data_3V06 # _entry.id 3V06 # _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 3V06 pdb_00003v06 10.2210/pdb3v06/pdb NDB NA1502 ? ? RCSB RCSB069428 ? ? WWPDB D_1000069428 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3V07 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3V06 _pdbx_database_status.recvd_initial_deposition_date 2011-12-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pallan, P.S.' 1 'Egli, M.' 2 # _citation.id primary _citation.title ;Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 51 _citation.page_first 7 _citation.page_last 9 _citation.year 2012 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22229409 _citation.pdbx_database_id_DOI 10.1021/bi201810r # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Yu, J.' 2 ? primary 'Allerson, C.R.' 3 ? primary 'Swayze, E.E.' 4 ? primary 'Seth, P.' 5 ? primary 'Egli, M.' 6 ? # _cell.entry_id 3V06 _cell.length_a 24.879 _cell.length_b 45.222 _cell.length_c 46.598 _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 3V06 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 ;DNA (5'-D(*GP*CP*GP*TP*AP*(F5H)P*AP*CP*GP*C)-3') ; 3091.049 2 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 1 ? ? ? ? 3 water nat water 18.015 77 ? ? ? ? # _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)(DC)(DG)(DT)(DA)(F5H)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTAXACGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 F5H n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3V06 _struct_ref.pdbx_db_accession 3V06 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3V06 A 1 ? 10 ? 3V06 101 ? 110 ? 101 110 2 1 3V06 B 1 ? 10 ? 3V06 201 ? 210 ? 201 210 # 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 F5H 'DNA linking' . '3,7-anhydro-1,5,6-trideoxy-5-fluoro-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-O-phosphono-D-glycero-L-altro-heptitol' ? 'C12 H18 F N2 O8 P' 368.252 HOH non-polymer . WATER ? 'H2 O' 18.015 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 # _exptl.entry_id 3V06 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.12 _exptl_crystal.density_percent_sol 41.98 _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 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;40 mM sodium cacodylate, 40 mM lithium chloride, 80 mM strontium chloride, 20 mM magnesium chloride, 12 mM spermine tetrahydrochloride, 10% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _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 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2010-07-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'C(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9787 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 21-ID-F' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 21-ID-F _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9787 # _reflns.entry_id 3V06 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 32.45 _reflns.d_resolution_high 1.53 _reflns.number_obs 8157 _reflns.number_all 8268 _reflns.percent_possible_obs 98.65 _reflns.pdbx_Rmerge_I_obs 0.070 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 46.3 _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 1.53 _reflns_shell.d_res_low 1.57 _reflns_shell.percent_possible_all 70.2 _reflns_shell.Rmerge_I_obs 0.446 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.7 _reflns_shell.pdbx_redundancy 8.5 _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3V06 _refine.ls_number_reflns_obs 7780 