data_1Y8L # _entry.id 1Y8L # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1Y8L pdb_00001y8l 10.2210/pdb1y8l/pdb NDB AD0041 ? ? RCSB RCSB031252 ? ? WWPDB D_1000031252 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1Y7F ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*) ; unspecified PDB 1Y84 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazolyl)ethyl] Thymidine (T*) ; unspecified PDB 1Y86 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(fluoro)ethyl] Thymidine (T*) ; unspecified PDB 1Y8V ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*) ; unspecified PDB 1Y9F ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*) ; unspecified PDB 1Y9S ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*) ; unspecified PDB 1WV5 ;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, MG-FORM ; unspecified PDB 1WV6 ;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, SR-FORM ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Y8L _pdbx_database_status.recvd_initial_deposition_date 2004-12-13 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Egli, M.' 1 'Minasov, G.' 2 'Tereshko, V.' 3 'Pallan, P.S.' 4 'Teplova, M.' 5 'Inamati, G.B.' 6 'Lesnik, E.A.' 7 'Owens, S.R.' 8 'Ross, B.S.' 9 'Prakash, T.P.' 10 'Manoharan, M.' 11 # _citation.id primary _citation.title ;Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 44 _citation.page_first 9045 _citation.page_last 9057 _citation.year 2005 _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 15966728 _citation.pdbx_database_id_DOI 10.1021/bi050574m # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Minasov, G.' 2 ? primary 'Tereshko, V.' 3 ? primary 'Pallan, P.S.' 4 ? primary 'Teplova, M.' 5 ? primary 'Inamati, G.B.' 6 ? primary 'Lesnik, E.A.' 7 ? primary 'Owens, S.R.' 8 ? primary 'Ross, B.S.' 9 ? primary 'Prakash, T.P.' 10 ? primary 'Manoharan, M.' 11 ? # _cell.entry_id 1Y8L _cell.length_a 24.636 _cell.length_b 45.020 _cell.length_c 45.132 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y8L _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 "5'-D(*GP*CP*GP*TP*AP*(TFE)P*AP*CP*GP*C)-3')" 3143.029 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 4 water nat water 18.015 111 ? ? ? ? # _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)(TFE)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _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 TFE n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1Y8L _struct_ref.pdbx_db_accession 1Y8L _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1Y8L A 1 ? 10 ? 1Y8L 1 ? 10 ? 1 10 2 1 1Y8L B 1 ? 10 ? 1Y8L 11 ? 20 ? 11 20 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 TFE 'RNA linking' n ;2'-O-[2-(TRIFLUORO)ETHYL] THYMIDINE-5'-MONOPHOSPHATE ; ? 'C12 H16 F3 N2 O9 P' 420.232 # _exptl.entry_id 1Y8L _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.99 _exptl_crystal.density_percent_sol 38.21 _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 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM NaCL, 12mM KCL, 20mM MgCL2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 Na-Cacodilate ? ? ? 1 3 1 Spermine ? ? ? 1 4 1 NaCL ? ? ? 1 5 1 KCL ? ? ? 1 6 1 MgCL2 ? ? ? 1 7 1 H2O ? ? ? 1 8 2 MPD ? ? ? 1 9 2 Na-Cacodilate ? ? ? 1 10 2 NaCl ? ? ? 1 11 2 KCl ? ? ? 