data_3GJL # _entry.id 3GJL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 3GJL pdb_00003gjl 10.2210/pdb3gjl/pdb NDB BD0112 ? ? RCSB RCSB051941 ? ? WWPDB D_1000051941 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3GJH . unspecified PDB 3GJJ . unspecified PDB 3GJK . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3GJL _pdbx_database_status.recvd_initial_deposition_date 2009-03-09 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Takenaka, A.' 1 'Juan, E.C.M.' 2 'Shimizu, S.' 3 'Haraguchi, T.' 4 'Xiao, M.' 5 'Kurose, T.' 6 'Ohkubo, A.' 7 'Sekine, M.' 8 'Shibata, T.' 9 'Millington, C.L.' 10 'Williams, D.M.' 11 # _citation.id primary _citation.title ;Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one ; _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Takenaka, A.' 1 ? primary 'Juan, E.C.M.' 2 ? primary 'Shimizu, S.' 3 ? primary 'Haraguchi, T.' 4 ? primary 'Xiao, M.' 5 ? primary 'Kurose, T.' 6 ? primary 'Ohkubo, A.' 7 ? primary 'Sekine, M.' 8 ? primary 'Shibata, T.' 9 ? primary 'Millington, C.M.' 10 ? primary 'William, D.M.' 11 ? # _cell.entry_id 3GJL _cell.length_a 26.477 _cell.length_b 26.477 _cell.length_c 98.958 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 3GJL _symmetry.space_group_name_H-M 'P 32 1 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*CP*GP*CP*GP*AP*A)-3'" 1818.231 1 ? ? ? ? 2 polymer syn "5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3'" 1838.251 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 42 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DG)(DC)(DG)(DA)(DA)' CGCGAA A ? 2 polydeoxyribonucleotide no yes '(DT)(DT)(B7C)(DG)(DC)(DG)' TTXGCG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 2 1 DT n 2 2 DT n 2 3 B7C n 2 4 DG n 2 5 DC n 2 6 DG n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 3GJL 3GJL 1 ? ? ? 2 PDB 3GJL 3GJL 2 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3GJL A 1 ? 6 ? 3GJL 1 ? 6 ? 1 6 2 2 3GJL B 1 ? 6 ? 3GJL 7 ? 12 ? 7 12 # 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 B7C 'DNA linking' n '3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one' ? 'C12 H16 N3 O7 P' 345.245 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # _exptl.entry_id 3GJL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.74 _exptl_crystal.density_percent_sol 55.08 _exptl_crystal.description ? # _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 ;25mM Sodium cacodylate (pH7.0), 6mM Spermine, tetrahydrochloride, 50mM NaCl, 5% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 270' _diffrn_detector.pdbx_collection_date 2006-12-17 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE AR-NW12A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline AR-NW12A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 3GJL _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.92 _reflns.number_obs 3233 _reflns.number_all 3233 _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.064 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 91.6 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 20.7 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.92 _reflns_shell.d_res_low 1.99 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.291 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 15.9 _reflns_shell.pdbx_redundancy 21.