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 32.45 _refine.ls_d_res_high 1.53 _refine.ls_percent_reflns_obs 97.03 _refine.ls_R_factor_obs 0.16997 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.16715 _refine.ls_R_factor_R_free 0.22693 _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 377 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.965 _refine.correlation_coeff_Fo_to_Fc_free 0.955 _refine.B_iso_mean 18.482 _refine.aniso_B[1][1] 0.31 _refine.aniso_B[2][2] -1.00 _refine.aniso_B[3][3] 0.69 _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 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 3EY2' _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 0.100 _refine.pdbx_overall_ESU_R_Free 0.090 _refine.overall_SU_ML 0.050 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.963 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 410 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 77 _refine_hist.number_atoms_total 488 _refine_hist.d_res_high 1.53 _refine_hist.d_res_low 32.45 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.022 0.021 ? 460 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2.493 2.972 ? 714 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.115 0.200 ? 82 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.025 0.020 ? 210 ? 'X-RAY DIFFRACTION' r_scbond_it 3.588 3.000 ? 458 ? 'X-RAY DIFFRACTION' r_scangle_it 4.422 4.500 ? 704 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr 2.724 3.000 ? 458 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.53 _refine_ls_shell.d_res_low 1.569 _refine_ls_shell.number_reflns_R_work 414 _refine_ls_shell.R_factor_R_work 0.167 _refine_ls_shell.percent_reflns_obs 70.18 _refine_ls_shell.R_factor_R_free 0.248 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 19 _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 3V06 _struct.title ;Crystal structure of S-6'-Me-3'-fluoro hexitol nucleic acid ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3V06 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;A-form DNA, 3'-fluoro hexitol nucleic acid, FHNA, S-6'-Me-FHNA, antisense oligonucleotides, 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 1 ? C N N 2 ? D N N 3 ? E 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 DA 5 "O3'" ? ? ? 1_555 A F5H 6 P ? ? A DA 105 A F5H 106 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? A F5H 6 "O4'" ? ? ? 1_555 A DA 7 P ? ? A F5H 106 A DA 107 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B F5H 6 P ? ? B DA 205 B F5H 206 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale4 covale both ? B F5H 6 "O4'" ? ? ? 1_555 B DA 7 P ? ? B F5H 206 B DA 207 1_555 ? ? ? ? ? ? ? 1.597 ? ? metalc1 metalc ? ? C SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 201 A HOH 318 1_555 ? ? ? ? ? ? ? 2.476 ? ? metalc2 metalc ? ? C SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 201 A HOH 334 1_555 ? ? ? ? ? ? ? 2.350 ? ? metalc3 metalc ? ? C SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 201 A HOH 335 1_555 ? ? ? ? ? ? ? 2.459 ? ? metalc4 metalc ? ? C SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 201 B HOH 317 1_555 ? ? ? ? ? ? ? 