data_2HPX # _entry.id 2HPX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2HPX pdb_00002hpx 10.2210/pdb2hpx/pdb RCSB RCSB038621 ? ? WWPDB D_1000038621 ? ? # 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 2007-05-29 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-08-08 5 'Structure model' 1 4 2024-05-01 # _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' 'Derived calculations' 5 4 'Structure model' 'Experimental preparation' 6 4 'Structure model' 'Source and taxonomy' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' 9 5 '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' ndb_struct_conf_na 2 4 'Structure model' pdbx_entity_src_syn 3 4 'Structure model' pdbx_nmr_ensemble 4 4 'Structure model' pdbx_nmr_exptl_sample 5 4 'Structure model' pdbx_nmr_exptl_sample_conditions 6 4 'Structure model' pdbx_nmr_sample_details 7 4 'Structure model' pdbx_nmr_software 8 4 'Structure model' pdbx_nmr_spectrometer 9 4 'Structure model' pdbx_struct_assembly 10 4 'Structure model' pdbx_struct_assembly_prop 11 4 'Structure model' pdbx_struct_oper_list 12 5 'Structure model' chem_comp_atom 13 5 'Structure model' chem_comp_bond 14 5 'Structure model' database_2 15 5 'Structure model' pdbx_nmr_software 16 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_pdbx_nmr_ensemble.conformer_selection_criteria' 2 4 'Structure model' '_pdbx_nmr_ensemble.conformers_calculated_total_number' 3 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.ionic_strength_units' 4 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.label' 5 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.pH_units' 6 4 'Structure model' '_pdbx_nmr_sample_details.contents' 7 4 'Structure model' '_pdbx_nmr_sample_details.label' 8 4 'Structure model' '_pdbx_nmr_sample_details.type' 9 4 'Structure model' '_pdbx_nmr_software.classification' 10 4 'Structure model' '_pdbx_nmr_spectrometer.manufacturer' 11 5 'Structure model' '_database_2.pdbx_DOI' 12 5 'Structure model' '_database_2.pdbx_database_accession' 13 5 'Structure model' '_pdbx_nmr_software.name' 14 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _database_PDB_caveat.id 1 _database_PDB_caveat.text ;chirality error at C1' of X4A ; # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2HPX _pdbx_database_status.recvd_initial_deposition_date 2006-07-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2HOU _pdbx_database_related.details ;13mer duplex DNA containing a 4'-oxidized abasic site, 10 structures ; _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Chen, J.' 1 'Dupradeau, F.Y.' 2 'Case, D.A.' 3 'Turner, C.J.' 4 'Stubbe, J.' 5 # _citation.id primary _citation.title ;Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 46 _citation.page_first 3096 _citation.page_last 3107 _citation.year 2007 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17323932 _citation.pdbx_database_id_DOI 10.1021/bi6024269 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, J.' 1 ? primary 'Dupradeau, F.Y.' 2 ? primary 'Case, D.A.' 3 ? primary 'Turner, C.J.' 4 ? primary 'Stubbe, J.' 5 ? # 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(*CP*CP*AP*AP*AP*GP*(X4A)P*AP*CP*CP*GP*GP*G)-3'" 3893.515 1 ? ? ? ;strand containing 4'-oxidized abasic site ; 2 polymer syn "5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'" 3958.571 1 ? ? ? 