data_3OZ3 # _entry.id 3OZ3 # _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 3OZ3 pdb_00003oz3 10.2210/pdb3oz3/pdb NDB NA0807 ? ? RCSB RCSB061752 ? ? WWPDB D_1000061752 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3OZ4 . unspecified PDB 3OZ5 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3OZ3 _pdbx_database_status.recvd_initial_deposition_date 2010-09-24 _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.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Seth, P.R.' 1 'Allerson, C.A.' 2 'Berdeja, A.' 3 'Siwkowski, A.' 4 'Pallan, P.S.' 5 'Gaus, H.' 6 'Prakash, T.P.' 7 'Watt, A.T.' 8 'Egli, M.' 9 'Swayze, E.E.' 10 # _citation.id primary _citation.title ;An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 132 _citation.page_first 14942 _citation.page_last 14950 _citation.year 2010 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20886816 _citation.pdbx_database_id_DOI 10.1021/ja105875e # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Seth, P.P.' 1 ? primary 'Allerson, C.R.' 2 ? primary 'Berdeja, A.' 3 ? primary 'Siwkowski, A.' 4 ? primary 'Pallan, P.S.' 5 ? primary 'Gaus, H.' 6 ? primary 'Prakash, T.P.' 7 ? primary 'Watt, A.T.' 8 ? primary 'Egli, M.' 9 ? primary 'Swayze, E.E.' 10 ? # _cell.entry_id 3OZ3 _cell.length_a 24.419 _cell.length_b 44.105 _cell.length_c 45.842 _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 3OZ3 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*CP*GP*TP*AP*(UVX)P*AP*CP*GP*C)-3') ; 3069.027 2 ? ? ? ? 2 non-polymer syn '(4S)-2-METHYL-2,4-PENTANEDIOL' 118.174 1 ? ? ? ? 3 water nat water 18.015 61 ? ? ? ? # _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)(UVX)(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 UVX 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 3OZ3 _struct_ref.pdbx_db_accession 3OZ3 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3OZ3 A 1 ? 10 ? 3OZ3 101 ? 110 ? 101 110 2 1 3OZ3 B 1 ? 10 ? 3OZ3 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 MPD non-polymer . '(4S)-2-METHYL-2,4-PENTANEDIOL' ? 'C6 H14 O2' 118.174 UVX 'DNA linking' n ;[(1R,3R,4R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methylidene-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate ; ? 'C12 H15 N2 O8 P' 346.230 # _exptl.entry_id 3OZ3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.01 _exptl_crystal.density_percent_sol 38.83 _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 6.0 _exptl_crystal_grow.pdbx_details ;20 mM sodium cacodylate, 6 mM sodium chloride, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _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 'sodium cacodylate' ? ? ? 1 2 1 'sodium chloride' ? ? ? 1 3 1 'potassium chloride' ? ? ? 1 4 1 'spermine tetrahydrochloride' ? ? ? 1 5 1 MPD ? ? ? 1 6 2 'sodium cacodylate' ? ? ? 1 7 2 'sodium chloride' ? ? ? 1 8 2 'potassium chloride' ? ? ? 1 9 2 'spermine tetrahydrochloride' ? ? ? 1 10 2 MPD ? ? ? # _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 2009-02-16 _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 ? _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 3OZ3 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.57 _reflns.number_obs 7592 _reflns.number_all 7637 _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.067 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 47.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.2 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.57 _reflns_shell.d_res_low 1.63 _reflns_shell.percent_possible_all 99.7 _reflns_shell.Rmerge_I_obs 0.248 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 13.2 _reflns_shell.pdbx_redundancy 5.