2.491 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 101 B DC 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 101 B DC 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 101 B DC 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 102 B DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 102 B DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 102 B DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 103 B DC 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 103 B DC 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 103 B DC 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 104 B DA 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 104 B DA 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 107 B DT 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 107 B DT 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 108 B DG 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 108 B DG 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 108 B DG 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 109 B DC 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 109 B DC 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 109 B DC 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 110 B DG 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 110 B DG 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 110 B DG 201 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 A _struct_site.pdbx_auth_comp_id SR _struct_site.pdbx_auth_seq_id 201 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE SR A 201' # 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 HOH D . ? HOH A 318 . ? 1_555 ? 2 AC1 4 HOH D . ? HOH A 334 . ? 1_555 ? 3 AC1 4 HOH D . ? HOH A 335 . ? 1_555 ? 4 AC1 4 HOH E . ? HOH B 317 . ? 1_555 ? # _database_PDB_matrix.entry_id 3V06 _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 3V06 _atom_sites.fract_transf_matrix[1][1] 0.040195 _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] 0.022113 _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] 0.021460 _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 F N O P SR # 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 1 101 101 DG DG A . n A 1 2 DC 2 102 102 DC DC A . n A 1 3 DG 3 103 103 DG DG A . n A 1 4 DT 4 104 104 DT DT A . n A 1 5 DA 5 105 105 DA DA A . n A 1 6 F5H 6 106 106 F5H F5H A . n A 1 7 DA 7 107 107 DA DA A . n A 1 8 DC 8 108 108 DC DC A . n A 1 9 DG 9 109 109 DG DG A . n A 1 10 DC 10 110 110 DC DC A . n B 1 1 DG 1 201 201 DG DG B . n B 1 2 DC 2 202 202 DC DC B . n B 1 3 DG 3 203 203 DG DG B . n B 1 4 DT 4 204 204 DT DT B . n B 1 5 DA 5 205 205 DA DA B . n B 1 6 F5H 6 206 206 F5H F5H B . n B 1 7 DA 7 207 207 DA DA B . n B 1 8 DC 8 208 208 DC DC B . n B 1 9 DG 9 209 209 DG DG B . n B 1 10 DC 10 210 210 DC DC B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SR 1 201 1 SR SR A . D 3 HOH 1 301 2 HOH HOH A . D 3 HOH 2 302 3 HOH HOH A . D 3 HOH 3 303 5 HOH HOH A . D 3 HOH 4 304 11 HOH HOH A . D 3 HOH 5 305 15 HOH HOH A . D 3 HOH 6 306 16 HOH HOH A . D 3 HOH 7 307 17 HOH HOH A . D 3 HOH 8 308 18 HOH HOH A . D 3 HOH 9 309 19 HOH HOH A . D 3 HOH 10 310 20 HOH HOH A . D 3 HOH 11 311 21 HOH HOH A . D 3 HOH 12 312 22 HOH HOH A . D 3 HOH 13 313 24 HOH HOH A . D 3 HOH 14 314 25 HOH HOH A . D 3 HOH 15 315 27 HOH HOH A . D 3 HOH 16 316 28 HOH HOH A . D 3 HOH 17 317 29 HOH HOH A . D 3 HOH 18 318 30 HOH HOH A . D 3 HOH 19 319 32 HOH HOH A . D 3 HOH 20 320 34 HOH HOH A . D 3 HOH 21 321 35 HOH HOH A . D 3 HOH 22 322 37 HOH HOH A . D 3 HOH 23 323 39 HOH HOH A . D 3 HOH 24 324 40 HOH HOH A . D 3 HOH 25 325 41 HOH HOH A . D 3 HOH 26 326 42 HOH HOH A . D 3 HOH 27 327 43 HOH HOH A . D 3 HOH 28 328 44 HOH HOH A . D 3 HOH 29 329 45 HOH HOH A . D 3 HOH 30 330 48 HOH HOH A . D 3 HOH 31 331 49 HOH HOH A . D 3 HOH 32 332 50 HOH HOH A . D 3 HOH 33 333 51 HOH HOH A . D 3 HOH 34 334 52 HOH HOH A . D 3 HOH 35 335 53 HOH HOH A . D 3 HOH 36 336 54 HOH HOH A . D 3 HOH 37 337 55 HOH HOH A . D 3 HOH 38 338 56 HOH HOH A . D 3 HOH 39 339 57 HOH HOH A . D 3 HOH 40 340 60 HOH HOH A . D 3 HOH 41 341 61 HOH HOH A . D 3 HOH 42 342 62 HOH HOH A . D 3 HOH 43 343 63 HOH HOH A . D 3 HOH 44 344 64 HOH HOH A . D 3 HOH 45 345 65 HOH HOH A . D 3 HOH 46 346 69 HOH HOH A . D 3 HOH 47 347 71 HOH HOH A . E 3 HOH 1 301 4 HOH HOH B . E 3 HOH 2 302 6 HOH HOH B . E 3 HOH 3 303 7 HOH HOH B . E 3 HOH 4 304 8 HOH HOH B . E 3 HOH 5 305 9 HOH HOH B . E 3 HOH 6 306 10 HOH HOH B . E 3 HOH 7 307 12 HOH HOH B . E 3 HOH 8 308 13 HOH HOH B . E 3 HOH 9 309 14 HOH HOH B . E 3 HOH 10 310 23 HOH HOH B . E 3 HOH 11 311 26 HOH HOH B . E 3 HOH 12 312 31 HOH HOH B . E 3 HOH 13 313 33 HOH HOH B . E 3 HOH 14 314 36 HOH HOH B . E 3 HOH 15 315 38 HOH HOH B . E 3 HOH 16 316 46 HOH HOH B . E 3 HOH 17 317 47 HOH HOH B . E 3 HOH 18 318 58 HOH HOH B . E 3 HOH 19 319 59 HOH HOH B . E 3 HOH 20 320 66 HOH HOH B . E 3 HOH 21 321 67 HOH HOH B . E 3 HOH 22 322 68 HOH HOH B . E 3 HOH 23 323 70 HOH HOH B . E 3 HOH 24 324 72 HOH HOH B . E 3 HOH 25 325 73 HOH HOH B . E 3 HOH 26 326 74 HOH HOH B . E 3 HOH 27 327 75 HOH HOH B . E 3 HOH 28 328 76 HOH HOH B . E 3 HOH 29 329 77 HOH HOH B . E 3 HOH 30 330 78 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 1260 ? 1 MORE -32 ? 1 'SSA (A^2)' 3670 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 318 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? D HOH . ? A HOH 334 ? 1_555 82.3 ? 2 O ? D HOH . ? A HOH 318 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? D HOH . ? A HOH 335 ? 1_555 74.1 ? 3 O ? D HOH . ? A HOH 334 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? D HOH . ? A HOH 335 ? 1_555 78.1 ? 4 O ? D HOH . ? A HOH 318 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? E HOH . ? B HOH 317 ? 1_555 144.4 ? 5 O ? D HOH . ? A HOH 334 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? E HOH . ? B HOH 317 ? 1_555 96.5 ? 6 O ? D HOH . ? A HOH 335 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? E HOH . ? B HOH 317 ? 1_555 70.9 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-02-08 2 'Structure model' 1 1 2023-09-13 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_initial_refinement_model 5 2 'Structure model' pdbx_struct_conn_angle 6 2 'Structure model' struct_conn 7 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 2 'Structure model' '_pdbx_struct_conn_angle.value' 6 2 'Structure model' '_struct_conn.pdbx_dist_value' 7 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 9 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 10 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 11 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MD2 'data collection' 'diffractometer software from EMBL (with LS-CAT developed extensions)' ? 1 CCP4 'model building' . ? 2 MOLREP phasing . ? 3 REFMAC refinement 5.5.0109 ? 4 HKL-2000 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 CCP4 phasing . ? 7 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N7 A DG 103 ? ? C8 A DG 103 ? ? 1.257 1.305 -0.048 0.006 N 2 1 N9 A DA 105 ? ? C4 A DA 105 ? ? 1.419 1.374 0.045 0.006 N 3 1 N1 B DT 204 ? ? C2 B DT 204 ? ? 1.428 1.376 0.052 0.008 N 4 1 C4 B DC 208 ? ? C5 B DC 208 ? ? 1.475 1.425 0.050 0.008 N # 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 C8 A DG 101 ? ? N9 A DG 101 ? ? C4 A DG 101 ? ? 