data_1Y86 # _entry.id 1Y86 # _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 1Y86 pdb_00001y86 10.2210/pdb1y86/pdb NDB AD0038 ? ? RCSB RCSB031237 ? ? WWPDB D_1000031237 ? ? # 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 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Y86 _pdbx_database_status.recvd_initial_deposition_date 2004-12-10 _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 1Y86 _cell.length_a 25.263 _cell.length_b 44.184 _cell.length_c 45.392 _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 1Y86 _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*(125)P*AP*CP*GP*C)-3'" 3107.048 2 ? ? ? ? 2 water nat water 18.015 101 ? ? ? ? # _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)(125)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTAUACGC _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 6 125 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 1Y86 _struct_ref.pdbx_db_accession 1Y86 _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 1Y86 A 1 ? 10 ? 1Y86 1 ? 10 ? 1 10 2 1 1Y86 B 1 ? 10 ? 1Y86 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 125 'RNA linking' n "2'-O-FLUOROETHYL-5-METHYL-URIDINE-5'-MONOPHOSPHATE" ? 'C12 H18 F N2 O9 P' 384.251 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 # _exptl.entry_id 1Y86 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.04 _exptl_crystal.density_percent_sol 39.66 _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 7.0 _exptl_crystal_grow.pdbx_details '10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM NaCL, pH 7.0, 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 H2O ? ? ? 1 6 ? MPD ? ? ? 1 7 ? 'Na Cacodilate' ? ? ? 1 8 ? NaCL ? ? ? # _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 1998-08-13 _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 1Y86 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.d_resolution_high 1.70 _reflns.d_resolution_low 30.0 _reflns.number_all 5893 _reflns.number_obs 5893 _reflns.percent_possible_obs 98.3 _reflns.pdbx_Rmerge_I_obs 0.074 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 25.2 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.0 _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 1.70 _reflns_shell.d_res_low 1.76 _reflns_shell.percent_possible_all 87.4 _reflns_shell.Rmerge_I_obs 0.281 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.6 _reflns_shell.pdbx_redundancy 4.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 499 _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 1Y86 _refine.ls_d_res_high 1.70 _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 5758 _refine.ls_number_reflns_obs 5758 _refine.ls_number_reflns_R_free 623 _refine.ls_percent_reflns_obs 96.8 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1707 _refine.ls_R_factor_R_free 0.1886 _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 23.7 _refine.aniso_B[1][1] -2.690 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] -2.393 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] 5.083 _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 412 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 103 _refine_hist.number_atoms_total 515 _refine_hist.d_res_high 1.70 _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_angle_d 0.0092 