1 12 2 MgCl2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 1998-07-07 _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 No _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1Y8L _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.d_resolution_high 1.50 _reflns.d_resolution_low 35.0 _reflns.number_all 7868 _reflns.number_obs 7868 _reflns.percent_possible_obs 91.8 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 26.2 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.0 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.50 _reflns_shell.d_res_low 1.55 _reflns_shell.percent_possible_all 75.6 _reflns_shell.Rmerge_I_obs 0.261 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.4 _reflns_shell.pdbx_redundancy 2.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 652 _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 1Y8L _refine.ls_d_res_high 1.50 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I 0.0 _refine.ls_number_reflns_all 7593 _refine.ls_number_reflns_obs 7593 _refine.ls_number_reflns_R_free 817 _refine.ls_percent_reflns_obs 89.4 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1709 _refine.ls_R_factor_R_free 0.2021 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'pdb entry 410D' _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details Random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model Isotropic _refine.B_iso_mean 18.7 _refine.aniso_B[1][1] 3.249 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] 1.506 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] -4.754 _refine.details 'Conjugate gradient refinement using maximum likelihood target for amplitudes' _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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 416 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 114 _refine_hist.number_atoms_total 545 _refine_hist.d_res_high 1.50 _refine_hist.d_res_low 20.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.31 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.50 _refine_ls_shell.d_res_low 1.53 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.03 _refine_ls_shell.percent_reflns_obs 68.08 _refine_ls_shell.R_factor_R_free 0.3269 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 34 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1Y8L _struct.title ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Y8L _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;A-DNA, O2'-modification, decamer, 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 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details 'Chains A and B form duplex' _struct_biol.pdbx_parent_biol_id ? # 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 TFE 6 P ? ? A DA 5 A TFE 6 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale both ? A TFE 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A TFE 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B TFE 6 P ? ? B DA 15 B TFE 16 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B TFE 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B TFE 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.598 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 102 1_555 ? ? ? ? ? ? ? 2.046 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 103 1_555 ? ? ? ? ? ? ? 2.280 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 104 1_555 ? ? ? ? ? ? ? 1.925 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 106 1_555 ? ? ? ? ? ? ? 2.101 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O A ? A MG 101 A HOH 107 1_555 ? ? ? ? ? ? ? 1.990 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O B ? A MG 101 B HOH 105 1_555 ? ? ? ? ? ? ? 