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 743 _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 3OZ3 _refine.ls_number_reflns_obs 6949 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _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 31.78 _refine.ls_d_res_high 1.57 _refine.ls_percent_reflns_obs 99.35 _refine.ls_R_factor_obs 0.16525 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.16318 _refine.ls_R_factor_R_free 0.20760 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 339 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.968 _refine.correlation_coeff_Fo_to_Fc_free 0.959 _refine.B_iso_mean 16.242 _refine.aniso_B[1][1] -0.58 _refine.aniso_B[2][2] -0.12 _refine.aniso_B[3][3] 0.70 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 3EY2' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.087 _refine.overall_SU_ML 0.055 _refine.overall_SU_B 3.466 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _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 8 _refine_hist.number_atoms_solvent 61 _refine_hist.number_atoms_total 477 _refine_hist.d_res_high 1.57 _refine_hist.d_res_low 31.78 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.022 0.021 ? 461 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.477 3.000 ? 702 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.411 0.200 ? 83 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.011 0.020 ? 216 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 4.086 3.000 ? 461 'X-RAY DIFFRACTION' ? r_scangle_it 4.741 4.500 ? 702 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 3.213 3.000 ? 461 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.570 _refine_ls_shell.d_res_low 1.611 _refine_ls_shell.number_reflns_R_work 504 _refine_ls_shell.R_factor_R_work 0.152 _refine_ls_shell.percent_reflns_obs 99.62 _refine_ls_shell.R_factor_R_free 0.279 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 26 _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 3OZ3 _struct.title 'Vinyl Carbocyclic LNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3OZ3 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-form DNA, vinyl carbocyclic LNA, antisense oligonucleotides, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A UVX 6 P ? ? A DA 105 A UVX 106 1_555 ? ? ? ? ? ? ? 1.564 ? ? covale2 covale both ? A UVX 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A UVX 106 A DA 107 1_555 ? ? ? ? ? ? ? 1.640 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B UVX 6 P ? ? B DA 205 B UVX 206 1_555 ? ? ? ? ? ? ? 1.585 ? ? covale4 covale both ? B UVX 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B UVX 206 B DA 207 1_555 ? ? ? ? ? ? ? 1.581 ? ? 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 ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MPD _struct_site.pdbx_auth_seq_id 211 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE MPD A 211' # 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 5 HOH D . ? HOH A 41 . ? 3_555 ? 2 AC1 5 DG A 1 ? DG A 101 . ? 3_555 ? 3 AC1 5 HOH E . ? HOH B 31 . ? 1_555 ? 4 AC1 5 UVX B 6 ? UVX B 206 . ? 1_555 ? 5 AC1 5 DA B 7 ? DA B 207 . ? 1_555 ? # _database_PDB_matrix.entry_id 3OZ3 _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 3OZ3 _atom_sites.fract_transf_matrix[1][1] 0.040952 _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] 0.022673 _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] 0.021814 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ # loop_ # 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 UVX 6 106 106 UVX UVX 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 UVX 6 206 206 UVX UVX 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 MPD 1 211 211 MPD MPD A . D 3 HOH 1 1 1 HOH HOH A . D 3 HOH 2 2 2 HOH HOH A . D 3 HOH 3 3 3 HOH HOH A . D 3 HOH 4 4 4 HOH HOH A . D 3 HOH 5 5 5 HOH HOH A . D 3 HOH 6 6 6 HOH HOH A . D 3 HOH 7 7 7 HOH HOH A . D 3 HOH 8 8 8 HOH HOH A . D 3 HOH 9 9 9 HOH HOH A . D 3 HOH 10 10 10 HOH HOH A . D 3 HOH 11 13 13 HOH HOH A . D 3 HOH 12 14 14 HOH HOH A . D 3 HOH 13 15 15 HOH HOH A . D 3 HOH 14 16 16 HOH HOH A . D 3 HOH 15 