.25 ? 6 DC A OP1 1 ATOM 107 O OP2 . DC A 1 6 ? 32.725 36.701 7.902 1.00 9.64 ? 6 DC A OP2 1 ATOM 108 O "O5'" . DC A 1 6 ? 33.299 38.098 5.953 1.00 8.66 ? 6 DC A "O5'" 1 ATOM 109 C "C5'" . DC A 1 6 ? 34.115 38.996 5.212 1.00 8.90 ? 6 DC A "C5'" 1 ATOM 110 C "C4'" . DC A 1 6 ? 33.433 39.330 3.903 1.00 8.84 ? 6 DC A "C4'" 1 ATOM 111 O "O4'" . DC A 1 6 ? 33.276 38.127 3.112 1.00 8.37 ? 6 DC A "O4'" 1 ATOM 112 C "C3'" . DC A 1 6 ? 32.008 39.846 4.052 1.00 9.06 ? 6 DC A "C3'" 1 ATOM 113 O "O3'" . DC A 1 6 ? 31.997 41.215 4.436 1.00 11.60 ? 6 DC A "O3'" 1 ATOM 114 C "C2'" . DC A 1 6 ? 31.474 39.623 2.646 1.00 9.16 ? 6 DC A "C2'" 1 ATOM 115 C "C1'" . DC A 1 6 ? 32.063 38.243 2.378 1.00 8.32 ? 6 DC A "C1'" 1 ATOM 116 N N1 . DC A 1 6 ? 31.150 37.101 2.714 1.00 7.75 ? 6 DC A N1 1 ATOM 117 C C2 . DC A 1 6 ? 30.116 36.786 1.819 1.00 7.70 ? 6 DC A C2 1 ATOM 118 O O2 . DC A 1 6 ? 29.989 37.475 0.796 1.00 7.91 ? 6 DC A O2 1 ATOM 119 N N3 . DC A 1 6 ? 29.291 35.742 2.101 1.00 7.18 ? 6 DC A N3 1 ATOM 120 C C4 . DC A 1 6 ? 29.457 35.031 3.220 1.00 7.76 ? 6 DC A C4 1 ATOM 121 N N4 . DC A 1 6 ? 28.618 34.015 3.441 1.00 8.11 ? 6 DC A N4 1 ATOM 122 C C5 . DC A 1 6 ? 30.498 35.334 4.154 1.00 7.58 ? 6 DC A C5 1 ATOM 123 C C6 . DC A 1 6 ? 31.310 36.364 3.862 1.00 7.28 ? 6 DC A C6 1 ATOM 124 P P . DA A 1 7 ? 30.748 41.815 5.233 1.00 12.50 ? 7 DA A P 1 ATOM 125 O OP1 . DA A 1 7 ? 31.143 43.167 5.712 1.00 13.31 ? 7 DA A OP1 1 ATOM 126 O OP2 . DA A 1 7 ? 30.200 40.812 6.184 1.00 12.61 ? 7 DA A OP2 1 ATOM 127 O "O5'" . DA A 1 7 ? 29.674 41.979 4.066 1.00 10.71 ? 7 DA A "O5'" 1 ATOM 128 C "C5'" . DA A 1 7 ? 29.871 42.930 3.021 1.00 10.74 ? 7 DA A "C5'" 1 ATOM 129 C "C4'" . DA A 1 7 ? 28.691 42.841 2.080 1.00 10.31 ? 7 DA A "C4'" 1 ATOM 130 O "O4'" . DA A 1 7 ? 28.595 41.503 1.539 1.00 10.39 ? 7 DA A "O4'" 1 ATOM 131 C "C3'" . DA A 1 7 ? 27.355 43.064 2.759 1.00 10.10 ? 7 DA A "C3'" 1 ATOM 132 O "O3'" . DA A 1 7 ? 27.099 44.453 2.799 1.00 11.17 ? 7 DA A "O3'" 1 ATOM 133 C "C2'" . DA A 1 7 ? 26.372 42.323 1.866 1.00 9.62 ? 7 DA A "C2'" 1 ATOM 134 C "C1'" . DA A 1 7 ? 27.228 41.153 1.415 1.00 8.62 ? 7 DA A "C1'" 1 ATOM 135 N N9 . DA A 1 7 ? 27.059 39.889 2.126 1.00 7.80 ? 7 DA A N9 1 ATOM 136 C C8 . DA A 1 7 ? 27.800 39.405 3.176 1.00 7.82 ? 7 DA A C8 1 ATOM 137 N N7 . DA A 1 7 ? 27.417 38.216 3.582 1.00 7.61 ? 7 DA A N7 1 ATOM 138 C C5 . DA A 1 7 ? 26.367 37.889 2.732 1.00 7.83 ? 7 DA A C5 1 ATOM 139 C C6 . DA A 1 7 ? 25.528 36.753 2.631 1.00 7.91 ? 7 DA A C6 1 ATOM 140 N N6 . DA A 1 7 ? 25.646 35.687 3.429 1.00 7.48 ? 7 DA A N6 1 ATOM 141 N N1 . DA A 1 7 ? 24.565 36.759 1.671 1.00 7.87 ? 7 DA A N1 1 ATOM 142 C C2 . DA A 1 7 ? 24.451 37.829 0.872 1.00 8.14 ? 7 DA A C2 1 ATOM 143 N N3 . DA A 1 7 ? 25.180 38.948 0.868 1.00 8.36 ? 7 DA A N3 1 ATOM 144 C C4 . DA A 1 7 ? 26.129 38.914 1.832 1.00 7.77 ? 