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3GJL _refine.ls_number_reflns_obs 3165 _refine.ls_number_reflns_all 3205 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 22.34 _refine.ls_d_res_high 1.92 _refine.ls_percent_reflns_obs 99.3 _refine.ls_R_factor_obs 0.227 _refine.ls_R_factor_all 0.227 _refine.ls_R_factor_R_work 0.225 _refine.ls_R_factor_R_free 0.264 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.4 _refine.ls_number_reflns_R_free 139 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.952 _refine.correlation_coeff_Fo_to_Fc_free 0.937 _refine.B_iso_mean 25.343 _refine.aniso_B[1][1] -0.06 _refine.aniso_B[2][2] -0.06 _refine.aniso_B[3][3] 0.09 _refine.aniso_B[1][2] -0.03 _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 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 1ehv _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model isotropic _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.162 _refine.pdbx_overall_ESU_R_Free 0.151 _refine.overall_SU_ML 0.094 _refine.overall_SU_B 3.325 _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 246 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 42 _refine_hist.number_atoms_total 289 _refine_hist.d_res_high 1.92 _refine_hist.d_res_low 22.34 # 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 0.013 0.021 ? 276 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.209 3.000 ? 423 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.086 0.200 ? 46 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.011 0.020 ? 127 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.154 0.200 ? 71 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.312 0.200 ? 163 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.186 0.200 ? 12 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.443 0.200 ? 1 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.447 0.200 ? 27 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.062 0.200 ? 10 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined 0.457 0.200 ? 3 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 1.798 3.000 ? 333 'X-RAY DIFFRACTION' ? r_scangle_it 2.407 4.500 ? 423 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.921 _refine_ls_shell.d_res_low 1.971 _refine_ls_shell.number_reflns_R_work 206 _refine_ls_shell.R_factor_R_work 0.255 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.413 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 11 _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 3GJL _struct.title 'crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GJL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, duplex, bicyclic cytosine, 7, 8-dihydropyridol[2, 3-d]pyrimidin-2-one' # 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 ? D N N 4 ? E N N 4 ? # _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 ? B DT 2 "O3'" ? ? ? 1_555 B B7C 3 P ? ? B DT 8 B B7C 9 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale2 covale both ? B B7C 3 "O3'" ? ? ? 1_555 B DG 4 P ? ? B B7C 9 B DG 10 1_555 ? ? ? ? ? ? ? 1.606 ? ? metalc1 metalc ? ? C NA . NA ? ? ? 1_555 B DG 6 OP1 ? ? B NA 1 B DG 12 1_555 ? ? ? ? ? ? ? 1.906 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 1 O4 ? ? A DA 6 B DT 7 1_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 B _struct_site.pdbx_auth_comp_id NA _struct_site.pdbx_auth_seq_id 1 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE NA B 1' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DC A 1 ? DC A 1 . ? 