21 21 HOH HOH A . D 3 HOH 16 22 22 HOH HOH A . D 3 HOH 17 25 25 HOH HOH A . D 3 HOH 18 27 27 HOH HOH A . D 3 HOH 19 28 28 HOH HOH A . D 3 HOH 20 29 29 HOH HOH A . D 3 HOH 21 30 30 HOH HOH A . D 3 HOH 22 32 32 HOH HOH A . D 3 HOH 23 34 34 HOH HOH A . D 3 HOH 24 36 36 HOH HOH A . D 3 HOH 25 41 41 HOH HOH A . D 3 HOH 26 42 42 HOH HOH A . D 3 HOH 27 43 43 HOH HOH A . D 3 HOH 28 44 44 HOH HOH A . D 3 HOH 29 45 45 HOH HOH A . D 3 HOH 30 48 48 HOH HOH A . D 3 HOH 31 57 57 HOH HOH A . D 3 HOH 32 60 60 HOH HOH A . D 3 HOH 33 61 61 HOH HOH A . D 3 HOH 34 63 63 HOH HOH A . D 3 HOH 35 65 65 HOH HOH A . E 3 HOH 1 11 11 HOH HOH B . E 3 HOH 2 12 12 HOH HOH B . E 3 HOH 3 17 17 HOH HOH B . E 3 HOH 4 18 18 HOH HOH B . E 3 HOH 5 19 19 HOH HOH B . E 3 HOH 6 20 20 HOH HOH B . E 3 HOH 7 23 23 HOH HOH B . E 3 HOH 8 24 24 HOH HOH B . E 3 HOH 9 26 26 HOH HOH B . E 3 HOH 10 31 31 HOH HOH B . E 3 HOH 11 33 33 HOH HOH B . E 3 HOH 12 35 35 HOH HOH B . E 3 HOH 13 46 46 HOH HOH B . E 3 HOH 14 47 47 HOH HOH B . E 3 HOH 15 49 49 HOH HOH B . E 3 HOH 16 50 50 HOH HOH B . E 3 HOH 17 51 51 HOH HOH B . E 3 HOH 18 52 52 HOH HOH B . E 3 HOH 19 53 53 HOH HOH B . E 3 HOH 20 54 54 HOH HOH B . E 3 HOH 21 55 55 HOH HOH B . E 3 HOH 22 56 56 HOH HOH B . E 3 HOH 23 58 58 HOH HOH B . E 3 HOH 24 59 59 HOH HOH B . E 3 HOH 25 62 62 HOH HOH B . E 3 HOH 26 64 64 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 UVX 6 A UVX 106 ? DU ? 2 B UVX 6 B UVX 206 ? DU ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1230 ? 1 MORE -7 ? 1 'SSA (A^2)' 3810 ? # _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 2010-11-24 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-09-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 MOLREP phasing . ? 2 CCP4 'model building' . ? 3 REFMAC refinement 5.5.0109 ? 4 HKL-2000 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 CCP4 phasing . ? 7 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DA 107 ? ? "C3'" A DA 107 ? ? 1.380 1.419 -0.039 0.006 N 2 1 "C5'" A DC 110 ? ? "C4'" A DC 110 ? ? 1.561 1.512 0.049 0.007 N 3 1 "C5'" B DG 201 ? ? "C4'" B DG 201 ? ? 1.556 1.512 0.044 0.007 N 4 1 C4 B DT 204 ? ? C5 B DT 204 ? ? 1.503 1.445 0.058 0.009 N 5 1 C6 B DT 204 ? ? N1 B DT 204 ? ? 1.420 1.378 0.042 0.007 N 6 1 C6 B DA 205 ? ? N6 B DA 205 ? ? 1.405 1.335 0.070 0.008 N 7 1 "O3'" B DG 209 ? ? "C3'" B DG 209 ? ? 1.383 1.419 -0.036 0.006 N 8 1 "O3'" B DC 210 ? ? "C3'" B DC 210 ? ? 1.381 1.419 -0.038 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 110 ? ? "C4'" A DC 110 ? ? "C3'" A DC 110 ? ? 101.84 104.50 -2.66 0.40 N 2 1 "O4'" B DT 204 ? ? "C4'" B DT 204 ? ? "C3'" B DT 204 ? ? 101.85 104.50 -2.65 0.40 N 3 1 "O4'" B DG 209 ? ? "C1'" B DG 209 ? ? "C2'" B DG 209 ? ? 109.87 106.80 3.07 0.50 N 4 1 "O4'" B DG 209 ? ? "C1'" B DG 209 ? ? N9 B DG 209 ? ? 110.11 108.30 1.81 0.30 N 5 1 "O4'" B DC 210 ? ? "C1'" B DC 210 ? ? "C2'" B DC 210 ? ? 110.16 106.80 3.36 0.50 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MPD C1 C N N 147 MPD C2 C N N 148 MPD O2 O N N 149 MPD CM C N N 150 MPD C3 C N N 151 MPD C4 C N S 152 MPD O4 O N N 153 MPD C5 C N N 154 MPD H11 H N N 155 MPD H12 H N N 156 MPD H13 H N N 157 MPD HO2 H N N 158 MPD HM1 H N N 159 MPD HM2 H N N 160 MPD HM3 H N N 161 MPD H31 H N N 162 MPD H32 H N N 163 MPD H4 H N N 164 MPD HO4 H N N 165 MPD H51 H N N 166 MPD H52 H N N 167 MPD H53 H N N 168 UVX P P N N 169 UVX N1 N N N 170 UVX C2 C N N 171 UVX O2 O N N 172 UVX N3 N N N 173 UVX C4 C N N 174 UVX O4 O N N 175 UVX C5 C N N 176 UVX C6 C N N 177 UVX "C1'" C N R 178 UVX "C2'" C N R 179 UVX "C3'" C N S 180 UVX "O3'" O N N 181 UVX "C4'" C N R 182 UVX "O4'" O N N 183 UVX "C5'" C N N 184 UVX "O5'" O N N 185 UVX "C6'" C N N 186 UVX "C7'" C N N 187 UVX "C8'" C N N 188 UVX OP1 O N N 189 UVX OP2 O N N 190 UVX OP3 O N N 191 UVX H5 H N N 192 UVX H6 H N N 193 UVX "H1'" H N N 194 UVX "H2'" H N N 195 UVX "H3'" H N N 196 