7 DA A C4 1 ATOM 145 P P . DC A 1 8 ? 26.210 45.061 3.972 1.00 12.05 ? 8 DC A P 1 ATOM 146 O OP1 . DC A 1 8 ? 26.241 46.534 3.785 1.00 13.06 ? 8 DC A OP1 1 ATOM 147 O OP2 . DC A 1 8 ? 26.633 44.487 5.270 1.00 13.42 ? 8 DC A OP2 1 ATOM 148 O "O5'" . DC A 1 8 ? 24.739 44.550 3.635 1.00 10.98 ? 8 DC A "O5'" 1 ATOM 149 C "C5'" . DC A 1 8 ? 24.082 45.070 2.478 1.00 12.10 ? 8 DC A "C5'" 1 ATOM 150 C "C4'" . DC A 1 8 ? 22.739 44.413 2.247 1.00 12.17 ? 8 DC A "C4'" 1 ATOM 151 O "O4'" . DC A 1 8 ? 22.941 42.978 2.152 1.00 11.58 ? 8 DC A "O4'" 1 ATOM 152 C "C3'" . DC A 1 8 ? 21.697 44.661 3.337 1.00 13.10 ? 8 DC A "C3'" 1 ATOM 153 O "O3'" . DC A 1 8 ? 20.459 45.014 2.731 1.00 15.88 ? 8 DC A "O3'" 1 ATOM 154 C "C2'" . DC A 1 8 ? 21.588 43.326 4.064 1.00 12.36 ? 8 DC A "C2'" 1 ATOM 155 C "C1'" . DC A 1 8 ? 22.026 42.318 3.000 1.00 11.18 ? 8 DC A "C1'" 1 ATOM 156 N N1 . DC A 1 8 ? 22.660 41.111 3.609 1.00 10.63 ? 8 DC A N1 1 ATOM 157 C C2 . DC A 1 8 ? 22.120 39.835 3.369 1.00 10.15 ? 8 DC A C2 1 ATOM 158 O O2 . DC A 1 8 ? 21.129 39.713 2.636 1.00 10.11 ? 8 DC A O2 1 ATOM 159 N N3 . DC A 1 8 ? 22.703 38.758 3.962 1.00 9.75 ? 8 DC A N3 1 ATOM 160 C C4 . DC A 1 8 ? 23.775 38.913 4.752 1.00 9.68 ? 8 DC A C4 1 ATOM 161 N N4 . DC A 1 8 ? 24.308 37.819 5.314 1.00 9.22 ? 8 DC A N4 1 ATOM 162 C C5 . DC A 1 8 ? 24.348 40.201 4.997 1.00 9.76 ? 8 DC A C5 1 ATOM 163 C C6 . DC A 1 8 ? 23.760 41.254 4.418 1.00 10.05 ? 8 DC A C6 1 HETATM 164 MG MG . MG B 2 . ? 30.594 21.925 2.266 1.00 31.29 ? 11 MG A MG 1 HETATM 165 O O . HOH C 3 . ? 26.127 47.810 1.437 1.00 13.71 ? 21 HOH A O 1 HETATM 166 O O . HOH C 3 . ? 26.150 16.493 -0.750 1.00 14.32 ? 22 HOH A O 1 HETATM 167 O O . HOH C 3 . ? 20.901 38.797 -0.009 1.00 14.62 ? 23 HOH A O 1 HETATM 168 O O . HOH C 3 . ? 31.380 25.824 -2.831 1.00 12.64 ? 24 HOH A O 1 HETATM 169 O O . HOH C 3 . ? 30.001 31.134 4.980 1.00 22.12 ? 25 HOH A O 1 HETATM 170 O O . HOH C 3 . ? 30.445 24.463 6.091 1.00 21.24 ? 26 HOH A O 1 HETATM 171 O O . HOH C 3 . ? 28.446 19.637 -7.900 1.00 16.25 ? 27 HOH A O 1 HETATM 172 O O . HOH C 3 . ? 27.354 16.965 -8.501 1.00 13.17 ? 28 HOH A O 1 HETATM 173 O O . HOH C 3 . ? 17.937 38.605 0.026 1.00 20.65 ? 29 HOH A O 1 HETATM 174 O O . HOH C 3 . ? 22.697 39.803 -2.060 1.00 19.48 ? 30 HOH A O 1 HETATM 175 O O . HOH C 3 . ? 38.849 16.919 -2.726 1.00 16.74 ? 31 HOH A O 1 HETATM 176 O O . HOH C 3 . ? 30.500 24.434 -0.487 1.00 20.02 ? 32 HOH A O 1 HETATM 177 O O . HOH C 3 . ? 24.599 15.506 1.395 1.00 23.24 ? 33 HOH A O 1 HETATM 178 O O . HOH C 3 . ? 31.516 34.034 7.443 1.00 17.86 ? 34 HOH A O 1 HETATM 179 O O . HOH C 3 . ? 25.912 42.750 7.039 1.00 21.98 ? 35 HOH A O 1 HETATM 180 O O . HOH C 3 . ? 29.131 21.894 0.102 1.00 21.99 ? 36 HOH A O 1 HETATM 181 O O . HOH C 3 . ? 31.412 22.863 -6.608 1.00 25.02 ? 37 HOH A O 1 HETATM 182 O O . HOH C 3 . ? 