data_1HZ2 # _entry.id 1HZ2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1HZ2 pdb_00001hz2 10.2210/pdb1hz2/pdb RCSB RCSB012701 ? ? WWPDB D_1000012701 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1HZ2 _pdbx_database_status.recvd_initial_deposition_date 2001-01-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _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 'Dooley, P.A.' 1 'Tsarouhtsis, D.' 2 'Korbel, G.A.' 3 'Nechev, L.V.' 4 'Shearer, J.' 5 'Zegar, I.S.' 6 'Harris, C.M.' 7 'Stone, M.P.' 8 'Harris, T.M.' 9 # _citation.id primary _citation.title ;Structural studies of an oligodeoxynucleotide containing a trimethylene interstrand cross-link in a 5'-(CpG) motif: model of a malondialdehyde cross-link. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 123 _citation.page_first 1730 _citation.page_last 1739 _citation.year 2001 _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 11456774 _citation.pdbx_database_id_DOI 10.1021/ja003163w # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dooley, P.A.' 1 ? primary 'Tsarouhtsis, D.' 2 ? primary 'Korbel, G.A.' 3 ? primary 'Nechev, L.V.' 4 ? primary 'Shearer, J.' 5 ? primary 'Zegar, I.S.' 6 ? primary 'Harris, C.M.' 7 ? primary 'Stone, M.P.' 8 ? primary 'Harris, T.M.' 9 ? # _cell.entry_id 1HZ2 _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1HZ2 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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(*AP*GP*GP*CP*GP*CP*CP*T)-3') ; 2427.605 2 ? ? ? ? 2 non-polymer syn PROPANE 44.096 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DA)(DG)(DG)(DC)(DG)(DC)(DC)(DT)' _entity_poly.pdbx_seq_one_letter_code_can AGGCGCCT _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 DA n 1 2 DG n 1 3 DG n 1 4 DC n 1 5 DG n 1 6 DC n 1 7 DC n 1 8 DT n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1HZ2 _struct_ref.pdbx_db_accession 1HZ2 _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 1HZ2 A 1 ? 8 ? 1HZ2 1 ? 8 ? 1 8 2 1 1HZ2 B 1 ? 8 ? 1HZ2 9 ? 16 ? 9 16 # 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 TME non-polymer . PROPANE ? 'C3 H8' 44.096 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 DQF-COSY 3 1 1 PE-COSY 4 2 2 '2D NOESY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 303 ambient 7.1 ? ? K 2 298 ambient 7.1 ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '2 mM crosslinked duplex, 10 mM sodium phosphate buffer, 0.1 M NaCl, 50 mM EDTA, pH 7.1' '99.99% D2O' 2 '2 mM crosslinked duplex, 10 mM sodium phosphate buffer, 0.1 M NaCl, 50 mM EDTA, pH 7.1' '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AMX _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1HZ2 _pdbx_nmr_refine.method 'NOE-restrained molecular dynamics, simulated annealing' _pdbx_nmr_refine.details 'Further details about the structural refinement including the trimethylene chain can be found in the journal article' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1HZ2 _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal Felix 95 processing ? 