'template strand' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DC)(DC)(DA)(DA)(DA)(DG)(X4A)(DA)(DC)(DC)(DG)(DG)(DG)' CCAAAGNACCGGG A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DC)(DG)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG)' CCCGGTACTTTGG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DA n 1 4 DA n 1 5 DA n 1 6 DG n 1 7 X4A n 1 8 DA n 1 9 DC n 1 10 DC n 1 11 DG n 1 12 DG n 1 13 DG n 2 1 DC n 2 2 DC n 2 3 DC n 2 4 DG n 2 5 DG n 2 6 DT n 2 7 DA n 2 8 DC n 2 9 DT n 2 10 DT n 2 11 DT n 2 12 DG n 2 13 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'synthetic construct' ? 32630 ? 2 1 sample ? ? 'synthetic construct' ? 32630 ? # 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 X4A 'DNA linking' . '[(2R,3S,5S)-2,3,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C5 H11 O8 P' 230.110 # 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 DC 1 1 1 DC DC5 A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 X4A 7 7 7 X4A X4A A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DG 13 13 13 DG DG3 A . n B 2 1 DC 1 14 14 DC DC5 B . n B 2 2 DC 2 15 15 DC DC B . n B 2 3 DC 3 16 16 DC DC B . n B 2 4 DG 4 17 17 DG DG B . n B 2 5 DG 5 18 18 DG DG B . n B 2 6 DT 6 19 19 DT DT B . n B 2 7 DA 7 20 20 DA DA B . n B 2 8 DC 8 21 21 DC DC B . n B 2 9 DT 9 22 22 DT DT B . n B 2 10 DT 10 23 23 DT DT B . n B 2 11 DT 11 24 24 DT DT B . n B 2 12 DG 12 25 25 DG DG B . n B 2 13 DG 13 26 26 DG DG3 B . n # _exptl.entry_id 2HPX _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _database_PDB_matrix.entry_id 2HPX _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 # _struct.entry_id 2HPX _struct.title ;13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2HPX _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'abasic site, DNA damage, bleomycin, molecular dynamics, 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 2 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 2HPX 2HPX ? ? ? 2 2 PDB 2HPX 2HPX ? ? ? # 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 2HPX A 1 ? 13 ? 2HPX 1 ? 13 ? 1 13 2 2 2HPX B 1 ? 13 ? 2HPX 14 ? 26 ? 14 26 # _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 # 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)' 1640 ? 1 MORE -7 ? 1 'SSA (A^2)' 5040 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 ? _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_ _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 DG 6 "O3'" ? ? ? 1_555 A X4A 7 P ? ? A DG 6 A X4A 7 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale2 covale both ? A X4A 7 "O3'" ? ? ? 1_555 A DA 8 P ? ? A X4A 7 A DA 8 1_555 ? ? ? ? ? ? ? 1.605 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 13 N1 ? ? A DC 1 B DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 13 O6 ? ? A DC 1 B DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 13 N2 ? ? A DC 1 B DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 2 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 2 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 2 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 11 N3 ? ? A DA 3 B DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 11 O4 ? ? A DA 3 B DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 4 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 4 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 5 B DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 5 B DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 6 