28.058 16.946 2.594 1.00 23.32 ? 38 HOH A O 1 HETATM 183 O O . HOH C 3 . ? 36.191 22.681 8.803 1.00 29.16 ? 39 HOH A O 1 HETATM 184 O O . HOH C 3 . ? 31.869 31.924 8.993 1.00 24.12 ? 40 HOH A O 1 HETATM 185 O O . HOH C 3 . ? 33.958 24.660 -6.285 1.00 20.77 ? 41 HOH A O 1 HETATM 186 O O . HOH C 3 . ? 27.858 20.417 -3.417 1.00 25.85 ? 42 HOH A O 1 HETATM 187 O O . HOH C 3 . ? 27.643 40.706 7.127 1.00 23.54 ? 43 HOH A O 1 HETATM 188 O O . HOH C 3 . ? 33.491 35.652 10.465 1.00 21.88 ? 44 HOH A O 1 HETATM 189 O O . HOH C 3 . ? 29.641 24.046 3.599 1.00 23.74 ? 45 HOH A O 1 HETATM 190 O O . HOH C 3 . ? 28.934 33.312 6.511 1.00 32.35 ? 46 HOH A O 1 HETATM 191 O O . HOH C 3 . ? 27.987 36.709 5.986 1.00 22.00 ? 47 HOH A O 1 HETATM 192 O O . HOH C 3 . ? 31.394 15.811 5.287 1.00 20.11 ? 48 HOH A O 1 HETATM 193 O O . HOH C 3 . ? 28.330 29.985 2.990 1.00 26.87 ? 49 HOH A O 1 HETATM 194 O O . HOH C 3 . ? 30.282 37.852 7.579 1.00 28.99 ? 50 HOH A O 1 HETATM 195 O O . HOH C 3 . ? 29.414 28.245 1.159 1.00 25.65 ? 51 HOH A O 1 HETATM 196 O O . HOH C 3 . ? 28.847 15.069 4.238 1.00 25.43 ? 52 HOH A O 1 HETATM 197 O O . HOH C 3 . ? 28.955 45.075 6.394 1.00 30.65 ? 53 HOH A O 1 HETATM 198 O O . HOH C 3 . ? 32.407 28.590 7.481 1.00 30.58 ? 54 HOH A O 1 HETATM 199 O O . HOH C 3 . ? 37.313 21.663 6.220 1.00 33.94 ? 55 HOH A O 1 HETATM 200 O O . HOH C 3 . ? 31.532 25.157 10.542 1.00 40.65 ? 56 HOH A O 1 HETATM 201 O O . HOH C 3 . ? 35.859 36.172 1.345 1.00 8.40 ? 57 HOH A O 1 HETATM 202 O O . HOH C 3 . ? 23.926 41.410 -0.257 1.00 14.40 ? 58 HOH A O 1 # 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 DG 1 1 1 DG G A . n A 1 2 UMS 2 2 2 UMS UMS A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 US2 4 4 4 US2 USM A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C 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 MG 1 11 11 MG MG A . C 3 HOH 1 21 21 HOH HOH A . C 3 HOH 2 22 22 HOH HOH A . C 3 HOH 3 23 23 HOH HOH A . C 3 HOH 4 24 24 HOH HOH A . C 3 HOH 5 25 25 HOH HOH A . C 3 HOH 6 26 26 HOH HOH A . C 3 HOH 7 27 27 HOH HOH A . C 3 HOH 8 28 28 HOH HOH A . C 3 HOH 9 29 29 HOH HOH A . C 3 HOH 10 30 30 HOH HOH A . C 3 HOH 11 31 31 HOH HOH A . C 3 HOH 12 32 32 HOH HOH A . C 3 HOH 13 33 33 HOH HOH A . C 3 HOH 14 34 34 HOH HOH A . C 3 HOH 15 35 35 HOH HOH A . C 3 HOH 16 36 36 HOH HOH A . C 3 HOH 17 37 37 HOH HOH A . C 3 HOH 18 38 38 HOH HOH A . C 3 HOH 19 39 39 HOH HOH A . C 3 HOH 20 40 40 HOH HOH A . C 3 HOH 21 41 41 HOH HOH A . C 3 HOH 22 42 42 HOH HOH A . C 3 HOH 23 43 43 HOH HOH A . C 3 HOH 24 44 44 HOH HOH A . C 3 HOH 25 45 45 HOH HOH A . C 3 HOH 26 46 46 HOH HOH A . C 3 HOH 27 47 47 HOH HOH A . C 3 HOH 28 48 48 HOH HOH A . C 3 HOH 29 49 49 HOH HOH A . C 3 HOH 30 50 50 HOH HOH A . C 3 HOH 31 51 51 HOH HOH A . C 3 HOH 32 52 52 HOH HOH A . C 3 HOH 33 53 53 HOH HOH A . C 3 HOH 34 54 54 HOH HOH A . C 3 HOH 35 55 55 HOH HOH A . C 3 HOH 36 56 56 HOH HOH A . C 3 HOH 37 57 57 HOH HOH A . C 3 HOH 38 58 58 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A UMS 2 A UMS 2 ? DU ? 