1 MARDIGRAS ? 'iterative matrix relaxation' 'Borgias, B. A.; James, T. l.' 2 X-PLOR 3.1 'structure solution' 'Brunger, A. T.' 3 CPANEL ? 'data analysis' 'Dr. J. Zdunek' 4 SPHINX/LINSHA ? 'data analysis' 'Widmer, H.; Wuthrich, K.' 5 X-PLOR 3.1 refinement 'Brunger, A. T.' 6 # _exptl.entry_id 1HZ2 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1HZ2 _struct.title ;SOLUTION NMR STRUCTURE OF SELF-COMPLEMENTARY DUPLEX 5'-D(AGGCG*CCT)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*. MODEL OF A MALONDIALDEHYDE CROSSLINK ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1HZ2 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA duplex, interstrand crosslink, 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 ? # _struct_biol.id 1 # 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 none ? A DG 5 N2 ? ? ? 1_555 C TME . C3 ? ? A DG 5 A TME 9 1_555 ? ? ? ? ? ? ? 1.461 ? ? covale2 covale none ? C TME . C1 ? ? ? 1_555 B DG 5 N2 ? ? A TME 9 B DG 13 1_555 ? ? ? ? ? ? ? 1.474 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 1 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 1 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 8 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 8 B DA 9 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 TME _struct_site.pdbx_auth_seq_id 9 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE TME A 9' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 DG A 5 ? DG A 5 . ? 1_555 ? 2 AC1 4 DC A 6 ? DC A 6 . ? 1_555 ? 3 AC1 4 DG B 5 ? DG B 13 . ? 1_555 ? 4 AC1 4 DC B 6 ? DC B 14 . ? 1_555 ? # _database_PDB_matrix.entry_id 1HZ2 _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 1HZ2 _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _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 H 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 DA 1 1 1 DA A A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DG 5 5 5 DG PX5 A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DT 8 8 8 DT T A . n B 1 1 DA 1 9 9 DA A B . n B 1 2 DG 2 10 10 DG G B . n B 1 3 DG 3 11 11 DG G B . n B 1 4 DC 4 12 12 DC C B . n B 1 5 DG 5 13 13 DG GPX B . n B 1 6 DC 6 14 14 DC C B . n B 1 7 DC 7 15 15 DC C B . n B 1 8 DT 8 16 16 DT T B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id TME _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 9 _pdbx_nonpoly_scheme.auth_seq_num 13 _pdbx_nonpoly_scheme.pdb_mon_id TME _pdbx_nonpoly_scheme.auth_mon_id GPX _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _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 # _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 2001-02-07 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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' # 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' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 N2 A DG 5 ? ? H31 A TME 9 ? ? 