data_3LTR # _entry.id 3LTR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3LTR pdb_00003ltr 10.2210/pdb3ltr/pdb NDB NA0451 ? ? RCSB RCSB057719 ? ? WWPDB D_1000057719 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3IJK . unspecified PDB 3LTU . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3LTR _pdbx_database_status.recvd_initial_deposition_date 2010-02-16 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.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 3LTR _cell.length_a 42.992 _cell.length_b 42.992 _cell.length_c 23.822 _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 3LTR _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*(T5O)P*AP*CP*AP*C)-3'" 2521.577 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 42 ? ? ? ? # _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)(T5O)(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 T5O 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 synthesizer' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3LTR _struct_ref.pdbx_db_accession 3LTR _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 3LTR _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 3LTR _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 T5O 'DNA linking' n ;2'-deoxy-5-methoxyuridine 5'-(dihydrogen phosphate) ; "5-methoxy-2'-deoxyuridine-5'-phosphate" 'C10 H15 N2 O9 P' 338.208 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 # _exptl.entry_id 3LTR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.65 _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 6.0 _exptl_crystal_grow.pdbx_details ;10% v / v MPD, 40 mM Na Cacodylate pH 6.0,12 mM Spermine tetra-HCl, 80 mM Sodium 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 210' _diffrn_detector.pdbx_collection_date 2009-07-15 _diffrn_detector.details Mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111)' _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 X12C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X12C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 3LTR _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.30 _reflns.number_obs 5389 _reflns.number_all 5922 _reflns.percent_possible_obs 91 _reflns.pdbx_Rmerge_I_obs 0.060 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 36.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 21.5 _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 1.30 _reflns_shell.d_res_low 1.35 _reflns_shell.percent_possible_all 58.1 _reflns_shell.Rmerge_I_obs 0.381 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.pdbx_redundancy 5.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 275 _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 3LTR _refine.ls_number_reflns_obs 5117 _refine.ls_number_reflns_all 5612 _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 30.40 _refine.ls_d_res_high 1.30 _refine.ls_percent_reflns_obs 91.05 _refine.ls_R_factor_obs 0.20260 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20164 _refine.ls_R_factor_R_free 0.22240 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 246 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.955 _refine.B_iso_mean 13.098 _refine.aniso_B[1][1] -0.25 _refine.aniso_B[2][2] -0.25 _refine.aniso_B[3][3] 0.50 _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 0.060 _refine.pdbx_overall_ESU_R_Free 0.061 _refine.overall_SU_ML 0.041 _refine.overall_SU_B 1.984 _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 3LTR _refine_analyze.Luzzati_coordinate_error_obs 0.060 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.061 _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 42 _refine_hist.number_atoms_total 206 _refine_hist.d_res_high 1.30 _refine_hist.d_res_low 30.40 # 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 0.006 0.021 ? 182 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.251 3.000 ? 278 'X-RAY DIFFRACTION' ? r_chiral_restr 0.060 0.200 ? 32 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.020 ? 83 'X-RAY DIFFRACTION' ? r_nbd_refined 0.158 0.200 ? 