2 A US2 4 A US2 4 ? DU ? # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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)' 2240 ? 1 MORE -12 ? 1 'SSA (A^2)' 2810 ? # 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' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 OP2 ? A DG 3 ? A DG 3 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 36 ? 1_555 130.6 ? 2 OP2 ? A DG 3 ? A DG 3 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 45 ? 1_555 99.3 ? 3 O ? C HOH . ? A HOH 36 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 45 ? 1_555 102.8 ? # 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 2010-03-09 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-06-13 4 'Structure model' 1 3 2012-09-26 5 'Structure model' 1 4 2023-09-06 # _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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Database references' 4 4 'Structure model' 'Database references' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_initial_refinement_model 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_conn.conn_type_id' 4 5 'Structure model' '_struct_conn.id' 5 5 'Structure model' '_struct_conn.pdbx_dist_value' 6 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 16 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 18 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 19 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 20 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 31.5133 _pdbx_refine_tls.origin_y 30.4882 _pdbx_refine_tls.origin_z 2.3842 _pdbx_refine_tls.T[1][1] 0.0169 _pdbx_refine_tls.T[2][2] -0.0057 _pdbx_refine_tls.T[3][3] 0.0077 _pdbx_refine_tls.T[1][2] -0.0065 _pdbx_refine_tls.T[1][3] 0.0054 _pdbx_refine_tls.T[2][3] -0.0025 _pdbx_refine_tls.L[1][1] 0.1824 _pdbx_refine_tls.L[2][2] 1.3050 _pdbx_refine_tls.L[3][3] 0.2928 _pdbx_refine_tls.L[1][2] -0.3805 _pdbx_refine_tls.L[1][3] -0.0034 _pdbx_refine_tls.L[2][3] 0.2072 _pdbx_refine_tls.S[1][1] -0.0049 _pdbx_refine_tls.S[1][2] 0.0122 _pdbx_refine_tls.S[1][3] 0.0094 _pdbx_refine_tls.S[2][1] 0.1295 _pdbx_refine_tls.S[2][2] 0.0189 _pdbx_refine_tls.S[2][3] -0.0139 _pdbx_refine_tls.S[3][1] 0.0248 _pdbx_refine_tls.S[3][2] -0.0403 _pdbx_refine_tls.S[3][3] -0.0140 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 8 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHASES phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 DC _pdbx_validate_rmsd_angle.auth_seq_id_1 8 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 DC _pdbx_validate_rmsd_angle.auth_seq_id_2 8 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N1 