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.41 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.70 _refine_ls_shell.d_res_low 1.75 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.2466 _refine_ls_shell.percent_reflns_obs 86.4 _refine_ls_shell.R_factor_R_free 0.3169 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 49 _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 1Y86 _struct.title ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(fluoro)ethyl] Thymidine (T*) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Y86 _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 2 ? # _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 125 6 P ? ? A DA 5 A 125 6 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? A 125 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A 125 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B 125 6 P ? ? B DA 15 B 125 16 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale4 covale both ? B 125 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B 125 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.619 ? ? 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 125 6 N3 ? ? A DA 5 B 125 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B 125 6 O4 ? ? A DA 5 B 125 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 125 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A 125 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 125 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A 125 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 ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1Y86 _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 1Y86 _atom_sites.fract_transf_matrix[1][1] 0.039584 _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] 0.022633 _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] 0.022030 _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 # 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 6 125 6 6 6 125 FET 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 6 125 6 16 16 125 FET 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 HOH 1 102 102 HOH HOH A . C 2 HOH 2 103 103 HOH HOH A . C 2 HOH 3 105 105 HOH HOH A . C 2 HOH 4 106 106 HOH HOH A . C 2 HOH 5 107 107 HOH HOH A . C 2 HOH 6 108 108 HOH HOH A . C 2 HOH 7 109 109 HOH HOH A . C 2 HOH 8 110 110 HOH HOH A . C 2 HOH 9 111 111 HOH HOH A . C 2 HOH 10 113 113 HOH HOH A . C 2 HOH 11 114 114 HOH HOH A . C 2 HOH 12 115 115 HOH HOH A . C 2 HOH 13 120 120 HOH HOH A . C 2 HOH 14 121 121 HOH HOH A . C 2 HOH 15 122 122 HOH HOH A . C 2 HOH 16 123 123 HOH HOH A . C 2 HOH 17 124 124 HOH HOH A . C 2 HOH 18 126 126 HOH HOH A . C 2 HOH 19 128 128 HOH HOH A . C 2 HOH 20 129 129 HOH HOH A . C 2 HOH 21 130 130 HOH HOH A . C 2 HOH 22 133 133 HOH HOH A . C 2 HOH 23 136 136 HOH HOH A . C 2 HOH 24 140 140 HOH HOH A . C 2 HOH 25 141 141 HOH HOH A . C 2 HOH 26 142 142 HOH HOH A . C 2 HOH 27 143 143 HOH HOH A . C 2 HOH 28 144 144 HOH HOH A . C 2 HOH 29 145 145 HOH HOH A . C 2 HOH 30 146 146 HOH HOH A . C 2 HOH 31 147 147 HOH HOH A . C 2 HOH 32 148 148 HOH HOH A . C 2 HOH 33 150 150 HOH HOH A . C 2 HOH 34 151 151 HOH HOH A . C 2 HOH 35 152 152 HOH HOH A . C 2 HOH 36 154 154 HOH HOH A . C 2 HOH 37 157 157 HOH HOH A . C 2 HOH 38 158 158 HOH HOH A . C 2 HOH 39 159 159 HOH HOH A . C 2 HOH 40 163 