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 6 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 6 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 8 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 8 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 9 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 9 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 9 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 10 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 10 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 10 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 12 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 12 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 12 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 N3 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 117.08 121.90 -4.82 0.70 N 2 1 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 117.06 121.90 -4.84 0.70 N 3 1 C4 A DA 3 ? ? C5 A DA 3 ? ? C6 A DA 3 ? ? 113.26 117.00 -3.74 0.50 N 4 1 C5 A DA 3 ? ? C6 A DA 3 ? ? N1 A DA 3 ? ? 121.12 117.70 3.42 0.50 N 5 1 N1 A DA 3 ? ? C6 A DA 3 ? ? N6 A DA 3 ? ? 113.82 118.60 -4.78 0.60 N 6 1 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.41 117.00 -3.59 0.50 N 7 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 121.01 117.70 3.31 0.50 N 8 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 113.71 118.60 -4.89 0.60 N 9 1 C4 A DA 5 ? ? C5 A DA 5 ? ? C6 A DA 5 ? ? 113.46 117.00 -3.54 0.50 N 10 1 C5 A DA 5 ? ? C6 A DA 5 ? ? N1 A DA 5 ? ? 121.32 117.70 3.62 0.50 N 11 1 N1 A DA 5 ? ? C6 A DA 5 ? ? N6 A DA 5 ? ? 113.81 118.60 -4.79 0.60 N 12 1 C4 A DA 8 ? ? C5 A DA 8 ? ? C6 A DA 8 ? ? 113.67 117.00 -3.33 0.50 N 13 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 121.18 117.70 3.48 0.50 N 14 1 N1 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 114.23 118.60 -4.37 0.60 N 15 1 N3 A DC 9 ? ? C2 A DC 9 ? ? O2 A DC 9 ? ? 116.72 121.90 -5.18 0.70 N 16 1 N3 A DC 10 ? ? C2 A DC 10 ? ? O2 A DC 10 ? ? 116.78 121.90 -5.12 0.70 N 17 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 110.61 108.30 2.31 0.30 N 18 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.05 108.30 2.75 0.30 N 19 1 N3 B DC 14 ? ? C2 B DC 14 ? ? O2 B DC 14 ? ? 117.01 121.90 -4.89 0.70 N 20 1 N3 B DC 15 ? ? C2 B DC 15 ? ? O2 B DC 15 ? ? 116.62 121.90 -5.28 0.70 N 21 1 N3 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 116.94 121.90 -4.96 0.70 N 22 1 C6 B DT 19 ? ? C5 B DT 19 ? ? C7 B DT 19 ? ? 118.45 122.90 -4.45 0.60 N 23 1 "O4'" B DA 20 ? ? "C1'" B DA 20 ? ? N9 B DA 20 ? ? 110.19 108.30 1.89 0.30 N 24 1 C4 B DA 20 ? ? C5 B DA 20 ? ? C6 B DA 20 ? ? 113.39 117.00 -3.61 0.50 N 25 1 C5 B DA 20 ? ? C6 B DA 20 ? ? N1 B DA 20 ? ? 121.62 117.70 3.92 0.50 N 26 1 N1 B DA 20 ? ? C6 B DA 20 ? ? N6 B DA 20 ? ? 113.62 118.60 -4.98 0.60 N 27 1 N3 B DC 21 ? ? C2 B DC 21 ? ? O2 B DC 21 ? ? 117.25 121.90 -4.65 0.70 N 28 1 "O4'" B DT 22 ? ? "C1'" B DT 22 ? ? N1 B DT 22 ? ? 110.12 108.30 1.82 0.30 N 29 1 C6 B DT 22 ? ? C5 B DT 22 ? ? C7 B DT 22 ? ? 119.27 122.90 -3.63 0.60 N 30 1 C6 B DT 23 ? ? C5 B DT 23 ? ? C7 B DT 23 ? ? 118.66 122.90 -4.24 0.60 N 31 1 C6 B DT 24 ? ? C5 B DT 24 ? ? C7 B DT 24 ? ? 118.69 122.90 -4.21 0.60 N 32 1 "O4'" B DG 26 ? ? "C1'" B DG 26 ? ? N9 B DG 26 ? ? 