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 DC _pdbx_validate_rmsd_angle.auth_seq_id_3 8 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 110.35 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 2.05 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.30 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 HOH O O N N 108 HOH H1 H N N 109 HOH H2 H N N 110 MG MG MG N N 111 UMS OP3 O N N 112 UMS P P N N 113 UMS OP1 O N N 114 UMS OP2 O N N 115 UMS "O5'" O N N 116 UMS "C5'" C N N 117 UMS "C4'" C N R 118 UMS "O4'" O N N 119 UMS "C3'" C N R 120 UMS "O3'" O N N 121 UMS "C2'" C N R 122 UMS "SE2'" SE N N 123 UMS "C1'" C N R 124 UMS "CA'" C N N 125 UMS N1 N N N 126 UMS C2 C N N 127 UMS O2 O N N 128 UMS N3 N N N 129 UMS C4 C N N 130 UMS O4 O N N 131 UMS C5 C N N 132 UMS C6 C N N 133 UMS HOP3 H N N 134 UMS HOP2 H N N 135 UMS "H5'" H N N 136 UMS "H5'2" H N N 137 UMS "H4'" H N N 138 UMS "H3'" H N N 139 UMS "HO3'" H N N 140 UMS "H2'" H N N 141 UMS "H1'" H N N 142 UMS "HA'" H N N 143 UMS "HA'2" H N N 144 UMS "HA'3" H N N 145 UMS H3 H N N 146 UMS H5 H N N 147 UMS H6 H N N 148 US2 P P N N 149 US2 N1 N N N 150 US2 C6 C N N 151 US2 C2 C N N 152 US2 O2 O N N 153 US2 N3 N N N 154 US2 C4 C N N 155 US2 O4 O N N 156 US2 C5 C N N 157 US2 S5 S N N 158 US2 C5A C N N 159 US2 "C1'" C N R 160 US2 "O4'" O N N 161 US2 "C4'" C N R 162 US2 "C3'" C N S 163 US2 "O3'" O N N 164 US2 "C2'" C N N 165 US2 "C5'" C N N 166 US2 "O5'" O N N 167 US2 O1P O N N 168 US2 O2P O N N 169 US2 H6 H N N 170 US2 HN3 H N N 171 US2 H15A H N N 172 US2 H25A H N N 173 US2 H35A H N N 174 US2 "H1'" H N N 175 US2 "H4'" H N N 176 US2 "H3'" H N N 177 US2 "HO3'" H N N 178 US2 "H12'" H N N 179 US2 "H22'" H N N 180 US2 "H15'" H N N 181 US2 "H25'" H N N 182 US2 O3P O N N 183 US2 HO2P H N N 184 US2 HO3P H N N 185 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 HOH O H1 sing N N 113 HOH O H2 sing N N 114 UMS OP3 P sing N N 115 UMS OP3 HOP3 sing N N 116 UMS P OP1 doub N N 117 UMS P OP2 sing N N 118 UMS P "O5'" sing N N 119 UMS OP2 HOP2 sing N N 120 UMS "O5'" "C5'" sing N N 121 UMS "C5'" "C4'" sing N N 122 UMS "C5'" "H5'" sing N N 123 UMS "C5'" "H5'2" sing N N 124 UMS "C4'" "O4'" sing N N 125 UMS "C4'" "C3'" sing N N 126 UMS "C4'" "H4'" sing N N 127 UMS "O4'" "C1'" sing N N 128 UMS "C3'" "O3'" sing N N 129 UMS "C3'" "C2'" sing N N 130 UMS "C3'" "H3'" sing N N 131 UMS "O3'" "HO3'" sing N N 132 UMS "C2'" "SE2'" sing N N 133 UMS "C2'" "C1'" sing N N 134 UMS "C2'" "H2'" sing N N 135 UMS "SE2'" "CA'" sing N N 136 UMS "C1'" N1 sing N N 137 UMS "C1'" "H1'" sing N N 138 UMS "CA'" "HA'" sing N N 139 UMS "CA'" "HA'2" sing N N 140 UMS "CA'" "HA'3" sing N N 141 UMS N1 C2 sing N N 142 UMS N1 C6 sing N N 143 UMS C2 O2 doub N N 144 UMS C2 N3 sing N N 145 UMS N3 C4 sing N N 146 UMS N3 H3 sing N N 147 UMS C4 O4 doub N N 148 UMS C4 C5 