163 HOH HOH A . C 2 HOH 41 164 164 HOH HOH A . C 2 HOH 42 165 165 HOH HOH A . C 2 HOH 43 166 166 HOH HOH A . C 2 HOH 44 167 167 HOH HOH A . C 2 HOH 45 172 172 HOH HOH A . C 2 HOH 46 175 175 HOH HOH A . C 2 HOH 47 179 179 HOH HOH A . C 2 HOH 48 181 181 HOH HOH A . C 2 HOH 49 183 183 HOH HOH A . C 2 HOH 50 184 184 HOH HOH A . C 2 HOH 51 185 185 HOH HOH A . C 2 HOH 52 187 187 HOH HOH A . C 2 HOH 53 188 188 HOH HOH A . C 2 HOH 54 189 189 HOH HOH A . C 2 HOH 55 190 190 HOH HOH A . C 2 HOH 56 191 191 HOH HOH A . C 2 HOH 57 195 195 HOH HOH A . C 2 HOH 58 199 199 HOH HOH A . C 2 HOH 59 200 200 HOH HOH A . C 2 HOH 60 201 201 HOH HOH A . D 2 HOH 1 101 101 HOH HOH B . D 2 HOH 2 104 104 HOH HOH B . D 2 HOH 3 112 112 HOH HOH B . D 2 HOH 4 116 116 HOH HOH B . D 2 HOH 5 117 117 HOH HOH B . D 2 HOH 6 118 118 HOH HOH B . D 2 HOH 7 119 119 HOH HOH B . D 2 HOH 8 125 125 HOH HOH B . D 2 HOH 9 127 127 HOH HOH B . D 2 HOH 10 131 131 HOH HOH B . D 2 HOH 11 132 132 HOH HOH B . D 2 HOH 12 134 134 HOH HOH B . D 2 HOH 13 135 135 HOH HOH B . D 2 HOH 14 137 137 HOH HOH B . D 2 HOH 15 138 138 HOH HOH B . D 2 HOH 16 139 139 HOH HOH B . D 2 HOH 17 149 149 HOH HOH B . D 2 HOH 18 153 153 HOH HOH B . D 2 HOH 19 155 155 HOH HOH B . D 2 HOH 20 156 156 HOH HOH B . D 2 HOH 21 160 160 HOH HOH B . D 2 HOH 22 161 161 HOH HOH B . D 2 HOH 23 162 162 HOH HOH B . D 2 HOH 24 168 168 HOH HOH B . D 2 HOH 25 169 169 HOH HOH B . D 2 HOH 26 170 170 HOH HOH B . D 2 HOH 27 171 171 HOH HOH B . D 2 HOH 28 173 173 HOH HOH B . D 2 HOH 29 174 174 HOH HOH B . D 2 HOH 30 176 176 HOH HOH B . D 2 HOH 31 177 177 HOH HOH B . D 2 HOH 32 178 178 HOH HOH B . D 2 HOH 33 180 180 HOH HOH B . D 2 HOH 34 182 182 HOH HOH B . D 2 HOH 35 186 186 HOH HOH B . D 2 HOH 36 192 192 HOH HOH B . D 2 HOH 37 193 193 HOH HOH B . D 2 HOH 38 194 194 HOH HOH B . D 2 HOH 39 196 196 HOH HOH B . D 2 HOH 40 197 197 HOH HOH B . D 2 HOH 41 198 198 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 125 6 A 125 6 ? U ? 2 B 125 6 B 125 16 ? U ? # _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 # _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_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' struct_conn # 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' '_struct_conn.pdbx_leaving_atom_flag' # 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_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN 2'-O-FLUOROETHYL-5-METHYL-URIDINE-5'-MONOPHOSPHATE is also known as 2'-O-FLUOROETHYL-THYMIDINE-5'-MONOPHOSPHATE ; # 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 125 P P N N 1 125 OP1 O N N 2 125 OP2 O N N 3 125 OP3 O N N 4 125 "O5'" O N N 5 125 "C5'" C N N 6 125 "C4'" C N R 7 125 "O4'" O N N 8 125 "C3'" C N R 9 125 "O3'" O N N 10 125 "C2'" C N R 11 125 "O2'" O N N 12 125 "C1'" C N R 13 125 N1 N N N 14 125 C2 C N N 15 125 O2 O N N 16 125 N3 N N N 17 125 C4 C N N 18 125 O4 O N N 19 125 C5 C N N 20 125 C5M C N N 21 125 C6 C N N 22 125 "CA'" C N N 23 125 "CB'" C N N 24 125 "FC'" F N N 25 125 HOP2 H N N 26 125 HOP3 H N N 27 125 "H5'" H N N 28 125 "H5''" H N N 29 125 "H4'" H N N 30 125 "H3'" H N N 31 125 "HO3'" H N N 32 125 "H2'" H N N 33 125 "H1'" H N N 34 125 H3 H N N 35 125 H71 H N N 36 125 H72 H N N 37 125 H73 H N N 38 125 H6 H N N 39 125 "HA'1" H N N 40 125 "HA'2" H N N 41 125 "HB'1" H N N 42 125 "HB'2" H N N 43 DA OP3 O N N 44 DA P P N N 45 DA OP1 O N N 46 DA OP2 O N N 47 DA "O5'" O N N 48 DA "C5'" C N N 49 DA "C4'" C N R 50 DA "O4'" O N N 51 DA "C3'" C N S 52 DA "O3'" O N N 53 DA "C2'" C N N 54 DA "C1'" C N R 55 DA N9 N Y N 56 DA C8 C Y N 57 DA N7 N Y N 58 DA C5 C Y N 59 DA C6 C Y N 60 DA N6 N N N 61 DA N1 N Y N 62 DA C2 C Y N 63 DA N3 N Y N 64 DA C4 C Y N 65 DA HOP3 H N N 66 DA HOP2 H N N 67 DA "H5'" H N N 68 DA "H5''" H N N 69 DA "H4'" H N N 70 DA "H3'" H N N 71 DA "HO3'" H N N 72 DA "H2'" H N N 73 DA "H2''" H N N 74 DA "H1'" H N N 75 DA H8 H N N 76 DA H61 H N N 77 DA H62 H N N 78 DA H2 H N N 79 DC OP3 O N N 80 DC P P N N 81 DC OP1 O N N 82 DC OP2 O N N 83 DC "O5'" O N N 84 DC "C5'" C N N 85 DC "C4'" C N R 86 DC "O4'" O N N 87 DC "C3'" C N S 88 DC "O3'" O N N 89 DC "C2'" C N N 90 DC "C1'" C N R 91 DC N1 N N N 92 DC C2 C N N 93 DC O2 O N N 94 DC N3 N N N 95 DC C4 C N N 96 DC N4 N N N 97 DC C5 C N N 98 DC C6 C N N 99 DC HOP3 H N N 100 DC HOP2 H N N 101 DC "H5'" H N N 102 DC "H5''" H N N 103 DC "H4'" H N N 104 DC "H3'" H N N 105 DC "HO3'" H N N 106 DC "H2'" H N N 107 DC "H2''" H N N 108 DC "H1'" H N N 109 DC H41 H N N 110 DC H42 H N N 111 DC H5 H N N 112 DC H6 H N N 113 DG OP3 O N N 114 DG P P N N 115 DG OP1 O N N 116 DG OP2 O N N 117 DG "O5'" O N N 118 DG "C5'" C N N 119 DG "C4'" C N R 120 DG "O4'" O N N 121 DG "C3'" C N S 122 DG "O3'" O N N 123 DG "C2'" C N N 124 DG "C1'" C N R 125 DG N9 N Y N 126 DG C8 C Y N 127 DG N7 N Y N 128 DG C5 C Y N 129 DG C6 C N N 130 DG O6 O N N 131 DG N1 N N N 132 DG C2 C N N 133 DG N2 N N N 134 DG N3 N N N 135 DG C4 C Y N 136 DG HOP3 H N N 137 DG HOP2 H N N 138 DG "H5'" H N N 139 DG "H5''" H N N 140 DG "H4'" H N N 141 DG "H3'" H N N 142 DG "HO3'" H N N 143 DG "H2'" H N N 144 DG "H2''" H N N 145 DG "H1'" H N N 146 DG H8 H N N 147 DG H1 H N N 148 DG H21 H N N 149 DG H22 H N N 150 DT OP3 O N N 151 DT P P N N 152 DT OP1 O N N 153 DT OP2 O N N 154 DT "O5'" O N N 155 DT "C5'" C N N 156 DT "C4'" C N R 157 DT "O4'" O N N 158 DT "C3'" C N S 159 DT "O3'" O N N 160 DT "C2'" C N N 161 DT "C1'" C N R 162 DT N1 N N N 163 DT C2 C N N 164 DT O2 O N N 165 DT N3 N N N 166 DT C4 C N N 167 DT O4 O N N 168 DT C5 C N N 169 DT C7 C N N 170 DT C6 C N N 171 DT HOP3 H N N 172 DT HOP2 H N N 173 DT "H5'" H N N 174 DT "H5''" H N N 175 DT "H4'" H N N 176 DT "H3'" H N N 177 DT "HO3'" H N N 178 DT "H2'" H N N 179 DT "H2''" H N N 180 DT "H1'" H N N 181 DT H3 H N N 182 DT H71 H N N 183 DT H72 H N N 184 DT H73 H N N 185 DT H6 H N N 186 HOH O O N N 187 HOH H1 H N N 188 HOH H2 H 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 125 P OP1 doub N N 1 125 P OP2 sing N N 2 125 P OP3 sing N N 3 125 P "O5'" sing N N 4 125 OP2 HOP2 sing N N 5 125 OP3 HOP3 sing N N 6 125 "O5'" "C5'" sing N N 7 125 "C5'" "C4'" sing N N 8 125 "C5'" "H5'" sing N N 9 125 "C5'" "H5''" sing N N 10 125 "C4'" "O4'" sing N N 11 125 "C4'" "C3'" sing N N 12 125 "C4'" "H4'" sing N N 13 125 "O4'" "C1'" sing N N 14 125 "C3'" "O3'" sing N N 15 125 "C3'" "C2'" sing N N 16 125 "C3'" "H3'" sing N N 17 125 "O3'" "HO3'" sing N N 18 125 "C2'" "O2'" sing N N 19 125 "C2'" "C1'" sing N N 20 125 "C2'" "H2'" sing N N 21 125 "O2'" "CA'" sing N N 22 125 "C1'" N1 sing N N 23 125 "C1'" "H1'" sing N N 24 125 N1 C2 sing N N 25 125 N1 C6 sing N N 26 125 C2 O2 doub N N 27 125 C2 N3 sing