UVX "HO3'" H N N 197 UVX "H5'" H N N 198 UVX "H5'A" H N N 199 UVX "H7'" H N N 200 UVX "H7'A" H N N 201 UVX "H8'" H N N 202 UVX "H8'A" H N N 203 UVX HOP2 H N N 204 UVX HOP3 H N N 205 UVX HN3 H N N 206 # 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 MPD C1 C2 sing N N 152 MPD C1 H11 sing N N 153 MPD C1 H12 sing N N 154 MPD C1 H13 sing N N 155 MPD C2 O2 sing N N 156 MPD C2 CM sing N N 157 MPD C2 C3 sing N N 158 MPD O2 HO2 sing N N 159 MPD CM HM1 sing N N 160 MPD CM HM2 sing N N 161 MPD CM HM3 sing N N 162 MPD C3 C4 sing N N 163 MPD C3 H31 sing N N 164 MPD C3 H32 sing N N 165 MPD C4 O4 sing N N 166 MPD C4 C5 sing N N 167 MPD C4 H4 sing N N 168 MPD O4 HO4 sing N N 169 MPD C5 H51 sing N N 170 MPD C5 H52 sing N N 171 MPD C5 H53 sing N N 172 UVX OP1 P doub N N 173 UVX OP3 P sing N N 174 UVX P "O5'" sing N N 175 UVX P OP2 sing N N 176 UVX "C1'" N1 sing N N 177 UVX N1 C6 sing N N 178 UVX N1 C2 sing N N 179 UVX O2 C2 doub N N 180 UVX C2 N3 sing N N 181 UVX N3 C4 sing N N 182 UVX C5 C4 sing N N 183 UVX C4 O4 doub N N 184 UVX C6 C5 doub N N 185 UVX C5 H5 sing N N 186 UVX C6 H6 sing N N 187 UVX "O4'" "C1'" sing N N 188 UVX "C1'" "C2'" sing N N 189 UVX "C1'" "H1'" sing N N 190 UVX "C6'" "C2'" sing N N 191 UVX "C3'" "C2'" sing N N 192 UVX "C2'" "H2'" sing N N 193 UVX "C4'" "C3'" sing N N 194 UVX "C3'" "O3'" sing N N 195 UVX "C3'" "H3'" sing N N 196 UVX "O3'" "HO3'" sing N N 197 UVX "C5'" "C4'" sing N N 198 UVX "C8'" "C4'" sing N N 199 UVX "C4'" "O4'" sing N N 200 UVX "C5'" "O5'" sing N N 201 UVX "C5'" "H5'" sing N N 202 UVX "C5'" "H5'A" sing N N 203 UVX "C8'" "C6'" sing N N 204 UVX "C6'" "C7'" doub N N 205 UVX "C7'" "H7'" sing N N 206 UVX "C7'" "H7'A" sing N N 207 UVX "C8'" "H8'" sing N N 208 UVX "C8'" "H8'A" sing N N 209 UVX OP2 HOP2 sing N N 210 UVX OP3 HOP3 sing N N 211 UVX N3 HN3 sing N N 212 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3OZ3 'a-form double helix' 3OZ3 '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 -0.253 -0.075 0.022 2.352 -4.592 -1.326 1 A_DG101:DC210_B A 101 ? B 210 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.208 -0.115 0.038 3.439 -10.316 0.393 2 A_DC102:DG209_B A 102 ? B 209 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.303 -0.146 0.151 -6.669 -16.702 -0.001 3 A_DG103:DC208_B A 103 ? B 208 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.161 -0.189 0.002 -3.061 -18.328 -1.368 4 A_DT104:DA207_B A 104 ? B 207 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.045 -0.157 0.016 5.779 -8.404 3.767 5 A_DA107:DT204_B A 107 ? B 204 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.290 -0.187 -0.174 9.952 -12.413 1.421 6 A_DC108:DG203_B A 108 ? B 203 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.317 -0.172 -0.109 -6.871 -10.106 0.443 7 A_DG109:DC202_B A 109 ? B 202 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.308 -0.134 0.171 -3.403 5.803 0.581 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 -1.572 3.263 1.077 0.282 38.795 -2.401 -0.232 3.257 0.424 -1.621 38.811 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 0.164 -2.255 3.391 0.378 8.989 24.506 -7.252 -0.269 2.426 20.323 -0.855 26.082 2 AA_DC102DG103:DC208DG209_BB A 102 ? B 209 ? A 103 ? B 208 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.080 -1.474 3.080 -1.428 4.577 37.495 -2.820 1.499 2.924 7.085 2.211 37.790 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 -0.085 -1.658 3.304 0.255 3.935 30.092 -3.941 0.213 3.067 7.538 -0.488 30.343 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 -0.342 -1.949 3.616 -1.358 11.416 28.862 -5.839 0.379 2.682 21.840 2.598 31.022 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 0.169 -1.746 3.332 -0.163 2.159 35.974 -3.129 -0.296 3.225 3.492 0.264 36.037 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 '(4S)-2-METHYL-2,4-PENTANEDIOL' MPD 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' #