data_4F2Y # _entry.id 4F2Y # _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 4F2Y pdb_00004f2y 10.2210/pdb4f2y/pdb NDB NA1781 ? ? RCSB RCSB072388 ? ? WWPDB D_1000072388 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4F2X _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4F2Y _pdbx_database_status.recvd_initial_deposition_date 2012-05-08 _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 ;Synthesis and Antisense Properties of Fluoro Cyclohexenyl Nucleic Acid (F-CeNA), a Nuclease Stable Mimic of 2'-Fluoro RNA. ; _citation.journal_abbrev J.Org.Chem. _citation.journal_volume 77 _citation.page_first 5074 _citation.page_last 5085 _citation.year 2012 _citation.journal_id_ASTM JOCEAH _citation.country US _citation.journal_id_ISSN 0022-3263 _citation.journal_id_CSD 0035 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22591005 _citation.pdbx_database_id_DOI 10.1021/jo300594b # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Seth, P.P.' 1 ? primary 'Yu, J.' 2 ? primary 'Jazayeri, A.' 3 ? primary 'Pallan, P.S.' 4 ? primary 'Allerson, C.R.' 5 ? primary 'Ostergaard, M.E.' 6 ? primary 'Liu, F.' 7 ? primary 'Herdewijn, P.' 8 ? primary 'Egli, M.' 9 ? primary 'Swayze, E.E.' 10 ? # _cell.entry_id 4F2Y _cell.length_a 24.775 _cell.length_b 38.299 _cell.length_c 47.746 _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 4F2Y _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*(XTF)P*AP*CP*GP*C)-3'" 3073.034 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 52 ? ? ? ? # _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)(XTF)(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 XTF 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 4F2Y _struct_ref.pdbx_db_accession 4F2Y _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code 'GCGTA(XTF)ACGC' _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 4F2Y A 1 ? 10 ? 4F2Y 101 ? 110 ? 101 110 2 1 4F2Y B 1 ? 10 ? 4F2Y 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 XTF 'DNA linking' n ;[(1R,4R,5S,6R)-5-fluoro-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate ; ? 'C12 H16 F N2 O7 P' 350.237 # _exptl.entry_id 4F2Y _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.84 _exptl_crystal.density_percent_sol 33.25 _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 5.5 _exptl_crystal_grow.pdbx_details ;40 mM sodium cacodylate, 20 mM cobalt hexamine, 40 mM lithium chloride, 20 mM magnesium chloride, 10% v/v MPD, pH 5.5, 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 2012-04-06 _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 'diamond(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 4F2Y _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.875 _reflns.d_resolution_high 1.59 _reflns.number_obs 6416 _reflns.number_all 6450 _reflns.percent_possible_obs 99.45 _reflns.pdbx_Rmerge_I_obs 0.091 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 59.43 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 14.2 _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 1.59 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs 0.53 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 9.8 _reflns_shell.pdbx_redundancy ? _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 4F2Y _refine.ls_number_reflns_obs 5930 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I 5.0 _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.875 _refine.ls_d_res_high 1.59 _refine.ls_percent_reflns_obs 99.60 _refine.ls_R_factor_obs 0.18694 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.18193 _refine.ls_R_factor_R_free 0.25331 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.6 _refine.ls_number_reflns_R_free 486 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.962 _refine.correlation_coeff_Fo_to_Fc_free 0.930 _refine.B_iso_mean 20.104 _refine.aniso_B[1][1] -0.38 _refine.aniso_B[2][2] 0.24 _refine.aniso_B[3][3] 0.14 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY ; _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 0.155 _refine.pdbx_overall_ESU_R_Free 0.116 _refine.overall_SU_ML 0.072 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.552 _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 408 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 52 _refine_hist.number_atoms_total 462 _refine_hist.d_res_high 1.59 _refine_hist.d_res_low 29.875 # 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 0.005 0.012 ? 