6_456 ? 2 AC1 6 DC A 1 ? DC A 1 . ? 1_455 ? 3 AC1 6 DC B 5 ? DC B 11 . ? 1_555 ? 4 AC1 6 DC B 5 ? DC B 11 . ? 6_566 ? 5 AC1 6 DG B 6 ? DG B 12 . ? 1_555 ? 6 AC1 6 DG B 6 ? DG B 12 . ? 6_566 ? # _database_PDB_matrix.entry_id 3GJL _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 3GJL _atom_sites.fract_transf_matrix[1][1] 0.037769 _atom_sites.fract_transf_matrix[1][2] 0.021806 _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] 0.043611 _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] 0.010105 _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 N NA O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n B 2 1 DT 1 7 7 DT DT B . n B 2 2 DT 2 8 8 DT DT B . n B 2 3 B7C 3 9 9 B7C B7C B . n B 2 4 DG 4 10 10 DG DG B . n B 2 5 DC 5 11 11 DC DC B . n B 2 6 DG 6 12 12 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 NA 1 1 1 NA NA B . D 4 HOH 1 7 1 HOH HOH A . D 4 HOH 2 8 8 HOH HOH A . D 4 HOH 3 9 9 HOH HOH A . D 4 HOH 4 10 2 HOH HOH A . D 4 HOH 5 11 11 HOH HOH A . D 4 HOH 6 12 12 HOH HOH A . D 4 HOH 7 16 16 HOH HOH A . D 4 HOH 8 17 6 HOH HOH A . D 4 HOH 9 27 27 HOH HOH A . D 4 HOH 10 28 28 HOH HOH A . D 4 HOH 11 29 29 HOH HOH A . D 4 HOH 12 30 30 HOH HOH A . D 4 HOH 13 31 31 HOH HOH A . D 4 HOH 14 34 34 HOH HOH A . D 4 HOH 15 35 35 HOH HOH A . D 4 HOH 16 36 36 HOH HOH A . D 4 HOH 17 37 37 HOH HOH A . E 4 HOH 1 3 3 HOH HOH B . E 4 HOH 2 4 4 HOH HOH B . E 4 HOH 3 5 5 HOH HOH B . E 4 HOH 4 13 13 HOH HOH B . E 4 HOH 5 14 14 HOH HOH B . E 4 HOH 6 15 15 HOH HOH B . E 4 HOH 7 16 7 HOH HOH B . E 4 HOH 8 17 17 HOH HOH B . E 4 HOH 9 18 18 HOH HOH B . E 4 HOH 10 19 19 HOH HOH B . E 4 HOH 11 20 20 HOH HOH B . E 4 HOH 12 21 21 HOH HOH B . E 4 HOH 13 22 22 HOH HOH B . E 4 HOH 14 23 23 HOH HOH B . E 4 HOH 15 24 24 HOH HOH B . E 4 HOH 16 25 25 HOH HOH B . E 4 HOH 17 26 26 HOH HOH B . E 4 HOH 18 27 10 HOH HOH B . E 4 HOH 19 32 32 HOH HOH B . E 4 HOH 20 33 33 HOH HOH B . E 4 HOH 21 38 38 HOH HOH B . E 4 HOH 22 39 39 HOH HOH B . E 4 HOH 23 40 40 HOH HOH B . E 4 HOH 24 41 41 HOH HOH B . E 4 HOH 25 42 42 HOH HOH B . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id B7C _pdbx_struct_mod_residue.label_seq_id 3 _pdbx_struct_mod_residue.auth_asym_id B _pdbx_struct_mod_residue.auth_comp_id B7C _pdbx_struct_mod_residue.auth_seq_id 9 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DC _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 460 ? 1 MORE -3 ? 1 'SSA (A^2)' 2660 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id NA _pdbx_struct_special_symmetry.auth_seq_id 1 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id NA _pdbx_struct_special_symmetry.label_seq_id . # 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 2010-03-31 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 5 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 6 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 7 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 11 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 13 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 14 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 17 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 18 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 AMoRE phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O3'" _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DA _pdbx_validate_symm_contact.auth_seq_id_1 6 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 P _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 DT _pdbx_validate_symm_contact.auth_seq_id_2 7 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 5_555 _pdbx_validate_symm_contact.dist 1.65 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 101.49 108.00 -6.51 0.70 N 2 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 110.31 108.30 2.01 0.30 N 3 1 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 110.84 108.30 2.54 0.30 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 B7C OP3 O N N 1 B7C P P N N 2 B7C OP1 O N N 3 B7C OP2 O N N 4 B7C "O5'" O N N 5 B7C N1 N N N 6 B7C C6 C N N 7 B7C C2 C N N 8 B7C O2 O N N 9 B7C N3 N N N 10 B7C C4 C N N 11 B7C N4 N N N 12 B7C C5 C N N 13 B7C C7 C N N 14 B7C C8 C N N 15 B7C C9 C N N 16 B7C "C2'" C N N 17 B7C "C5'" C N N 18 B7C "C4'" C N R 19 B7C "O4'" O N N 20 B7C "C1'" C N R 21 B7C "C3'" C N S 22 B7C "O3'" O N N 23 B7C HOP3 H N N 24 B7C HOP1 H N N 25 B7C H6 H N N 26 B7C HN4 H N N 27 B7C H7 H N N 28 B7C H8 H N N 29 B7C H9 H N N 30 B7C H9A H N N 31 B7C "H2'" H N N 32 B7C "H2'A" H N N 33 B7C "H5'" H N N 34 B7C "H5'A" H N N 35 B7C "H4'" H N N 36 B7C "H1'" H N N 37 B7C "H3'" H N N 38 B7C "HO3'" H N N 39 DA OP3 O N N 40 DA P P N N 41 DA OP1 O N N 42 DA OP2 O N N 43 DA "O5'" O N N 44 DA "C5'" C N N 45 DA "C4'" C N R 46 DA "O4'" O N N 47 DA "C3'" C N S 48 DA "O3'" O N N 49 DA "C2'" C N N 50 DA "C1'" C N R 51 DA N9 N Y N 52 DA C8 C Y N 53 DA N7 N Y N 54 DA C5 C Y N 55 DA C6 C Y N 56 DA N6 N N N 57 DA N1 N Y N 58 DA C2 C Y N 59 DA N3 N Y N 60 DA C4 C Y N 61 DA HOP3 H N N 62 DA HOP2 H N N 63 DA "H5'" H N N 64 DA "H5''" H N N 65 DA "H4'" H N N 66 DA "H3'" H N N 67 DA "HO3'" H N N 68 DA "H2'" H N N 69 DA "H2''" H N N 70 DA "H1'" H N N 71 DA H8 H N N 72 DA H61 H N N 73 DA H62 H N N 74 DA H2 H N N 75 DC OP3 O N N 76 DC P P N N 77 DC OP1 O N N 78 DC OP2 O N N 79 DC "O5'" O N N 80 DC "C5'" C N N 81 DC "C4'" C N R 82 DC "O4'" O N N 83 DC "C3'" C N S 84 DC "O3'" O N N 85 DC "C2'" C N N 86 DC "C1'" C N R 87 DC N1 N N N 88 DC C2 C N N 89 DC O2 O N N 90 DC N3 N N N 91 DC C4 C N N 92 DC N4 N N N 93 DC C5 C N N 94 DC C6 C N N 95 DC HOP3 H N N 96 DC HOP2 H N N 97 DC "H5'" H N N 98 DC "H5''" H N N 99 DC "H4'" H N N 100 DC "H3'" H N N 101 DC "HO3'" H N N 102 DC "H2'" H N N 103 DC "H2''" H N N 104 DC "H1'" H N N 105 DC H41 H N N 106 DC H42 H N N 107 DC H5 H N N 108 DC H6 H N N 109 DG OP3 O N N 110 DG P P N N 111 DG OP1 O N N 112 DG OP2 O N N 113 DG "O5'" O N N 114 DG "C5'" C N N 115 DG "C4'" C N R 116 DG "O4'" O N N 117 DG "C3'" C N S 118 DG "O3'" O N N 119 DG "C2'" C N N 120 DG "C1'" C N R 121 DG N9 N Y N 122 DG C8 C Y N 123 DG N7 N Y N 124 DG C5 C Y N 125 DG C6 C N N 126 DG O6 O N N 127 DG N1 N N N 128 DG C2 C N N 129 DG N2 N N N 130 DG N3 N N N 131 DG C4 C Y N 132 DG HOP3 H N N 133 DG HOP2 H N N 134 DG "H5'" H N N 135 DG "H5''" H N N 136 DG "H4'" H N N 137 DG "H3'" H N N 138 DG "HO3'" H N N 139 DG "H2'" H N N 140 DG "H2''" H N N 141 DG "H1'" H N N 142 DG H8 H N N 143 DG H1 H N N 144 DG H21 H N N 145 DG H22 H N N 146 DT OP3 O N N 147 DT P P N N 148 DT OP1 O N N 149 DT OP2 O N N 150 DT "O5'" O N N 151 DT "C5'" C N N 152 DT "C4'" C N R 