2.223 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B TFE 6 N3 ? ? A DA 5 B TFE 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B TFE 6 O4 ? ? A DA 5 B TFE 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A TFE 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A TFE 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A TFE 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A TFE 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B SPM 100 ? 11 'BINDING SITE FOR RESIDUE SPM B 100' AC2 Software A MG 101 ? 6 'BINDING SITE FOR RESIDUE MG A 101' # 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 11 DG A 9 ? DG A 9 . ? 4_545 ? 2 AC1 11 HOH E . ? HOH A 126 . ? 3_545 ? 3 AC1 11 HOH E . ? HOH A 146 . ? 3_545 ? 4 AC1 11 HOH E . ? HOH A 178 . ? 4_545 ? 5 AC1 11 DG B 3 ? DG B 13 . ? 1_555 ? 6 AC1 11 DT B 4 ? DT B 14 . ? 1_555 ? 7 AC1 11 DC B 8 ? DC B 18 . ? 3_645 ? 8 AC1 11 DG B 9 ? DG B 19 . ? 3_645 ? 9 AC1 11 HOH F . ? HOH B 130 . ? 1_555 ? 10 AC1 11 HOH F . ? HOH B 159 . ? 1_555 ? 11 AC1 11 HOH F . ? HOH B 184 . ? 3_645 ? 12 AC2 6 HOH E . ? HOH A 102 . ? 1_555 ? 13 AC2 6 HOH E . ? HOH A 103 . ? 1_555 ? 14 AC2 6 HOH E . ? HOH A 104 . ? 1_555 ? 15 AC2 6 HOH E . ? HOH A 106 . ? 1_555 ? 16 AC2 6 HOH E . ? HOH A 107 . ? 1_555 ? 17 AC2 6 HOH F . ? HOH B 105 . ? 1_555 ? # _database_PDB_matrix.entry_id 1Y8L _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 1Y8L _atom_sites.fract_transf_matrix[1][1] 0.040591 _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] 0.022212 _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] 0.022157 _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 MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 TFE 6 6 6 TFE TFE A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 TFE 6 16 16 TFE TFE B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C 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 MG 1 101 101 MG MG A . D 3 SPM 1 100 100 SPM SPM B . E 4 HOH 1 102 102 HOH HOH A . E 4 HOH 2 103 103 HOH HOH A . E 4 HOH 3 104 104 HOH HOH A . E 4 HOH 4 106 106 HOH HOH A . E 4 HOH 5 107 107 HOH HOH A . E 4 HOH 6 108 108 HOH HOH A . E 4 HOH 7 109 109 HOH HOH A . E 4 HOH 8 110 110 HOH HOH A . E 4 HOH 9 111 111 HOH HOH A . E 4 HOH 10 112 112 HOH HOH A . E 4 HOH 11 115 115 HOH HOH A . E 4 HOH 12 116 116 HOH HOH A . E 4 HOH 13 117 117 HOH HOH A . E 4 HOH 14 118 118 HOH HOH A . E 4 HOH 15 119 119 HOH HOH A . E 4 HOH 16 120 120 HOH HOH A . E 4 HOH 17 121 121 HOH HOH A . E 4 HOH 18 123 123 HOH HOH A . E 4 HOH 19 124 124 HOH HOH A . E 4 HOH 20 126 126 HOH HOH A . E 4 HOH 21 127 127 HOH HOH A . E 4 HOH 22 128 128 HOH HOH A . E 4 HOH 23 133 133 HOH HOH A . E 4 HOH 24 136 136 HOH HOH A . E 4 HOH 25 138 138 HOH HOH A . E 4 HOH 26 139 139 HOH HOH A . E 4 HOH 27 141 141 HOH HOH A . E 4 HOH 28 144 144 HOH HOH A . E 4 HOH 29 146 146 HOH HOH A . E 4 HOH 30 150 150 HOH HOH A . E 4 HOH 31 155 155 HOH HOH A . E 4 HOH 32 156 156 HOH HOH A . E 4 HOH 33 161 161 HOH HOH A . E 4 HOH 34 162 162 HOH HOH A . E 4 HOH 35 163 163 HOH HOH A . E 4 HOH 36 164 164 HOH HOH A . E 4 HOH 37 166 166 HOH HOH A . E 4 HOH 38 168 168 HOH HOH A . E 4 HOH 39 169 169 HOH HOH A . E 4 HOH 40 170 170 HOH HOH A . E 4 HOH 41 174 174 HOH HOH A . E 4 HOH 42 175 175 HOH HOH A . E 4 HOH 43 176 176 HOH HOH A . E 4 HOH 44 177 177 HOH HOH A . E 4 HOH 45 178 178 HOH HOH A . E 4 HOH 46 179 179 HOH HOH A . E 4 HOH 47 180 180 HOH HOH A . E 4 HOH 48 181 181 HOH HOH A . E 4 HOH 49 182 182 HOH HOH A . E 4 HOH 50 185 185 HOH HOH A . E 4 HOH 51 186 186 HOH HOH A . E 4 HOH 52 187 187 HOH HOH A . E 4 HOH 53 188 188 HOH HOH A . E 4 HOH 54 190 190 HOH HOH A . E 4 HOH 55 191 191 HOH HOH A . E 4 HOH 56 192 192 