456 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.365 1.517 ? 700 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.077 0.200 ? 64 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.010 0.020 ? 218 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr 3.220 3.000 ? 456 ? 'X-RAY DIFFRACTION' r_sphericity_free 22.969 5.000 ? 24 ? 'X-RAY DIFFRACTION' r_sphericity_bonded 11.461 5.000 ? 442 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.59 _refine_ls_shell.d_res_low 1.636 _refine_ls_shell.number_reflns_R_work 363 _refine_ls_shell.R_factor_R_work 0.146 _refine_ls_shell.percent_reflns_obs 94.87 _refine_ls_shell.R_factor_R_free 0.241 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 25 _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 4F2Y _struct.title ;Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4F2Y _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Fluoro Cyclohexenyl Nucleic Acid, F-CeNA, Modified DNA, A-form DNA, 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 ? E N N 3 ? F 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 XTF 6 P ? ? A DA 105 A XTF 106 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale2 covale both ? B DA 5 "O3'" ? ? ? 1_555 B XTF 6 P ? ? B DA 205 B XTF 206 1_555 ? ? ? ? ? ? ? 1.602 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 201 A HOH 301 1_555 ? ? ? ? ? ? ? 2.095 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 201 A HOH 302 1_555 ? ? ? ? ? ? ? 2.224 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 201 A HOH 303 1_555 ? ? ? ? ? ? ? 2.069 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 201 A HOH 304 1_555 ? ? ? ? ? ? ? 1.964 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 201 A HOH 305 1_555 ? ? ? ? ? ? ? 2.008 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 201 B HOH 402 1_555 ? ? ? ? ? ? ? 2.206 ? ? metalc7 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 403 1_555 ? ? ? ? ? ? ? 2.139 ? ? metalc8 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 404 1_555 ? ? ? ? ? ? ? 2.092 ? ? metalc9 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 405 1_555 ? ? ? ? ? ? ? 1.925 ? ? metalc10 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 406 1_555 ? ? ? ? ? ? ? 2.297 ? ? metalc11 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 408 1_555 ? ? ? ? ? ? ? 1.994 ? ? 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 ? ? # 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 A MG 201 ? 6 'BINDING SITE FOR RESIDUE MG A 201' AC2 Software B MG 301 ? 5 'BINDING SITE FOR RESIDUE MG B 301' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HOH E . ? HOH A 301 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH A 302 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 303 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 304 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH A 305 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH B 402 . ? 1_555 ? 7 AC2 5 HOH F . ? HOH B 403 . ? 1_555 ? 8 AC2 5 HOH F . ? HOH B 404 . ? 1_555 ? 9 AC2 5 HOH F . ? HOH B 405 . ? 1_555 ? 10 AC2 5 HOH F . ? HOH B 406 . ? 1_555 ? 11 AC2 5 HOH F . ? HOH B 408 . ? 1_555 ? # _database_PDB_matrix.entry_id 4F2Y _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 4F2Y _atom_sites.fract_transf_matrix[1][1] 0.040363 _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] 0.026110 _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] 0.020944 _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 1 101 101 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 XTF 6 106 106 XTF XTF 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 XTF 6 206 206 XTF XTF 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 MG 1 201 1 MG MG A . D 2 MG 1 301 2 MG MG B . E 3 HOH 1 301 3 HOH HOH A . E 3 HOH 2 302 4 HOH HOH A . E 3 HOH 3 303 5 HOH HOH A . E 3 HOH 4 304 7 HOH HOH A . E 3 HOH 5 305 8 HOH HOH A . E 3 HOH 6 306 19 HOH HOH A . E 3 HOH 7 307 21 HOH HOH A . E 3 HOH 8 308 24 HOH HOH A . E 3 HOH 9 309 28 HOH HOH A . E 3 HOH 10 310 29 HOH HOH A . E 3 HOH 11 311 30 HOH HOH A . E 3 HOH 12 312 32 HOH HOH A . E 3 HOH 13 313 36 HOH HOH A . E 3 HOH 14 314 37 HOH HOH A . E 3 HOH 15 315 44 HOH HOH