153 DT "O4'" O N N 154 DT "C3'" C N S 155 DT "O3'" O N N 156 DT "C2'" C N N 157 DT "C1'" C N R 158 DT N1 N N N 159 DT C2 C N N 160 DT O2 O N N 161 DT N3 N N N 162 DT C4 C N N 163 DT O4 O N N 164 DT C5 C N N 165 DT C7 C N N 166 DT C6 C N N 167 DT HOP3 H N N 168 DT HOP2 H N N 169 DT "H5'" H N N 170 DT "H5''" H N N 171 DT "H4'" H N N 172 DT "H3'" H N N 173 DT "HO3'" H N N 174 DT "H2'" H N N 175 DT "H2''" H N N 176 DT "H1'" H N N 177 DT H3 H N N 178 DT H71 H N N 179 DT H72 H N N 180 DT H73 H N N 181 DT H6 H N N 182 HOH O O N N 183 HOH H1 H N N 184 HOH H2 H N N 185 NA NA NA N N 186 # 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 B7C OP3 P sing N N 1 B7C P OP1 sing N N 2 B7C P OP2 doub N N 3 B7C P "O5'" sing N N 4 B7C "O5'" "C5'" sing N N 5 B7C N1 C6 sing N N 6 B7C N1 C2 sing N N 7 B7C N1 "C1'" sing N N 8 B7C C6 C5 doub N N 9 B7C C2 O2 doub N N 10 B7C C2 N3 sing N N 11 B7C N3 C4 doub N N 12 B7C C4 N4 sing N N 13 B7C C4 C5 sing N N 14 B7C N4 C9 sing N N 15 B7C C5 C7 sing N N 16 B7C C7 C8 doub N N 17 B7C C8 C9 sing N N 18 B7C "C2'" "C1'" sing N N 19 B7C "C2'" "C3'" sing N N 20 B7C "C5'" "C4'" sing N N 21 B7C "C4'" "O4'" sing N N 22 B7C "C4'" "C3'" sing N N 23 B7C "O4'" "C1'" sing N N 24 B7C "C3'" "O3'" sing N N 25 B7C OP3 HOP3 sing N N 26 B7C OP1 HOP1 sing N N 27 B7C C6 H6 sing N N 28 B7C N4 HN4 sing N N 29 B7C C7 H7 sing N N 30 B7C C8 H8 sing N N 31 B7C C9 H9 sing N N 32 B7C C9 H9A sing N N 33 B7C "C2'" "H2'" sing N N 34 B7C "C2'" "H2'A" sing N N 35 B7C "C5'" "H5'" sing N N 36 B7C "C5'" "H5'A" sing N N 37 B7C "C4'" "H4'" sing N N 38 B7C "C1'" "H1'" sing N N 39 B7C "C3'" "H3'" sing N N 40 B7C "O3'" "HO3'" sing N N 41 DA OP3 P sing N N 42 DA OP3 HOP3 sing N N 43 DA P OP1 doub N N 44 DA P OP2 sing N N 45 DA P "O5'" sing N N 46 DA OP2 HOP2 sing N N 47 DA "O5'" "C5'" sing N N 48 DA "C5'" "C4'" sing N N 49 DA "C5'" "H5'" sing N N 50 DA "C5'" "H5''" sing N N 51 DA "C4'" "O4'" sing N N 52 DA "C4'" "C3'" sing N N 53 DA "C4'" "H4'" sing N N 54 DA "O4'" "C1'" sing N N 55 DA "C3'" "O3'" sing N N 56 DA "C3'" "C2'" sing N N 57 DA "C3'" "H3'" sing N N 58 DA "O3'" "HO3'" sing N N 59 DA "C2'" "C1'" sing N N 60 DA "C2'" "H2'" sing N N 61 DA "C2'" "H2''" sing N N 62 DA "C1'" N9 sing N N 63 DA "C1'" "H1'" sing N N 64 DA N9 C8 sing Y N 65 DA N9 C4 sing Y N 66 DA C8 N7 doub Y N 67 DA C8 H8 sing N N 68 DA N7 C5 sing Y N 69 DA C5 C6 sing Y N 70 DA C5 C4 doub Y N 71 DA C6 N6 sing N N 72 DA C6 N1 doub Y N 73 DA N6 H61 sing N N 74 DA N6 H62 sing N N 75 DA N1 C2 sing Y N 76 DA C2 N3 doub Y N 77 DA C2 H2 sing N N 78 DA N3 C4 sing Y N 79 DC OP3 P sing N N 80 DC OP3 HOP3 sing N N 81 DC P OP1 doub N N 82 DC P OP2 sing N N 83 DC P "O5'" sing N N 84 DC OP2 HOP2 sing N N 85 DC "O5'" "C5'" sing N N 86 DC "C5'" "C4'" sing N N 87 DC "C5'" "H5'" sing N N 88 DC "C5'" "H5''" sing N N 89 DC "C4'" "O4'" sing N N 90 DC "C4'" "C3'" sing N N 91 DC "C4'" "H4'" sing N N 92 DC "O4'" "C1'" sing N N 93 DC "C3'" "O3'" sing N N 94 DC "C3'" "C2'" sing N N 95 DC "C3'" "H3'" sing N N 96 DC "O3'" "HO3'" sing N N 97 DC "C2'" "C1'" sing N N 98 DC "C2'" "H2'" sing N N 99 DC "C2'" "H2''" sing N N 100 DC "C1'" N1 sing N N 101 DC "C1'" "H1'" sing N N 102 DC N1 C2 sing N N 103 DC N1 C6 sing N N 104 DC C2 O2 doub N N 105 DC C2 N3 sing N N 106 DC N3 C4 doub N N 107 DC C4 N4 sing N N 108 DC C4 C5 sing N N 109 DC N4 H41 sing N N 