110.95 108.30 2.65 0.30 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DG _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 6 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.074 _pdbx_validate_planes.type 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 2HPX _pdbx_nmr_ensemble.conformers_calculated_total_number 30 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 2HPX _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 ;2.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 mM EDTA, 100% D2O ; '100% D2O' sample_1 solution ? 2 ;2.0 mM duplex DNA containing a 4'-oxidized abasic site, 0.2 mM EDTA, 90%D2O/10% H2O ; '90%D2O/10% H2O' sample_2 solution ? # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;duplex DNA containing a 4'-oxidized abasic site ; 2.0 ? mM 'natural abundance' 1 ;duplex DNA containing a 4'-oxidized abasic site ; 2.0 ? mM 'natural abundance' 2 'sodium phosphate' 10 ? mM 'natural abundance' 1 'sodium phosphate' 10 ? mM 'natural abundance' 4 EDTA 0.2 ? mM 'natural abundance' 1 EDTA 0.2 ? mM 'natural abundance' 2 # 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 _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 1 298 1 6.5 '10 mM sodium phosphate' atm K sample_conditions_1 pH mM 2 277 1 6.5 '10 mM sodium phosphate' atm K sample_conditions_2 pH mM # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 '2D TOCSY' 1 3 1 E-COSY 1 4 1 PH-COSY 1 5 1 HP-HSQC 1 6 2 '2D NOESY' 2 # _pdbx_nmr_details.entry_id 2HPX _pdbx_nmr_details.text 'The structure model was determined using standard 2D homonuclear and heteronuclear techniques' # _pdbx_nmr_refine.entry_id 2HPX _pdbx_nmr_refine.method ;simulated annealing matrix relaxation ; _pdbx_nmr_refine.details ;the structures are based on 410 NOE-derived distance constraints, 43 dihedral angle restraints,8 distance restraints from hydrogen bonds. ; _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement Amber 8.0 'Case, D.A. et al.' 1 'data analysis' Felix 2000 ? 2 'data analysis' MARDIGRAS ? ? 3 # 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 X4A OP3 O N N 144 X4A P P N N 145 X4A OP1 O N N 146 X4A OP2 O N N 147 X4A "O5'" O N N 148 X4A "C5'" C N N 149 X4A "C4'" C N R 150 X4A O4A O N N 151 X4A "O4'" O N N 152 X4A "C1'" C N S 153 X4A O1A O N N 154 X4A "C3'" C N S 155 X4A "C2'" C N N 156 X4A "O3'" O N N 157 X4A HOP3 H N N 158 X4A HOP2 H N N 159 X4A "H5'" H N N 160 X4A "H5''" H N N 161 X4A H4A H N N 162 X4A "H1'" H N N 163 X4A H1A H N N 164 X4A "H3'" H N N 165 X4A "H2'" H N N 166 X4A "H2''" H N N 167 X4A "HO3'" H N N 168 # 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 X4A OP3 P sing N N 150 X4A OP3 HOP3 sing N N 151 X4A P OP1 doub N N 152 X4A P OP2 sing N N 153 X4A P "O5'" sing N N 154 X4A OP2 HOP2 sing N N 155 X4A "O5'" "C5'" sing N N 156 X4A "C5'" "C4'" sing N N 157 X4A "C5'" "H5'" sing N N 158 X4A "C5'" "H5''" sing N N 159 X4A "C4'" O4A sing N N 160 X4A "C4'" "O4'" sing N N 161 X4A "C4'" "C3'" sing N N 162 X4A O4A H4A sing N N 163 X4A "O4'" "C1'" sing N N 164 X4A "C1'" O1A sing N N 165 X4A "C1'" "C2'" sing N N 166 X4A "C1'" "H1'" sing N N 167 X4A O1A H1A sing N N 168 X4A "C3'" "C2'" sing N N 169 X4A "C3'" "O3'" sing N N 170 X4A "C3'" "H3'" sing N N 171 X4A "C2'" "H2'" sing N N 172 X4A "C2'" "H2''" sing N N 173 X4A "O3'" "HO3'" sing N N 174 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2HPX 'double helix' 2HPX 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 13 1_555 0.291 -0.144 -0.007 3.674 -6.156 -0.315 1 A_DC1:DG26_B A 1 ? B 26 ? 