A . E 3 HOH 16 316 45 HOH HOH A . E 3 HOH 17 317 46 HOH HOH A . E 3 HOH 18 318 49 HOH HOH A . E 3 HOH 19 319 50 HOH HOH A . E 3 HOH 20 320 51 HOH HOH A . F 3 HOH 1 401 18 HOH HOH B . F 3 HOH 2 402 6 HOH HOH B . F 3 HOH 3 403 9 HOH HOH B . F 3 HOH 4 404 10 HOH HOH B . F 3 HOH 5 405 11 HOH HOH B . F 3 HOH 6 406 12 HOH HOH B . F 3 HOH 7 407 13 HOH HOH B . F 3 HOH 8 408 14 HOH HOH B . F 3 HOH 9 409 15 HOH HOH B . F 3 HOH 10 410 16 HOH HOH B . F 3 HOH 11 411 17 HOH HOH B . F 3 HOH 12 412 20 HOH HOH B . F 3 HOH 13 413 22 HOH HOH B . F 3 HOH 14 414 23 HOH HOH B . F 3 HOH 15 415 25 HOH HOH B . F 3 HOH 16 416 26 HOH HOH B . F 3 HOH 17 417 27 HOH HOH B . F 3 HOH 18 418 31 HOH HOH B . F 3 HOH 19 419 33 HOH HOH B . F 3 HOH 20 420 34 HOH HOH B . F 3 HOH 21 421 35 HOH HOH B . F 3 HOH 22 422 38 HOH HOH B . F 3 HOH 23 423 39 HOH HOH B . F 3 HOH 24 424 40 HOH HOH B . F 3 HOH 25 425 41 HOH HOH B . F 3 HOH 26 426 42 HOH HOH B . F 3 HOH 27 427 43 HOH HOH B . F 3 HOH 28 428 47 HOH HOH B . F 3 HOH 29 429 48 HOH HOH B . F 3 HOH 30 430 52 HOH HOH B . F 3 HOH 31 431 53 HOH HOH B . F 3 HOH 32 432 54 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 XTF 6 A XTF 106 ? DT ? 2 B XTF 6 B XTF 206 ? DT ? # _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,F # 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)' 1120 ? 1 MORE -11 ? 1 'SSA (A^2)' 3800 ? # _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 301 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 302 ? 1_555 91.6 ? 2 O ? E HOH . ? A HOH 301 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 303 ? 1_555 86.6 ? 3 O ? E HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 303 ? 1_555 87.4 ? 4 O ? E HOH . ? A HOH 301 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 304 ? 1_555 174.8 ? 5 O ? E HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 304 ? 1_555 92.8 ? 6 O ? E HOH . ? A HOH 303 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 304 ? 1_555 96.4 ? 7 O ? E HOH . ? A HOH 301 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 305 ? 1_555 90.1 ? 8 O ? E HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 305 ? 1_555 92.0 ? 9 O ? E HOH . ? A HOH 303 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 305 ? 1_555 176.6 ? 10 O ? E HOH . ? A HOH 304 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? E HOH . ? A HOH 305 ? 1_555 87.0 ? 11 O ? E HOH . ? A HOH 301 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? F HOH . ? B HOH 402 ? 1_555 83.3 ? 12 O ? E HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? F HOH . ? B HOH 402 ? 1_555 172.8 ? 13 O ? E HOH . ? A HOH 303 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? F HOH . ? B HOH 402 ? 1_555 87.2 ? 14 O ? E HOH . ? A HOH 304 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? F HOH . ? B HOH 402 ? 1_555 92.6 ? 15 O ? E HOH . ? A HOH 305 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? F HOH . ? B HOH 402 ? 1_555 93.0 ? 16 O ? F HOH . ? B HOH 403 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 404 ? 1_555 89.0 ? 17 O ? F HOH . ? B HOH 403 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 405 ? 1_555 90.5 ? 18 O ? F HOH . ? B HOH 404 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 405 ? 1_555 88.0 ? 19 O ? F HOH . ? B HOH 403 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 406 ? 1_555 173.1 ? 20 O ? F HOH . ? B HOH 404 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 406 ? 1_555 87.9 ? 21 O ? F HOH . ? B HOH 405 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 406 ? 1_555 95.6 ? 22 O ? F HOH . ? B HOH 403 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 408 ? 1_555 89.3 ? 23 O ? F HOH . ? B HOH 404 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 408 ? 1_555 85.6 ? 24 O ? F HOH . ? B HOH 405 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 408 ? 1_555 173.6 ? 25 O ? F HOH . ? B HOH 406 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 408 ? 1_555 84.3 ? # 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 2012-05-30 2 'Structure model' 1 1 2012-06-13 3 'Structure model' 1 2 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.value' 13 3 'Structure model' '_struct_conn.pdbx_dist_value' 14 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 15 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 16 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 19 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 21 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 22 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 23 3 '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 5.6.0117 ? 