HOH HOH A . E 4 HOH 57 193 193 HOH HOH A . E 4 HOH 58 194 194 HOH HOH A . E 4 HOH 59 196 196 HOH HOH A . E 4 HOH 60 197 197 HOH HOH A . E 4 HOH 61 198 198 HOH HOH A . E 4 HOH 62 199 199 HOH HOH A . E 4 HOH 63 200 200 HOH HOH A . E 4 HOH 64 201 201 HOH HOH A . E 4 HOH 65 202 202 HOH HOH A . E 4 HOH 66 204 204 HOH HOH A . E 4 HOH 67 205 205 HOH HOH A . F 4 HOH 1 105 105 HOH HOH B . F 4 HOH 2 113 113 HOH HOH B . F 4 HOH 3 114 114 HOH HOH B . F 4 HOH 4 122 122 HOH HOH B . F 4 HOH 5 125 125 HOH HOH B . F 4 HOH 6 129 129 HOH HOH B . F 4 HOH 7 130 130 HOH HOH B . F 4 HOH 8 131 131 HOH HOH B . F 4 HOH 9 132 132 HOH HOH B . F 4 HOH 10 134 134 HOH HOH B . F 4 HOH 11 135 135 HOH HOH B . F 4 HOH 12 137 137 HOH HOH B . F 4 HOH 13 140 140 HOH HOH B . F 4 HOH 14 142 142 HOH HOH B . F 4 HOH 15 143 143 HOH HOH B . F 4 HOH 16 145 145 HOH HOH B . F 4 HOH 17 147 147 HOH HOH B . F 4 HOH 18 148 148 HOH HOH B . F 4 HOH 19 149 149 HOH HOH B . F 4 HOH 20 151 151 HOH HOH B . F 4 HOH 21 152 152 HOH HOH B . F 4 HOH 22 153 153 HOH HOH B . F 4 HOH 23 154 154 HOH HOH B . F 4 HOH 24 157 157 HOH HOH B . F 4 HOH 25 158 158 HOH HOH B . F 4 HOH 26 159 159 HOH HOH B . F 4 HOH 27 160 160 HOH HOH B . F 4 HOH 28 165 165 HOH HOH B . F 4 HOH 29 167 167 HOH HOH B . F 4 HOH 30 171 171 HOH HOH B . F 4 HOH 31 172 172 HOH HOH B . F 4 HOH 32 173 173 HOH HOH B . F 4 HOH 33 183 183 HOH HOH B . F 4 HOH 34 184 184 HOH HOH B . F 4 HOH 35 189 189 HOH HOH B . F 4 HOH 36 195 195 HOH HOH B . F 4 HOH 37 203 203 HOH HOH B . F 4 HOH 38 206 206 HOH HOH B . F 4 HOH 39 207 207 HOH HOH B . F 4 HOH 40 208 208 HOH HOH B . F 4 HOH 41 209 209 HOH HOH B . F 4 HOH 42 210 210 HOH HOH B . F 4 HOH 43 211 211 HOH HOH B . F 4 HOH 44 212 212 HOH HOH B . # 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 TFE 6 A TFE 6 ? DT ? 2 B TFE 6 B TFE 16 ? DT ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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 ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 103 ? 1_555 95.4 ? 2 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 104 ? 1_555 81.9 ? 3 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 104 ? 1_555 177.3 ? 4 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 85.2 ? 5 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 72.6 ? 6 O ? E HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 107.1 ? 7 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O A E HOH . ? A HOH 107 ? 1_555 94.7 ? 8 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O A E HOH . ? A HOH 107 ? 1_555 103.2 ? 9 O ? E HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O A E HOH . ? A HOH 107 ? 1_555 77.1 ? 10 O ? E HOH . ? A HOH 106 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O A E HOH . ? A HOH 107 ? 1_555 175.8 ? 11 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O B F HOH . ? B HOH 105 ? 1_555 150.9 ? 12 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O B F HOH . ? B HOH 105 ? 1_555 93.5 ? 13 O ? E HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O B F HOH . ? B HOH 105 ? 1_555 88.8 ? 14 O ? E HOH . ? A HOH 106 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O B F HOH . ? B HOH 105 ? 1_555 123.9 ? 15 O A E HOH . ? A HOH 107 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O B F HOH . ? B HOH 105 ? 