N N 28 125 N3 C4 sing N N 29 125 N3 H3 sing N N 30 125 C4 O4 doub N N 31 125 C4 C5 sing N N 32 125 C5 C5M sing N N 33 125 C5 C6 doub N N 34 125 C5M H71 sing N N 35 125 C5M H72 sing N N 36 125 C5M H73 sing N N 37 125 C6 H6 sing N N 38 125 "CA'" "CB'" sing N N 39 125 "CA'" "HA'1" sing N N 40 125 "CA'" "HA'2" sing N N 41 125 "CB'" "FC'" sing N N 42 125 "CB'" "HB'1" sing N N 43 125 "CB'" "HB'2" sing N N 44 DA OP3 P sing N N 45 DA OP3 HOP3 sing N N 46 DA P OP1 doub N N 47 DA P OP2 sing N N 48 DA P "O5'" sing N N 49 DA OP2 HOP2 sing N N 50 DA "O5'" "C5'" sing N N 51 DA "C5'" "C4'" sing N N 52 DA "C5'" "H5'" sing N N 53 DA "C5'" "H5''" sing N N 54 DA "C4'" "O4'" sing N N 55 DA "C4'" "C3'" sing N N 56 DA "C4'" "H4'" sing N N 57 DA "O4'" "C1'" sing N N 58 DA "C3'" "O3'" sing N N 59 DA "C3'" "C2'" sing N N 60 DA "C3'" "H3'" sing N N 61 DA "O3'" "HO3'" sing N N 62 DA "C2'" "C1'" sing N N 63 DA "C2'" "H2'" sing N N 64 DA "C2'" "H2''" sing N N 65 DA "C1'" N9 sing N N 66 DA "C1'" "H1'" sing N N 67 DA N9 C8 sing Y N 68 DA N9 C4 sing Y N 69 DA C8 N7 doub Y N 70 DA C8 H8 sing N N 71 DA N7 C5 sing Y N 72 DA C5 C6 sing Y N 73 DA C5 C4 doub Y N 74 DA C6 N6 sing N N 75 DA C6 N1 doub Y N 76 DA N6 H61 sing N N 77 DA N6 H62 sing N N 78 DA N1 C2 sing Y N 79 DA C2 N3 doub Y N 80 DA C2 H2 sing N N 81 DA N3 C4 sing Y N 82 DC OP3 P sing N N 83 DC OP3 HOP3 sing N N 84 DC P OP1 doub N N 85 DC P OP2 sing N N 86 DC P "O5'" sing N N 87 DC OP2 HOP2 sing N N 88 DC "O5'" "C5'" sing N N 89 DC "C5'" "C4'" sing N N 90 DC "C5'" "H5'" sing N N 91 DC "C5'" "H5''" sing N N 92 DC "C4'" "O4'" sing N N 93 DC "C4'" "C3'" sing N N 94 DC "C4'" "H4'" sing N N 95 DC "O4'" "C1'" sing N N 96 DC "C3'" "O3'" sing N N 97 DC "C3'" "C2'" sing N N 98 DC "C3'" "H3'" sing N N 99 DC "O3'" "HO3'" sing N N 100 DC "C2'" "C1'" sing N N 101 DC "C2'" "H2'" sing N N 102 DC "C2'" "H2''" sing N N 103 DC "C1'" N1 sing N N 104 DC "C1'" "H1'" sing N N 105 DC N1 C2 sing N N 106 DC N1 C6 sing N N 107 DC C2 O2 doub N N 108 DC C2 N3 sing N N 109 DC N3 C4 doub N N 110 DC C4 N4 sing N N 111 DC C4 C5 sing N N 112 DC N4 H41 sing N N 113 DC N4 H42 sing N N 114 DC C5 C6 doub N N 115 DC C5 H5 sing N N 116 DC C6 H6 sing N N 117 DG OP3 P sing N N 118 DG OP3 HOP3 sing N N 119 DG P OP1 doub N N 120 DG P OP2 sing N N 121 DG P "O5'" sing N N 122 DG OP2 HOP2 sing N N 123 DG "O5'" "C5'" sing N N 124 DG "C5'" "C4'" sing N N 125 DG "C5'" "H5'" sing N N 126 DG "C5'" "H5''" sing N N 127 DG "C4'" "O4'" sing N N 128 DG "C4'" "C3'" sing N N 129 DG "C4'" "H4'" sing N N 130 DG "O4'" "C1'" sing N N 131 DG "C3'" "O3'" sing N N 132 DG "C3'" "C2'" sing N N 133 DG "C3'" "H3'" sing N N 134 DG "O3'" "HO3'" sing N N 135 DG "C2'" "C1'" sing N N 136 DG "C2'" "H2'" sing N N 137 DG "C2'" "H2''" sing N N 138 DG "C1'" N9 sing N N 139 DG "C1'" "H1'" sing N N 140 DG N9 C8 sing Y N 141 DG N9 C4 sing Y N 142 DG C8 N7 doub Y N 143 DG C8 H8 sing N N 144 DG N7 C5 sing Y N 145 DG C5 C6 sing N N 146 DG C5 C4 doub Y N 147 DG C6 O6 doub N N 148 DG C6 N1 sing N N 149 DG N1 C2 sing N N 150 DG N1 H1 sing N N 151 DG C2 N2 sing N N 152 DG C2 N3 doub N N 153 DG N2 H21 sing N N 154 DG N2 H22 sing N N 155 DG N3 C4 sing N N 156 DT OP3 P sing N N 157 DT OP3 HOP3 sing N N 158 DT P OP1 doub N N 159 DT P OP2 sing N N 160 DT P "O5'" sing N N 161 DT OP2 HOP2 sing N N 162 DT "O5'" "C5'" sing N N 163 DT "C5'" "C4'" sing N N 164 DT "C5'" "H5'" sing N N 165 DT "C5'" "H5''" sing N N 166 DT "C4'" "O4'" sing N N 167 DT "C4'" "C3'" sing N N 168 DT "C4'" "H4'" sing N N 169 DT "O4'" "C1'" sing N N 170 DT "C3'" "O3'" sing N N 171 DT "C3'" "C2'" sing N N 172 DT "C3'" "H3'" sing N N 173 DT "O3'" "HO3'" sing N N 174 DT "C2'" "C1'" sing N N 175 DT "C2'" "H2'" sing N N 176 DT "C2'" "H2''" sing N N 177 DT "C1'" N1 sing N N 178 DT "C1'" "H1'" sing N N 179 DT N1 C2 sing N N 180 DT N1 C6 sing N N 181 DT C2 O2 doub N N 182 DT C2 N3 sing N N 183 DT N3 C4 sing N N 184 DT N3 H3 sing N N 185 DT C4 O4 doub N N 186 DT C4 C5 sing N N 187 DT C5 C7 sing N N 188 DT C5 C6 doub N N 189 DT C7 H71 sing N N 190 DT C7 H72 sing N N 191 DT C7 H73 sing N N 192 DT C6 H6 sing N N 193 HOH O H1 sing N N 194 HOH O H2 sing N N 195 # _ndb_struct_conf_na.entry_id 1Y86 _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 -0.316 -0.149 0.274 1.683 -4.682 -1.030 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.193 -0.116 0.017 6.742 -15.134 1.675 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.342 -0.110 0.002 -8.689 -15.144 1.405 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.107 -0.142 -0.117 -5.336 -15.993 0.591 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B 125 6 1_555 0.192 -0.068 0.246 -1.297 -13.587 -6.481 5 A_DA5:12516_B A 5 ? B 16 ? 20 1 1 A 125 6 1_555 B DA 5 1_555 0.000 -0.118 0.372 3.377 -14.936 3.794 6 A_1256:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.013 -0.158 -0.030 4.746 -11.074 3.087 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.174 -0.195 -0.167 8.226 -11.940 -0.008 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.206 -0.077 -0.191 -6.329 -10.886 3.343 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.266 -0.094 0.010 -2.163 5.552 -0.071 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 0.364 -1.537 3.178 3.115 -0.058 39.690 -2.251 -0.183 3.198 -0.085 -4.580 39.807 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 0.234 -2.095 3.523 1.034 10.740 25.333 -6.920 -0.251 2.454 23.194 -2.234 27.501 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 -1.049 -1.415 3.077 -0.815 5.876 36.972 -2.908 1.538 2.849 9.193 1.275 37.428 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 125 6 1_555 0.577 -1.604 3.098 0.306 19.606 25.663 -5.665 -0.996 1.527 37.883 -0.592 32.197 4 AA_DT4DA5:12516DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B 125 6 1_555 A 125 6 1_555 B DA 5 1_555 0.893 -1.406 3.129 0.893 5.652 32.854 -3.321 -1.420 2.877 9.899 -1.564 33.335 5 AA_DA51256:DA1512516_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A 125 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.251 -1.424 3.033 1.785 13.621 31.005 -4.291 0.673 2.213 24.055 -3.152 33.843 6 AA_1256DA7: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 0.195 -1.635 3.275 0.842 2.703 31.770 -3.458 -0.205 3.133 4.925 -1.534 31.893 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 -0.162 -1.968 3.537 0.789 13.220 27.984 -6.134 0.449 2.380 25.601 -1.528 30.903 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 0.096 -1.638 3.335 -0.398 0.973 34.880 -2.881 -0.221 3.288 1.622 0.663 34.895 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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' #