102.88 106.40 -3.52 0.40 N 2 1 N9 A DG 101 ? ? C4 A DG 101 ? ? C5 A DG 101 ? ? 108.47 105.40 3.07 0.40 N 3 1 N1 A DC 102 ? ? C2 A DC 102 ? ? O2 A DC 102 ? ? 114.86 118.90 -4.04 0.60 N 4 1 "O4'" A DT 104 ? ? "C4'" A DT 104 ? ? "C3'" A DT 104 ? ? 100.89 104.50 -3.61 0.40 N 5 1 C6 A DT 104 ? ? C5 A DT 104 ? ? C7 A DT 104 ? ? 118.54 122.90 -4.36 0.60 N 6 1 C6 A DA 105 ? ? N1 A DA 105 ? ? C2 A DA 105 ? ? 123.05 118.60 4.45 0.60 N 7 1 N1 A DA 105 ? ? C2 A DA 105 ? ? N3 A DA 105 ? ? 125.96 129.30 -3.34 0.50 N 8 1 C5 A DA 105 ? ? C6 A DA 105 ? ? N1 A DA 105 ? ? 114.63 117.70 -3.07 0.50 N 9 1 "O3'" A DA 105 ? ? P A F5H 106 ? ? "O5'" A F5H 106 ? ? 88.59 104.00 -15.41 1.90 Y 10 1 "O4'" A DC 108 ? ? "C4'" A DC 108 ? ? "C3'" A DC 108 ? ? 101.63 104.50 -2.87 0.40 N 11 1 "O4'" A DG 109 ? ? "C4'" A DG 109 ? ? "C3'" A DG 109 ? ? 101.01 104.50 -3.49 0.40 N 12 1 C4 A DG 109 ? ? C5 A DG 109 ? ? N7 A DG 109 ? ? 114.09 110.80 3.29 0.40 N 13 1 C5 A DG 109 ? ? N7 A DG 109 ? ? C8 A DG 109 ? ? 99.66 104.30 -4.64 0.50 N 14 1 C6 A DG 109 ? ? C5 A DG 109 ? ? N7 A DG 109 ? ? 126.65 130.40 -3.75 0.60 N 15 1 C6 A DC 110 ? ? N1 A DC 110 ? ? C2 A DC 110 ? ? 123.03 120.30 2.73 0.40 N 16 1 "O4'" B DG 203 ? ? "C4'" B DG 203 ? ? "C3'" B DG 203 ? ? 99.87 104.50 -4.63 0.40 N 17 1 "O4'" B DT 204 ? ? "C1'" B DT 204 ? ? N1 B DT 204 ? ? 110.33 108.30 2.03 0.30 N 18 1 "O3'" B DA 205 ? ? P B F5H 206 ? ? "O5'" B F5H 206 ? ? 90.08 104.00 -13.92 1.90 Y 19 1 C6 B DA 207 ? ? N1 B DA 207 ? ? C2 B DA 207 ? ? 122.29 118.60 3.69 0.60 N 20 1 N1 B DA 207 ? ? C2 B DA 207 ? ? N3 B DA 207 ? ? 123.13 129.30 -6.17 0.50 N 21 1 C2 B DA 207 ? ? N3 B DA 207 ? ? C4 B DA 207 ? ? 114.81 110.60 4.21 0.50 N 22 1 "C4'" B DC 208 ? ? "C3'" B DC 208 ? ? "C2'" B DC 208 ? ? 96.61 102.20 -5.59 0.70 N 23 1 "C3'" B DG 209 ? ? "C2'" B DG 209 ? ? "C1'" B DG 209 ? ? 97.41 102.40 -4.99 0.80 N 24 1 "O4'" B DG 209 ? ? "C1'" B DG 209 ? ? "C2'" B DG 209 ? ? 112.94 106.80 6.14 0.50 N 25 1 C5 B DG 209 ? ? N7 B DG 209 ? ? C8 B DG 209 ? ? 107.40 104.30 3.10 0.50 N 26 1 "O5'" B DC 210 ? ? "C5'" B DC 210 ? ? "C4'" B DC 210 ? ? 104.51 109.40 -4.89 0.80 N 27 1 "O4'" B DC 210 ? ? "C4'" B DC 210 ? ? "C3'" B DC 210 ? ? 101.11 104.50 -3.39 0.40 N 28 1 "O4'" B DC 210 ? ? "C1'" B DC 210 ? ? "C2'" B DC 210 ? ? 110.03 106.80 3.23 0.50 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 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 F5H P P N N 144 F5H N1 N N N 145 F5H C2 C N N 146 F5H O2 O N N 147 F5H N3 N N N 148 F5H C4 C N N 149 F5H O4 O N N 150 F5H C5 C N N 151 F5H C6 C N N 152 F5H C7 C N N 153 F5H "C1'" C N N 154 F5H O1P O N N 155 F5H "C2'" C N R 156 F5H O2P O N N 157 F5H "C3'" C N S 158 F5H "F3'" F N N 159 F5H O3P O N N 160 F5H "C4'" C N R 161 F5H "O4'" O N N 162 F5H "C5'" C N S 163 F5H "O5'" O N N 164 F5H "C6'" C N S 165 F5H "O6'" O N N 166 F5H "C7'" C N N 167 F5H HN3 H N N 168 F5H H6 H N N 169 F5H H7 H N N 170 F5H H7A H N N 171 F5H H7B H N N 172 F5H "H1'" H N N 173 F5H "H1'A" H N N 174 F5H HO1P H N N 175 F5H "H2'" H N N 176 F5H "H3'" H N N 177 F5H HO3P H N N 178 F5H "H4'" H N N 179 F5H "HO4'" H N N 180 F5H "H5'" H N N 181 F5H "H6'" H N N 182 F5H "H7'" H N N 183 F5H "H7'A" H N N 184 F5H "H7'B" H N N 185 HOH O O N N 186 HOH H1 H N N 187 HOH H2 H N N 188 SR SR SR N N 189 # 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 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 F5H O2P P doub N N 150 F5H "O6'" P sing N N 151 F5H P O1P sing N N 152 F5H P O3P sing N N 153 F5H C2 N1 sing N N 154 F5H C6 N1 sing N N 155 F5H N1 "C2'" sing N N 156 