110 DC N4 H42 sing N N 111 DC C5 C6 doub N N 112 DC C5 H5 sing N N 113 DC C6 H6 sing N N 114 DG OP3 P sing N N 115 DG OP3 HOP3 sing N N 116 DG P OP1 doub N N 117 DG P OP2 sing N N 118 DG P "O5'" sing N N 119 DG OP2 HOP2 sing N N 120 DG "O5'" "C5'" sing N N 121 DG "C5'" "C4'" sing N N 122 DG "C5'" "H5'" sing N N 123 DG "C5'" "H5''" sing N N 124 DG "C4'" "O4'" sing N N 125 DG "C4'" "C3'" sing N N 126 DG "C4'" "H4'" sing N N 127 DG "O4'" "C1'" sing N N 128 DG "C3'" "O3'" sing N N 129 DG "C3'" "C2'" sing N N 130 DG "C3'" "H3'" sing N N 131 DG "O3'" "HO3'" sing N N 132 DG "C2'" "C1'" sing N N 133 DG "C2'" "H2'" sing N N 134 DG "C2'" "H2''" sing N N 135 DG "C1'" N9 sing N N 136 DG "C1'" "H1'" sing N N 137 DG N9 C8 sing Y N 138 DG N9 C4 sing Y N 139 DG C8 N7 doub Y N 140 DG C8 H8 sing N N 141 DG N7 C5 sing Y N 142 DG C5 C6 sing N N 143 DG C5 C4 doub Y N 144 DG C6 O6 doub N N 145 DG C6 N1 sing N N 146 DG N1 C2 sing N N 147 DG N1 H1 sing N N 148 DG C2 N2 sing N N 149 DG C2 N3 doub N N 150 DG N2 H21 sing N N 151 DG N2 H22 sing N N 152 DG N3 C4 sing N N 153 DT OP3 P sing N N 154 DT OP3 HOP3 sing N N 155 DT P OP1 doub N N 156 DT P OP2 sing N N 157 DT P "O5'" sing N N 158 DT OP2 HOP2 sing N N 159 DT "O5'" "C5'" sing N N 160 DT "C5'" "C4'" sing N N 161 DT "C5'" "H5'" sing N N 162 DT "C5'" "H5''" sing N N 163 DT "C4'" "O4'" sing N N 164 DT "C4'" "C3'" sing N N 165 DT "C4'" "H4'" sing N N 166 DT "O4'" "C1'" sing N N 167 DT "C3'" "O3'" sing N N 168 DT "C3'" "C2'" sing N N 169 DT "C3'" "H3'" sing N N 170 DT "O3'" "HO3'" sing N N 171 DT "C2'" "C1'" sing N N 172 DT "C2'" "H2'" sing N N 173 DT "C2'" "H2''" sing N N 174 DT "C1'" N1 sing N N 175 DT "C1'" "H1'" sing N N 176 DT N1 C2 sing N N 177 DT N1 C6 sing N N 178 DT C2 O2 doub N N 179 DT C2 N3 sing N N 180 DT N3 C4 sing N N 181 DT N3 H3 sing N N 182 DT C4 O4 doub N N 183 DT C4 C5 sing N N 184 DT C5 C7 sing N N 185 DT C5 C6 doub N N 186 DT C7 H71 sing N N 187 DT C7 H72 sing N N 188 DT C7 H73 sing N N 189 DT C6 H6 sing N N 190 HOH O H1 sing N N 191 HOH O H2 sing N N 192 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3GJL 'double helix' 3GJL 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 2 1_555 B DC 5 1_555 -0.226 -0.180 0.269 -7.982 -0.800 -1.478 1 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 0.257 -0.113 0.148 -2.087 2.293 0.953 2 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DA 5 1_555 B DT 2 1_555 -0.009 -0.089 -0.017 1.800 -18.773 4.442 3 A_DA5:DT8_B A 5 ? B 8 ? 20 1 1 A DA 6 1_555 B DT 1 1_555 -0.002 -0.085 0.038 -0.067 -18.820 5.475 4 A_DA6:DT7_B A 6 ? B 7 ? 20 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 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 0.873 0.334 3.360 1.419 -6.238 36.851 1.362 -1.170 3.292 -9.778 -2.224 37.383 1 AA_DG2DC3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 4 1_555 A DA 5 1_555 B DT 2 1_555 0.004 0.099 6.374 3.719 4.817 67.276 -0.272 0.275 6.360 4.339 -3.350 67.518 2 AA_DC3DA5:DT8DG10_BB A 3 ? B 10 ? A 5 ? B 8 ? 1 A DA 5 1_555 B DT 2 1_555 A DA 6 1_555 B DT 1 1_555 0.090 -0.285 3.269 -0.408 -2.459 35.567 -0.108 -0.207 3.279 -4.019 0.666 35.652 3 AA_DA5DA6:DT7DT8_BB A 5 ? B 8 ? A 6 ? B 7 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SODIUM ION' NA 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1EHV _pdbx_initial_refinement_model.details ? #