1.30 2 1 "H2''" B DC 14 ? ? "O5'" B DC 15 ? ? 1.51 3 1 "H2''" A DC 6 ? ? "O5'" A DC 7 ? ? 1.55 # 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 C8 A DA 1 ? ? N9 A DA 1 ? ? 1.266 1.373 -0.107 0.008 N 2 1 C8 A DG 2 ? ? N9 A DG 2 ? ? 1.310 1.374 -0.064 0.007 N 3 1 "C4'" A DC 4 ? ? "C3'" A DC 4 ? ? 1.441 1.521 -0.080 0.010 N 4 1 "C3'" A DC 4 ? ? "C2'" A DC 4 ? ? 1.618 1.518 0.100 0.012 N 5 1 "C2'" A DC 4 ? ? "C1'" A DC 4 ? ? 1.587 1.519 0.068 0.010 N 6 1 C8 A DG 5 ? ? N9 A DG 5 ? ? 1.326 1.374 -0.048 0.007 N 7 1 N9 A DG 5 ? ? C4 A DG 5 ? ? 1.325 1.375 -0.050 0.008 N 8 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? 1.332 1.418 -0.086 0.012 N 9 1 "O4'" A DC 6 ? ? "C4'" A DC 6 ? ? 1.317 1.446 -0.129 0.010 N 10 1 "C1'" A DC 6 ? ? N1 A DC 6 ? ? 1.354 1.468 -0.114 0.014 N 11 1 N1 A DC 6 ? ? C6 A DC 6 ? ? 1.267 1.367 -0.100 0.006 N 12 1 C5 A DC 6 ? ? C6 A DC 6 ? ? 1.233 1.339 -0.106 0.008 N 13 1 "C3'" A DC 7 ? ? "C2'" A DC 7 ? ? 1.595 1.518 0.077 0.012 N 14 1 C5 A DT 8 ? ? C6 A DT 8 ? ? 1.413 1.339 0.074 0.007 N 15 1 C5 A DT 8 ? ? C7 A DT 8 ? ? 1.571 1.496 0.075 0.006 N 16 1 C8 B DA 9 ? ? N9 B DA 9 ? ? 1.266 1.373 -0.107 0.008 N 17 1 C8 B DG 10 ? ? N9 B DG 10 ? ? 1.310 1.374 -0.064 0.007 N 18 1 "C4'" B DC 12 ? ? "C3'" B DC 12 ? ? 1.441 1.521 -0.080 0.010 N 19 1 "C3'" B DC 12 ? ? "C2'" B DC 12 ? ? 1.620 1.518 0.102 0.012 N 20 1 "C2'" B DC 12 ? ? "C1'" B DC 12 ? ? 1.583 1.519 0.064 0.010 N 21 1 C8 B DG 13 ? ? N9 B DG 13 ? ? 1.328 1.374 -0.046 0.007 N 22 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? 1.332 1.418 -0.086 0.012 N 23 1 "O4'" B DC 14 ? ? "C4'" B DC 14 ? ? 1.316 1.446 -0.130 0.010 N 24 1 "C1'" B DC 14 ? ? N1 B DC 14 ? ? 1.353 1.468 -0.115 0.014 N 25 1 N1 B DC 14 ? ? C6 B DC 14 ? ? 1.262 1.367 -0.105 0.006 N 26 1 C5 B DC 14 ? ? C6 B DC 14 ? ? 1.233 1.339 -0.106 0.008 N 27 1 "C3'" B DC 15 ? ? "C2'" B DC 15 ? ? 1.603 1.518 0.085 0.012 N 28 1 C5 B DT 16 ? ? C6 B DT 16 ? ? 1.411 1.339 0.072 0.007 N 29 1 C5 B DT 16 ? ? C7 B DT 16 ? ? 1.565 1.496 0.069 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 C5 A DA 1 ? ? N7 A DA 1 ? ? C8 A DA 1 ? ? 100.12 103.90 -3.78 0.50 N 2 1 N7 A DA 1 ? ? C8 A DA 1 ? ? N9 A DA 1 ? ? 119.60 113.80 5.80 0.50 N 3 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.14 108.30 2.84 0.30 N 4 1 C5 A DG 2 ? ? N7 A DG 2 ? ? C8 A DG 2 ? ? 100.95 104.30 -3.35 0.50 N 5 1 N7 A DG 2 ? ? C8 A DG 2 ? ? N9 A DG 2 ? ? 118.70 113.10 5.60 0.50 N 6 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 117.04 113.10 3.94 0.50 N 7 1 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 103.31 106.40 -3.09 0.40 N 8 1 "O4'" A DC 4 ? ? "C4'" A DC 4 ? ? "C3'" A DC 4 ? ? 110.31 106.00 4.31 0.60 N 9 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 112.26 108.30 3.96 0.30 N 10 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 119.52 108.30 11.22 0.30 N 11 1 C5 A DG 5 ? ? N7 A DG 5 ? ? C8 A DG 5 ? ? 