4 HKL-2000 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 CCP4 phasing . ? 7 # 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 XTF F F N N 148 XTF "C2'" C N S 149 XTF "C1'" C N R 150 XTF N1 N N N 151 XTF C6 C N N 152 XTF C5 C N N 153 XTF C5M C N N 154 XTF C2 C N N 155 XTF O2 O N N 156 XTF N3 N N N 157 XTF C4 C N N 158 XTF O4 O N N 159 XTF "C7'" C N N 160 XTF "C6'" C N N 161 XTF "C3'" C N R 162 XTF "O3'" O N N 163 XTF "C4'" C N R 164 XTF "C5'" C N N 165 XTF "O5'" O N N 166 XTF P P N N 167 XTF OP1 O N N 168 XTF OP2 O N N 169 XTF H1 H N N 170 XTF H2 H N N 171 XTF H3 H N N 172 XTF H4 H N N 173 XTF H5 H N N 174 XTF H6 H N N 175 XTF H7 H N N 176 XTF H8 H N N 177 XTF H9 H N N 178 XTF H10 H N N 179 XTF H11 H N N 180 XTF H12 H N N 181 XTF H13 H N N 182 XTF H14 H N N 183 XTF H16 H N N 184 XTF OP3 O N N 185 XTF H18 H N N 186 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 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 XTF F "C2'" sing N N 152 XTF "O3'" "C3'" sing N N 153 XTF "C2'" "C3'" sing N N 154 XTF "C2'" "C1'" sing N N 155 XTF "C3'" "C4'" sing N N 156 XTF "C1'" N1 sing N N 157 XTF "C1'" "C7'" sing N N 158 XTF "O5'" "C5'" sing N N 159 XTF "O5'" P sing N N 160 XTF OP2 P sing N N 161 XTF N1 C6 sing N N 162 XTF N1 C2 sing N N 163 XTF O2 C2 doub N N 164 XTF C6 C5 doub N N 165 XTF C2 N3 sing N N 166 XTF "C4'" "C5'" sing N N 167 XTF "C4'" "C6'" sing N N 168 XTF C5 C4 sing N N 169 XTF C5 C5M sing N N 170 XTF N3 C4 sing N N 171 XTF C4 O4 doub N N 172 XTF P OP1 doub N N 173 XTF "C7'" "C6'" doub N N 174 XTF "C2'" H1 sing N N 175 XTF "C1'" H2 sing N N 176 XTF C6 H3 sing N N 177 XTF C5M H4 sing N N 178 XTF C5M H5 sing N N 179 XTF C5M H6 sing N N 180 XTF N3 H7 sing N N 181 XTF "C7'" H8 sing N N 182 XTF "C6'" H9 sing N N 183 XTF "C3'" H10 sing N N 184 XTF "O3'" H11 sing N N 185 XTF "C4'" H12 sing N N 186 XTF "C5'" H13 sing N N 187 XTF "C5'" H14 sing N N 188 XTF OP2 H16 sing N N 189 XTF P OP3 sing N N 190 XTF OP3 H18 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4F2Y 'a-form double helix' 4F2Y '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 -0.888 -0.228 0.330 11.712 -18.988 1.105 1 A_DG101:DC210_B A 101 ? B 210 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.165 -0.193 0.006 8.464 -21.782 1.246 2 A_DC102:DG209_B A 102 ? B 209 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.401 -0.178 0.305 -2.089 -10.608 2.351 3 A_DG103:DC208_B A 103 ? B 208 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.143 -0.186 0.152 -0.901 -17.948 -0.458 4 A_DT104:DA207_B A 104 ? B 207 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.071 -0.093 0.333 2.065 -8.591 4.322 5 A_DA107:DT204_B A 107 ? B 204 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.403 -0.079 -0.037 8.577 -14.627 6.331 6 A_DC108:DG203_B A 108 ? B 203 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.093 -0.160 0.020 -6.898 -9.539 -1.253 7 A_DG109:DC202_B A 109 ? B 202 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.429 -0.044 0.152 0.901 0.031 3.029 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 0.241 -1.152 3.241 1.307 3.946 43.165 -1.934 -0.202 3.135 5.349 -1.772 43.355 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 -0.072 -1.924 3.283 -3.928 11.646 27.660 -5.799 -0.572 2.293 22.977 7.749 30.219 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 -0.926 -1.535 3.204 -1.926 6.987 33.315 -3.666 1.293 2.879 12.010 3.311 34.073 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 0.597 -1.929 3.156 4.185 3.523 30.812 -4.207 -0.359 2.976 6.565 -7.799 31.282 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 -0.441 -2.220 3.543 0.080 11.274 27.046 -6.720 0.890 2.439 22.884 -0.163 29.262 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 0.435 -1.580 3.138 0.362 0.535 35.395 -2.673 -0.664 3.119 0.880 -0.595 35.401 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 'MAGNESIUM ION' MG 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3EY2 _pdbx_initial_refinement_model.details 'PDB ENTRY 3EY2' #