59 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.276 0.200 ? 108 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.151 0.200 ? 28 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.187 0.200 ? 19 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.088 0.200 ? 15 'X-RAY DIFFRACTION' ? r_scbond_it 0.895 3.000 ? 261 'X-RAY DIFFRACTION' ? r_scangle_it 1.318 4.500 ? 278 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.30 _refine_ls_shell.d_res_low 1.332 _refine_ls_shell.number_reflns_R_work 174 _refine_ls_shell.R_factor_R_work 0.396 _refine_ls_shell.percent_reflns_obs 43.90 _refine_ls_shell.R_factor_R_free 0.423 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _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 3LTR _struct.title '5-OMe-dU containing DNA 8mer' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3LTR _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;DNA, oligonucleotide, 2'-SeMe, 5-OMe, selenium, 5-methoxy-uridine ; # 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 ? ? metalc1 metalc ? ? A UMS 2 O4 ? ? ? 1_555 B MG . MG ? ? A UMS 2 A MG 11 1_555 ? ? ? ? ? ? ? 2.895 ? ? metalc2 metalc ? ? A DG 3 O6 ? ? ? 1_555 B MG . MG ? ? A DG 3 A MG 11 1_555 ? ? ? ? ? ? ? 2.927 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 11 A HOH 120 1_555 ? ? ? ? ? ? ? 2.631 ? ? 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 T5O 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A T5O 4 A DA 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A T5O 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A T5O 4 A DA 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A T5O 4 N3 ? ? A DA 5 A T5O 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A T5O 4 O4 ? ? A DA 5 A T5O 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A UMS 2 N3 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A UMS 2 O4 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 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 3 _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 3 UMS A 2 ? UMS A 2 . ? 1_555 ? 2 AC1 3 DG A 3 ? DG A 3 . ? 1_555 ? 3 AC1 3 HOH C . ? HOH A 120 . ? 1_555 ? # _database_PDB_matrix.entry_id 3LTR _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 3LTR _atom_sites.fract_transf_matrix[1][1] 0.023260 _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] 0.023260 _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] 0.041978 _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 SE # 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 T5O 4 4 4 T5O T5O 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 1 101 101 HOH HOH A . C 3 HOH 2 102 102 HOH HOH A . C 3 HOH 3 103 103 HOH HOH A . C 3 HOH 4 104 104 HOH HOH A . C 3 HOH 5 105 105 HOH HOH A . C 3 HOH 6 106 106 HOH HOH A . C 3 HOH 7 107 107 HOH HOH A . C 3 HOH 8 108 108 HOH HOH A . C 3 HOH 9 109 109 HOH HOH A . C 3 HOH 10 110 110 HOH HOH A . C 3 HOH 11 111 111 HOH HOH A . C 3 HOH 12 112 112 HOH HOH A . C 3 HOH 13 113 113 HOH HOH A . C 3 HOH 14 114 114 HOH HOH A . C 3 HOH 15 115 115 HOH HOH A . C 3 HOH 16 116 116 HOH HOH A . C 3 HOH 17 117 117 HOH HOH A . C 3 HOH 18 118 118 HOH HOH A . C 3 HOH 19 119 119 HOH HOH A . C 3 HOH 20 120 120 HOH HOH A . C 3 HOH 21 121 121 HOH HOH A . C 3 HOH 22 122 122 HOH HOH A . C 3 HOH 23 123 123 HOH HOH A . C 3 HOH 24 124 124 HOH HOH A . C 3 HOH 25 125 125 HOH HOH A . C 3 HOH 26 126 126 HOH HOH A . C 3 HOH 27 127 127 HOH HOH A . C 3 HOH 28 128 128 HOH HOH A . C 3 HOH 29 129 129 HOH HOH A . C 3 HOH 30 130 130 HOH HOH A . C 3 HOH 31 131 131 HOH HOH A . C 3 HOH 32 132 132 HOH HOH A . C 3 HOH 33 133 133 HOH HOH A . C 3 HOH 34 134 134 HOH HOH A . C 3 HOH 35 135 135 HOH HOH A . C 3 HOH 36 136 136 HOH HOH A . C 3 HOH 37 137 137 HOH HOH A . C 3 HOH 38 138 138 HOH HOH A . C 3 HOH 39 139 139 HOH HOH A . C 3 HOH 40 140 140 HOH HOH A . C 3 HOH 41 141 141 HOH HOH A . C 3 HOH 42 142 142 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 T5O 4 A T5O 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)' 2250 ? 