1_555 56.3 ? # 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 2005-06-28 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_alt_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.value' 12 4 'Structure model' '_struct_conn.conn_type_id' 13 4 'Structure model' '_struct_conn.id' 14 4 'Structure model' '_struct_conn.pdbx_dist_value' 15 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 16 4 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 17 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 18 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 31 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 32 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 33 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement . ? 4 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DG _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 19 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.056 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MG MG MG N N 147 SPM N1 N N N 148 SPM C2 C N N 149 SPM C3 C N N 150 SPM C4 C N N 151 SPM N5 N N N 152 SPM C6 C N N 153 SPM C7 C N N 154 SPM C8 C N N 155 SPM C9 C N N 156 SPM N10 N N N 157 SPM C11 C N N 158 SPM C12 C N N 159 SPM C13 C N N 160 SPM N14 N N N 161 SPM HN11 H N N 162 SPM HN12 H N N 163 SPM H21 H N N 164 SPM H22 H N N 165 SPM H31 H N N 166 SPM H32 H N N 167 SPM H41 H N N 168 SPM H42 H N N 169 SPM HN5 H N N 170 SPM H61 H N N 171 SPM H62 H N N 172 SPM H71 H N N 173 SPM H72 H N N 174 SPM H81 H N N 175 SPM H82 H N N 176 SPM H91 H N N 177 SPM H92 H N N 178 SPM HN0 H N N 179 SPM H111 H N N 180 SPM H112 H N N 181 SPM H121 H N N 182 SPM H122 H N N 183 SPM H131 H N N 184 SPM H132 H N N 185 SPM HN41 H N N 186 SPM HN42 H N N 187 TFE P P N N 188 TFE OP1 O N N 189 TFE OP2 O N N 190 TFE "O5'" O N N 191 TFE "C5'" C N N 192 TFE "C4'" C N R 193 TFE "O4'" O N N 194 TFE "C1'" C N R 195 TFE N1 N N N 196 TFE C6 C N N 197 TFE C2 C N N 198 TFE O2 O N N 199 TFE N3 N N N 200 TFE C4 C N N 201 TFE O4 O N N 202 TFE C5 C N N 203 TFE C5M C N N 204 TFE "C2'" C N R 205 TFE "O2'" O N N 206 TFE "CB'" C N N 207 TFE "CC'" C N N 208 TFE "FD'" F N N 209 TFE "FE'" F N N 210 TFE "FF'" F N N 211 TFE "C3'" C N R 212 TFE "O3'" O N N 213 TFE OP3 O N N 214 TFE HOP2 H N N 215 TFE "H5'" H N N 216 TFE "H5''" H N N 217 TFE "H4'" H N N 218 TFE "H1'" H N N 219 TFE H6 H N N 220 TFE HN3 H N N 221 TFE H71 H N N 222 TFE H72 H N N 223 TFE H73 H N N 224 TFE "H2'" H N N 225 TFE "HB'1" H N N 226 TFE "HB'2" H N N 227 TFE "H3'" H N N 228 TFE "HO3'" H N N 229 TFE HOP3 H N N 230 # 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 HOH O H1 sing N N 150 HOH O H2 sing N N 151 SPM N1 C2 sing N N 152 SPM N1 HN11 sing N N 153 SPM N1 HN12 sing N N 154 SPM C2 C3 sing N N 155 SPM C2 H21 sing N N 156 SPM C2 H22 sing N N 157 SPM C3 C4 sing N N 158 SPM C3 H31 sing N N 159 SPM C3 H32 sing N N 160 SPM C4 N5 sing N N 161 SPM C4 H41 sing N N 162 SPM C4 H42 sing N N 163 SPM N5 C6 sing N N 164 SPM N5 HN5 sing N N 165 SPM C6 C7 sing N N 166 SPM C6 H61 sing N N 167 SPM C6 H62 sing N N 168 SPM C7 C8 sing N N 169 SPM C7 H71 sing N N 170 SPM C7 H72 sing N N 171 SPM C8 C9 sing N N 172 SPM C8 H81 sing N N 173 SPM C8 H82 sing N N 174 SPM C9 N10 sing N N 175 SPM C9 H91 sing N N 176 SPM C9 H92 sing N N 177 SPM N10 C11 sing N N 178 SPM N10 HN0 sing N N 179 SPM C11 C12 sing N N 180 SPM C11 H111 sing N N 181 SPM C11 H112 sing N N 182 SPM C12 C13 sing N N 183 SPM C12 H121 sing N N 184 SPM C12 H122 sing N N 185 SPM C13 N14 sing N N 186 SPM C13 H131 sing N N 187 SPM C13 H132 sing N N 188 SPM N14 HN41 sing N N 189 SPM N14 HN42 sing N N 190 TFE P OP1 doub N N 191 TFE P OP2 sing N N 192 TFE P "O5'" sing N N 193 TFE P OP3 sing N N 194 TFE OP2 HOP2 sing N N 195 TFE "O5'" "C5'" sing N N 196 TFE "C5'" "C4'" sing N N 197 TFE "C5'" "H5'" sing N N 198 TFE "C5'" "H5''" sing N N 199 TFE "C4'" "O4'" sing N N 200 TFE "C4'" "C3'" sing N N 201 TFE "C4'" "H4'" sing N N 202 TFE "O4'" "C1'" sing N N 203 TFE "C1'" N1 sing N N 204 TFE "C1'" "C2'" sing N N 205 TFE "C1'" "H1'" sing N N 206 TFE N1 C6 sing N N 207 TFE N1 C2 sing N N 208 TFE C6 C5 doub N N 209 TFE C6 H6 sing N N 210 TFE C2 O2 doub N N 211 TFE C2 N3 sing N N 212 TFE N3 C4 sing N N 213 TFE N3 HN3 sing N N 214 TFE C4 O4 doub N N 215 TFE C4 C5 sing N N 216 TFE C5 C5M sing N N 217 TFE C5M H71 sing N N 218 TFE C5M H72 sing N N 219 TFE C5M H73 sing N N 220 TFE "C2'" "O2'" sing N N 221 TFE "C2'" "C3'" sing N N 222 TFE "C2'" "H2'" sing N N 223 TFE "O2'" "CB'" sing N N 224 TFE "CB'" "CC'" sing N N 225 TFE "CB'" "HB'1" sing N N 226 TFE "CB'" "HB'2" sing N N 227 TFE "CC'" "FD'" sing N N 228 TFE "CC'" "FE'" sing N N 229 TFE "CC'" "FF'" sing N N 230 TFE "C3'" "O3'" sing N N 231 TFE "C3'" "H3'" sing N N 232 TFE "O3'" "HO3'" sing N N 233 TFE OP3 HOP3 sing N N 234 # _ndb_struct_conf_na.entry_id 1Y8L _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 B DC 10 1_555 -0.362 -0.198 0.103 3.026 -9.868 -2.289 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.061 -0.017 -0.115 6.629 -16.977 0.325 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.382 -0.173 -0.033 -8.621 -15.567 1.608 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.153 -0.144 -0.029 -3.113 -16.309 0.440 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B TFE 6 1_555 0.220 -0.115 0.194 -0.629 -12.292 -3.126 5 A_DA5:TFE16_B A 5 ? B 16 ? 20 1 1 A TFE 6 1_555 B DA 5 1_555 -0.166 -0.128 0.187 6.595 -11.840 2.953 6 A_TFE6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.092 -0.182 -0.086 3.250 -14.536 1.482 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.207 -0.151 -0.193 10.600 -15.175 1.092 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.175 -0.144 0.008 -6.494 -11.669 1.638 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.255 -0.130 0.004 -2.347 5.129 -0.118 10 A_DC10:DG11_B A 10 ? B 11 ? 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 0.366 -1.344 3.165 3.216 0.437 39.795 -2.018 -0.176 3.169 0.641 -4.715 39.921 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.325 -2.107 3.556 0.203 12.559 25.082 -7.151 -0.625 2.264 26.874 -0.434 28.006 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.088 -1.385 3.048 -3.279 6.579 36.529 -2.963 1.307 2.848 10.367 5.167 37.237 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B TFE 6 1_555 0.573 -1.509 3.169 0.743 17.899 25.898 -5.598 -0.942 1.792 35.092 -1.456 31.403 4 AA_DT4DA5:TFE16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B TFE 6 1_555 A TFE 6 1_555 B DA 5 1_555 0.640 -1.377 3.107 1.001 6.347 31.072 -3.584 -1.004 2.797 11.691 -1.844 31.714 5 AA_DA5TFE6:DA15TFE16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A TFE 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.139 -1.343 3.200 1.903 13.545 31.588 -4.179 0.503 2.426 23.549 -3.309 34.353 6 AA_TFE6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.218 -1.601 3.208 1.356 5.839 31.511 -3.885 -0.165 2.879 10.632 -2.469 32.062 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.332 -1.924 3.596 -1.635 13.614 29.077 -5.875 0.312 2.485 25.410 3.052 32.085 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.200 -1.614 3.302 1.362 2.097 35.211 -2.971 -0.129 3.209 3.460 -2.248 35.297 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 SPERMINE SPM 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 410D _pdbx_initial_refinement_model.details 'pdb entry 410D' #