F5H N3 C2 sing N N 157 F5H C2 O2 doub N N 158 F5H C4 N3 sing N N 159 F5H N3 HN3 sing N N 160 F5H O4 C4 doub N N 161 F5H C4 C5 sing N N 162 F5H C7 C5 sing N N 163 F5H C5 C6 doub N N 164 F5H C6 H6 sing N N 165 F5H C7 H7 sing N N 166 F5H C7 H7A sing N N 167 F5H C7 H7B sing N N 168 F5H "C2'" "C1'" sing N N 169 F5H "C1'" "O5'" sing N N 170 F5H "C1'" "H1'" sing N N 171 F5H "C1'" "H1'A" sing N N 172 F5H O1P HO1P sing N N 173 F5H "C3'" "C2'" sing N N 174 F5H "C2'" "H2'" sing N N 175 F5H "C3'" "C4'" sing N N 176 F5H "C3'" "F3'" sing N N 177 F5H "C3'" "H3'" sing N N 178 F5H O3P HO3P sing N N 179 F5H "O4'" "C4'" sing N N 180 F5H "C4'" "C5'" sing N N 181 F5H "C4'" "H4'" sing N N 182 F5H "O4'" "HO4'" sing N N 183 F5H "C5'" "O5'" sing N N 184 F5H "C5'" "C6'" sing N N 185 F5H "C5'" "H5'" sing N N 186 F5H "O6'" "C6'" sing N N 187 F5H "C6'" "C7'" sing N N 188 F5H "C6'" "H6'" sing N N 189 F5H "C7'" "H7'" sing N N 190 F5H "C7'" "H7'A" sing N N 191 F5H "C7'" "H7'B" sing N N 192 HOH O H1 sing N N 193 HOH O H2 sing N N 194 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3V06 'a-form double helix' 3V06 '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 B DC 10 1_555 -0.342 -0.160 0.289 7.059 -8.444 -0.931 1 A_DG101:DC210_B A 101 ? B 210 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.261 -0.143 0.040 9.676 -19.243 0.665 2 A_DC102:DG209_B A 102 ? B 209 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.314 -0.163 0.231 -3.869 -17.126 0.941 3 A_DG103:DC208_B A 103 ? B 208 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.109 -0.087 -0.162 -0.554 -17.616 1.592 4 A_DT104:DA207_B A 104 ? B 207 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.049 -0.155 0.131 2.536 -9.833 1.855 5 A_DA107:DT204_B A 107 ? B 204 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.250 -0.127 -0.054 8.483 -13.304 1.463 6 A_DC108:DG203_B A 108 ? B 203 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.241 -0.206 -0.173 -7.473 -9.997 -1.007 7 A_DG109:DC202_B A 109 ? B 202 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.277 -0.071 0.064 -0.947 4.211 0.784 8 A_DC110:DG201_B A 110 ? B 201 ? 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 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.474 -1.255 3.181 2.733 0.830 38.712 -1.987 -0.389 3.179 1.250 -4.116 38.814 1 AA_DG101DC102:DG209DC210_BB A 101 ? B 210 ? A 102 ? B 209 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 -0.134 -1.906 3.372 -2.805 12.548 29.057 -5.607 -0.228 2.369 23.605 5.276 31.718 2 AA_DC102DG103:DC208DG209_BB A 102 ? B 209 ? A 103 ? B 208 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.009 -1.418 3.075 -0.259 5.846 34.934 -3.111 1.625 2.816 9.655 0.427 35.406 3 AA_DG103DT104:DA207DC208_BB A 103 ? B 208 ? A 104 ? B 207 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.234 -1.779 3.185 1.259 4.571 29.602 -4.321 -0.210 2.891 8.874 -2.443 29.971 4 AA_DA107DC108:DG203DT204_BB A 107 ? B 204 ? A 108 ? B 203 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.484 -2.004 3.548 1.287 13.028 29.413 -5.857 1.095 2.441 24.204 -2.391 32.136 5 AA_DC108DG109:DC202DG203_BB A 108 ? B 203 ? A 109 ? B 202 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.491 -1.628 3.238 0.138 1.009 34.531 -2.894 -0.805 3.193 1.699 -0.232 34.545 6 AA_DG109DC110:DG201DC202_BB A 109 ? B 202 ? A 110 ? B 201 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 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 3EY2 _pdbx_initial_refinement_model.details 'PDB ENTRY 3EY2' #