sing N N 149 UMS C5 C6 doub N N 150 UMS C5 H5 sing N N 151 UMS C6 H6 sing N N 152 US2 P O2P sing N N 153 US2 N1 C6 sing N N 154 US2 N1 "C1'" sing N N 155 US2 C6 H6 sing N N 156 US2 C2 N1 sing N N 157 US2 O2 C2 doub N N 158 US2 N3 C4 sing N N 159 US2 N3 C2 sing N N 160 US2 N3 HN3 sing N N 161 US2 C4 C5 sing N N 162 US2 O4 C4 doub N N 163 US2 C5 S5 sing N N 164 US2 C5 C6 doub N N 165 US2 S5 C5A sing N N 166 US2 C5A H15A sing N N 167 US2 C5A H25A sing N N 168 US2 C5A H35A sing N N 169 US2 "C1'" "O4'" sing N N 170 US2 "C1'" "C2'" sing N N 171 US2 "C1'" "H1'" sing N N 172 US2 "O4'" "C4'" sing N N 173 US2 "C4'" "C3'" sing N N 174 US2 "C4'" "C5'" sing N N 175 US2 "C4'" "H4'" sing N N 176 US2 "C3'" "O3'" sing N N 177 US2 "C3'" "H3'" sing N N 178 US2 "O3'" "HO3'" sing N N 179 US2 "C2'" "C3'" sing N N 180 US2 "C2'" "H12'" sing N N 181 US2 "C2'" "H22'" sing N N 182 US2 "C5'" "H15'" sing N N 183 US2 "C5'" "H25'" sing N N 184 US2 "O5'" "C5'" sing N N 185 US2 "O5'" P sing N N 186 US2 O1P P doub N N 187 US2 P O3P sing N N 188 US2 O2P HO2P sing N N 189 US2 O3P HO3P sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3IKI 'a-form double helix' 3IKI 'internal loop' # 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 DG 1 1_555 A DC 8 7_555 -0.350 -0.123 -0.340 -19.369 -13.573 -2.360 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A UMS 2 1_555 A DA 7 7_555 -0.037 -0.094 0.142 -5.623 -11.049 2.831 2 A_UMS2:DA7_A A 2 ? A 7 ? 20 1 1 A DG 3 1_555 A DC 6 7_555 -0.255 -0.231 0.247 -4.548 -13.598 -0.012 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A DG 1 1_555 A DC 8 1_555 -0.350 -0.123 -0.340 -19.369 -13.573 -2.360 4 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A UMS 2 1_555 A DA 7 1_555 -0.037 -0.094 0.142 -5.623 -11.049 2.831 5 A_UMS2:DA7_A A 2 ? A 7 ? 20 1 1 A DG 3 1_555 A DC 6 1_555 -0.255 -0.231 0.247 -4.548 -13.598 -0.012 6 A_DG3:DC6_A A 3 ? A 6 ? 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 DG 1 1_555 A DC 8 7_555 A UMS 2 1_555 A DA 7 7_555 0.539 -0.832 3.040 -2.846 13.421 30.709 -3.364 -1.341 2.419 23.902 5.068 33.567 1 AA_DG1UMS2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A UMS 2 1_555 A DA 7 7_555 A DG 3 1_555 A DC 6 7_555 0.694 -1.478 3.075 0.004 11.978 28.509 -4.762 -1.303 2.283 23.076 -0.008 30.875 2 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 1 1_555 A DC 8 1_555 A UMS 2 1_555 A DA 7 1_555 0.539 -0.832 3.040 -2.846 13.421 30.709 -3.364 -1.341 2.419 23.902 5.068 33.567 3 AA_DG1UMS2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A UMS 2 1_555 A DA 7 1_555 A DG 3 1_555 A DC 6 1_555 0.694 -1.478 3.075 0.004 11.978 28.509 -4.762 -1.303 2.283 23.076 -0.008 30.875 4 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 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 1DNS _pdbx_initial_refinement_model.details ? #