1 MORE -11 ? 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 O4 ? A UMS 2 ? A UMS 2 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O6 ? A DG 3 ? A DG 3 ? 1_555 70.7 ? 2 O4 ? A UMS 2 ? A UMS 2 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 120 ? 1_555 80.2 ? 3 O6 ? A DG 3 ? A DG 3 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 120 ? 1_555 89.7 ? # 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' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 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' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.value' 16 5 'Structure model' '_struct_conn.pdbx_dist_value' 17 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 18 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 25 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 29 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 30 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 31 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 11.4486 _pdbx_refine_tls.origin_y 12.5770 _pdbx_refine_tls.origin_z 2.4137 _pdbx_refine_tls.T[1][1] 0.0704 _pdbx_refine_tls.T[2][2] 0.0549 _pdbx_refine_tls.T[3][3] 0.0671 _pdbx_refine_tls.T[1][2] -0.0063 _pdbx_refine_tls.T[1][3] -0.0152 _pdbx_refine_tls.T[2][3] 0.0005 _pdbx_refine_tls.L[1][1] 0.9159 _pdbx_refine_tls.L[2][2] 3.9115 _pdbx_refine_tls.L[3][3] 0.4272 _pdbx_refine_tls.L[1][2] -1.0744 _pdbx_refine_tls.L[1][3] 0.1786 _pdbx_refine_tls.L[2][3] -0.8824 _pdbx_refine_tls.S[1][1] -0.0595 _pdbx_refine_tls.S[1][2] -0.0351 _pdbx_refine_tls.S[1][3] -0.0042 _pdbx_refine_tls.S[2][1] 0.2754 _pdbx_refine_tls.S[2][2] 0.0474 _pdbx_refine_tls.S[2][3] -0.0337 _pdbx_refine_tls.S[3][1] -0.0654 _pdbx_refine_tls.S[3][2] 0.0470 _pdbx_refine_tls.S[3][3] 0.0120 # _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 DG _pdbx_validate_rmsd_angle.auth_seq_id_1 3 _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 DG _pdbx_validate_rmsd_angle.auth_seq_id_2 3 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 DG _pdbx_validate_rmsd_angle.auth_seq_id_3 3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 110.59 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 2.29 _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 T5O P P N N 112 T5O N1 N N N 113 T5O C2 C N N 114 T5O O2 O N N 115 T5O N3 N N N 116 T5O C4 C N N 117 T5O O4 O N N 118 T5O C5 C N N 119 T5O O5 O N N 120 T5O C6 C N N 121 T5O "C1'" C N R 122 T5O OP3 O N N 123 T5O "C2'" C N N 124 T5O OP2 O N N 125 T5O "C3'" C N S 126 T5O "O3'" O N N 127 T5O "C4'" C N R 128 T5O "O4'" O N N 129 T5O "C5'" C N N 130 T5O "O5'" O N N 131 T5O C7 C N N 132 T5O H6 H N N 133 T5O "H1'" H N N 134 T5O HOP3 H N N 135 T5O "H2'" H N N 136 T5O "H2'A" H N N 137 T5O HOP2 H N N 138 T5O "H3'" H N N 139 T5O "HO3'" H N N 140 T5O "H4'" H N N 141 T5O "H5'" H N N 142 T5O "H5'A" H N N 143 T5O HC7 H N N 144 T5O HC7A H N N 145 T5O HC7B H N N 146 T5O HN3 H N N 147 T5O OP1 O N N 148 UMS OP3 O N N 149 UMS P P N N 150 UMS OP1 O N N 151 UMS OP2 O N N 152 UMS "O5'" O N N 153 UMS "C5'" C N N 154 UMS "C4'" C N R 155 UMS "O4'" O N N 156 UMS "C3'" C N R 157 UMS "O3'" O N N 158 UMS "C2'" C N R 159 UMS "SE2'" SE N N 160 UMS "C1'" C N R 161 UMS "CA'" C N N 162 UMS N1 N N N 163 UMS C2 C N N 164 UMS O2 O N N 165 UMS N3 N N N 166 UMS C4 C N N 167 UMS O4 O N N 168 UMS C5 C N N 169 UMS C6 C N N 170 UMS HOP3 H N N 171 UMS HOP2 H N N 172 UMS "H5'" H N N 173 UMS "H5'2" H N N 174 UMS "H4'" H N N 175 UMS "H3'" H N N 176 UMS "HO3'" H N N 177 UMS "H2'" H N N 178 UMS "H1'" H N N 179 UMS "HA'" H N N 180 UMS "HA'2" H N N 181 UMS "HA'3" H N N 182 UMS H3 H N N 183 UMS H5 H N N 184 UMS H6 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 T5O P OP3 sing N N 115 T5O N1 C6 sing N N 116 T5O N1 "C1'" sing N N 117 T5O C2 N1 sing N N 118 T5O O2 C2 doub N N 119 T5O N3 C2 sing N N 120 T5O N3 C4 sing N N 121 T5O N3 HN3 sing N N 122 T5O C4 C5 sing N N 123 T5O O4 C4 doub N N 124 T5O C5 O5 sing N N 125 T5O C5 C6 doub N N 126 T5O O5 C7 sing N N 127 T5O C6 