100.75 104.30 -3.55 0.50 N 12 1 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.55 113.10 3.45 0.50 N 13 1 N3 A DG 5 ? ? C4 A DG 5 ? ? N9 A DG 5 ? ? 122.36 126.00 -3.64 0.60 N 14 1 "C5'" A DC 6 ? ? "C4'" A DC 6 ? ? "O4'" A DC 6 ? ? 96.70 109.30 -12.60 1.90 N 15 1 C6 A DC 6 ? ? N1 A DC 6 ? ? C2 A DC 6 ? ? 125.65 120.30 5.35 0.40 N 16 1 C6 A DC 6 ? ? N1 A DC 6 ? ? "C1'" A DC 6 ? ? 108.72 120.80 -12.08 1.20 N 17 1 C2 A DC 6 ? ? N1 A DC 6 ? ? "C1'" A DC 6 ? ? 125.46 118.80 6.66 1.10 N 18 1 "C3'" A DC 6 ? ? "O3'" A DC 6 ? ? P A DC 7 ? ? 130.28 119.70 10.58 1.20 Y 19 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 112.63 108.30 4.33 0.30 N 20 1 C5 B DA 9 ? ? N7 B DA 9 ? ? C8 B DA 9 ? ? 100.12 103.90 -3.78 0.50 N 21 1 N7 B DA 9 ? ? C8 B DA 9 ? ? N9 B DA 9 ? ? 119.51 113.80 5.71 0.50 N 22 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? N9 B DG 10 ? ? 111.12 108.30 2.82 0.30 N 23 1 C5 B DG 10 ? ? N7 B DG 10 ? ? C8 B DG 10 ? ? 100.96 104.30 -3.34 0.50 N 24 1 N7 B DG 10 ? ? C8 B DG 10 ? ? N9 B DG 10 ? ? 118.68 113.10 5.58 0.50 N 25 1 N7 B DG 11 ? ? C8 B DG 11 ? ? N9 B DG 11 ? ? 117.12 113.10 4.02 0.50 N 26 1 C8 B DG 11 ? ? N9 B DG 11 ? ? C4 B DG 11 ? ? 103.03 106.40 -3.37 0.40 N 27 1 "O4'" B DC 12 ? ? "C4'" B DC 12 ? ? "C3'" B DC 12 ? ? 109.79 106.00 3.79 0.60 N 28 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 112.94 108.30 4.64 0.30 N 29 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 120.88 108.30 12.58 0.30 N 30 1 N7 B DG 13 ? ? C8 B DG 13 ? ? N9 B DG 13 ? ? 117.27 113.10 4.17 0.50 N 31 1 "C5'" B DC 14 ? ? "C4'" B DC 14 ? ? "O4'" B DC 14 ? ? 97.06 109.30 -12.24 1.90 N 32 1 C6 B DC 14 ? ? N1 B DC 14 ? ? C2 B DC 14 ? ? 125.54 120.30 5.24 0.40 N 33 1 N3 B DC 14 ? ? C4 B DC 14 ? ? C5 B DC 14 ? ? 119.44 121.90 -2.46 0.40 N 34 1 C6 B DC 14 ? ? N1 B DC 14 ? ? "C1'" B DC 14 ? ? 109.04 120.80 -11.76 1.20 N 35 1 "C3'" B DC 14 ? ? "O3'" B DC 14 ? ? P B DC 15 ? ? 130.37 119.70 10.67 1.20 Y 36 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 111.82 108.30 3.52 0.30 N 37 1 "O4'" B DT 16 ? ? "C1'" B DT 16 ? ? N1 B DT 16 ? ? 110.96 108.30 2.66 0.30 N 38 1 C5 B DT 16 ? ? C6 B DT 16 ? ? N1 B DT 16 ? ? 119.93 123.70 -3.77 0.60 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 3 ? ? 0.048 'SIDE CHAIN' 2 1 DG B 11 ? ? 0.051 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 1HZ2 _ndb_struct_conf_na.feature '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 DA 1 1_555 B DT 8 1_555 0.279 -1.667 -2.036 41.310 12.341 -16.842 1 A_DA1:DT16_B A 1 ? B 16 ? 20 1 1 A DG 3 1_555 B DC 6 1_555 -1.697 -0.639 0.020 -12.719 -23.644 7.809 2 A_DG3:DC14_B A 3 ? B 14 ? 19 1 1 A DC 6 1_555 B DG 3 1_555 -1.567 -0.392 -0.117 -11.215 -18.023 -7.016 3 A_DC6:DG11_B A 6 ? B 11 ? 19 1 1 A DT 8 1_555 B DA 1 1_555 -0.335 -1.869 -2.100 -40.891 13.720 -24.121 4 A_DT8:DA9_B A 8 ? B 9 ? 20 1 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name PROPANE _pdbx_entity_nonpoly.comp_id TME #