19 1 1 A DC 2 1_555 B DG 12 1_555 0.467 -0.186 0.033 2.148 -4.715 0.444 2 A_DC2:DG25_B A 2 ? B 25 ? 19 1 1 A DA 3 1_555 B DT 11 1_555 0.252 -0.073 -0.214 -1.926 -9.547 0.301 3 A_DA3:DT24_B A 3 ? B 24 ? 20 1 1 A DA 4 1_555 B DT 10 1_555 0.110 -0.076 -0.142 -1.829 -10.441 2.521 4 A_DA4:DT23_B A 4 ? B 23 ? 20 1 1 A DA 5 1_555 B DT 9 1_555 0.056 -0.072 0.137 -0.411 -3.178 -0.877 5 A_DA5:DT22_B A 5 ? B 22 ? 20 1 1 A DG 6 1_555 B DC 8 1_555 -0.462 -0.129 0.327 15.721 -2.471 -0.324 6 A_DG6:DC21_B A 6 ? B 21 ? 19 1 1 A DA 8 1_555 B DT 6 1_555 0.082 -0.046 0.005 -4.830 -5.915 1.185 7 A_DA8:DT19_B A 8 ? B 19 ? 20 1 1 A DC 9 1_555 B DG 5 1_555 0.483 -0.165 0.099 -0.526 -6.832 -0.547 8 A_DC9:DG18_B A 9 ? B 18 ? 19 1 1 A DC 10 1_555 B DG 4 1_555 0.336 -0.132 0.148 -3.703 -1.790 -0.568 9 A_DC10:DG17_B A 10 ? B 17 ? 19 1 1 A DG 11 1_555 B DC 3 1_555 -0.475 -0.183 -0.024 3.035 -2.253 -0.890 10 A_DG11:DC16_B A 11 ? B 16 ? 19 1 1 A DG 12 1_555 B DC 2 1_555 -0.487 -0.141 -0.294 -3.931 -3.042 0.674 11 A_DG12:DC15_B A 12 ? B 15 ? 19 1 1 A DG 13 1_555 B DC 1 1_555 -0.416 -0.156 -0.248 -6.573 1.120 -0.449 12 A_DG13:DC14_B A 13 ? B 14 ? 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 DC 1 1_555 B DG 13 1_555 A DC 2 1_555 B DG 12 1_555 -0.177 -1.012 3.473 -0.177 2.645 32.982 -2.246 0.279 3.385 4.649 0.310 33.085 1 AA_DC1DC2:DG25DG26_BB A 1 ? B 26 ? A 2 ? B 25 ? 1 A DC 2 1_555 B DG 12 1_555 A DA 3 1_555 B DT 11 1_555 -0.153 -0.852 3.440 2.485 7.592 32.961 -2.710 0.671 3.152 13.141 -4.302 33.889 2 AA_DC2DA3:DT24DG25_BB A 2 ? B 25 ? A 3 ? B 24 ? 1 A DA 3 1_555 B DT 11 1_555 A DA 4 1_555 B DT 10 1_555 -0.167 -0.891 3.475 -1.361 0.936 31.842 -1.802 0.042 3.452 1.704 2.478 31.883 3 AA_DA3DA4:DT23DT24_BB A 3 ? B 24 ? A 4 ? B 23 ? 1 A DA 4 1_555 B DT 10 1_555 A DA 5 1_555 B DT 9 1_555 -0.379 -0.850 3.438 -2.692 4.109 34.684 -2.056 0.209 3.338 6.850 4.487 35.020 4 AA_DA4DA5:DT22DT23_BB A 4 ? B 23 ? A 5 ? B 22 ? 1 A DA 5 1_555 B DT 9 1_555 A DG 6 1_555 B DC 8 1_555 0.539 -0.602 3.114 -1.194 -1.475 24.545 -0.981 -1.614 3.115 -3.464 2.803 24.617 5 AA_DA5DG6:DC21DT22_BB A 5 ? B 22 ? A 6 ? B 21 ? 1 A DG 6 1_555 B DC 8 1_555 A DA 8 1_555 B DT 6 1_555 -1.266 -1.460 6.883 -5.580 17.182 74.637 -2.230 0.682 6.540 13.975 4.538 76.482 6 AA_DG6DA8:DT19DC21_BB A 6 ? B 21 ? A 8 ? B 19 ? 1 A DA 8 1_555 B DT 6 1_555 A DC 9 1_555 B DG 5 1_555 -0.162 -0.603 3.333 -1.946 0.480 33.215 -1.135 -0.047 3.328 0.839 3.401 33.274 7 AA_DA8DC9:DG18DT19_BB A 8 ? B 19 ? A 9 ? B 18 ? 1 A DC 9 1_555 B DG 5 1_555 A DC 10 1_555 B DG 4 1_555 0.212 -1.076 3.484 0.354 2.866 32.121 -2.473 -0.315 3.380 5.166 -0.638 32.247 8 AA_DC9DC10:DG17DG18_BB A 9 ? B 18 ? A 10 ? B 17 ? 1 A DC 10 1_555 B DG 4 1_555 A DG 11 1_555 B DC 3 1_555 0.038 -0.652 3.160 0.180 4.938 30.095 -2.176 -0.038 3.017 9.430 -0.344 30.489 9 AA_DC10DG11:DC16DG17_BB A 10 ? B 17 ? A 11 ? B 16 ? 1 A DG 11 1_555 B DC 3 1_555 A DG 12 1_555 B DC 2 1_555 0.443 -1.503 3.609 2.720 0.872 30.247 -3.062 -0.243 3.590 1.666 -5.197 30.378 10 AA_DG11DG12:DC15DC16_BB A 11 ? B 16 ? A 12 ? B 15 ? 1 A DG 12 1_555 B DC 2 1_555 A DG 13 1_555 B DC 1 1_555 0.073 -1.307 3.591 -0.765 0.369 33.052 -2.365 -0.269 3.574 0.648 1.344 33.063 11 AA_DG12DG13:DC14DC15_BB A 12 ? B 15 ? A 13 ? B 14 ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 Custom-built Home-built 750 ? 2 Custom-built Home-built 591 ? # _atom_sites.entry_id 2HPX _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_