H6 sing N N 128 T5O "C1'" "O4'" sing N N 129 T5O "C1'" "C2'" sing N N 130 T5O "C1'" "H1'" sing N N 131 T5O OP3 HOP3 sing N N 132 T5O "C2'" "C3'" sing N N 133 T5O "C2'" "H2'" sing N N 134 T5O "C2'" "H2'A" sing N N 135 T5O OP2 P sing N N 136 T5O OP2 HOP2 sing N N 137 T5O "C3'" "O3'" sing N N 138 T5O "C3'" "H3'" sing N N 139 T5O "O3'" "HO3'" sing N N 140 T5O "C4'" "C3'" sing N N 141 T5O "C4'" "C5'" sing N N 142 T5O "C4'" "H4'" sing N N 143 T5O "O4'" "C4'" sing N N 144 T5O "C5'" "H5'" sing N N 145 T5O "C5'" "H5'A" sing N N 146 T5O "O5'" P sing N N 147 T5O "O5'" "C5'" sing N N 148 T5O C7 HC7 sing N N 149 T5O C7 HC7A sing N N 150 T5O C7 HC7B sing N N 151 T5O P OP1 doub N N 152 UMS OP3 P sing N N 153 UMS OP3 HOP3 sing N N 154 UMS P OP1 doub N N 155 UMS P OP2 sing N N 156 UMS P "O5'" sing N N 157 UMS OP2 HOP2 sing N N 158 UMS "O5'" "C5'" sing N N 159 UMS "C5'" "C4'" sing N N 160 UMS "C5'" "H5'" sing N N 161 UMS "C5'" "H5'2" sing N N 162 UMS "C4'" "O4'" sing N N 163 UMS "C4'" "C3'" sing N N 164 UMS "C4'" "H4'" sing N N 165 UMS "O4'" "C1'" sing N N 166 UMS "C3'" "O3'" sing N N 167 UMS "C3'" "C2'" sing N N 168 UMS "C3'" "H3'" sing N N 169 UMS "O3'" "HO3'" sing N N 170 UMS "C2'" "SE2'" sing N N 171 UMS "C2'" "C1'" sing N N 172 UMS "C2'" "H2'" sing N N 173 UMS "SE2'" "CA'" sing N N 174 UMS "C1'" N1 sing N N 175 UMS "C1'" "H1'" sing N N 176 UMS "CA'" "HA'" sing N N 177 UMS "CA'" "HA'2" sing N N 178 UMS "CA'" "HA'3" sing N N 179 UMS N1 C2 sing N N 180 UMS N1 C6 sing N N 181 UMS C2 O2 doub N N 182 UMS C2 N3 sing N N 183 UMS N3 C4 sing N N 184 UMS N3 H3 sing N N 185 UMS C4 O4 doub N N 186 UMS C4 C5 sing N N 187 UMS C5 C6 doub N N 188 UMS C5 H5 sing N N 189 UMS C6 H6 sing N N 190 # _ndb_struct_conf_na.entry_id 3LTR _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 A DC 8 7_555 -0.350 -0.108 -0.316 -20.419 -13.058 -1.533 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A UMS 2 1_555 A DA 7 7_555 -0.034 -0.070 0.225 -9.472 -11.128 2.460 2 A_UMS2:DA7_A A 2 ? A 7 ? 20 1 1 A DG 3 1_555 A DC 6 7_555 -0.269 -0.190 0.293 -4.456 -12.941 0.248 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A T5O 4 1_555 A DA 5 7_555 -0.167 -0.176 0.306 -4.517 -11.497 -5.746 4 A_T5O4:DA5_A A 4 ? A 5 ? 20 1 1 A DA 5 1_555 A T5O 4 7_555 0.167 -0.176 0.306 4.517 -11.497 -5.746 5 A_DA5:T5O4_A A 5 ? A 4 ? 20 1 1 A DC 6 1_555 A DG 3 7_555 0.269 -0.190 0.293 4.456 -12.941 0.248 6 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DA 7 1_555 A UMS 2 7_555 0.034 -0.070 0.225 9.472 -11.128 2.460 7 A_DA7:UMS2_A A 7 ? A 2 ? 20 1 1 A DC 8 1_555 A DG 1 7_555 0.350 -0.108 -0.316 20.419 -13.058 -1.533 8 A_DC8:DG1_A A 8 ? 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 DG 1 1_555 A DC 8 7_555 A UMS 2 1_555 A DA 7 7_555 0.449 -0.894 3.140 -2.979 12.900 31.118 -3.431 -1.210 2.529 22.797 5.264 33.754 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 0.750 -1.468 2.963 1.314 11.804 28.972 -4.573 -1.185 2.239 22.440 -2.499 31.264 2 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 7_555 A T5O 4 1_555 A DA 5 7_555 -0.163 -1.877 3.311 1.874 -0.170 34.214 -3.158 0.574 3.306 -0.288 -3.182 34.264 3 AA_DG3T5O4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A T5O 4 1_555 A DA 5 7_555 A DA 5 1_555 A T5O 4 7_555 0.000 -1.566 2.955 0.000 5.975 29.994 -3.986 0.000 2.601 11.402 0.000 30.570 4 AA_T5O4DA5:T5O4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A T5O 4 7_555 A DC 6 1_555 A DG 3 7_555 0.163 -1.877 3.311 -1.874 -0.170 34.214 -3.158 -0.574 3.306 -0.288 3.182 34.264 5 AA_DA5DC6:DG3T5O4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 7_555 A DA 7 1_555 A UMS 2 7_555 -0.750 -1.468 2.963 -1.315 11.804 28.972 -4.573 1.185 2.239 22.440 2.499 31.264 6 AA_DC6DA7:UMS2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A DA 7 1_555 A UMS 2 7_555 A DC 8 1_555 A DG 1 7_555 -0.449 -0.894 3.140 2.979 12.900 31.118 -3.431 1.210 2.529 22.797 -5.264 33.754 7 AA_DA7DC8:DG1UMS2_AA A 7 ? A 2 ? A 8 ? A 1 ? # 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 ? #