data_2LAR # _entry.id 2LAR # _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 2LAR pdb_00002lar 10.2210/pdb2lar/pdb RCSB RCSB102167 ? ? BMRB 17535 ? 10.13018/BMR17535 WWPDB D_1000102167 ? ? # 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 2011-10-12 2 'Structure model' 1 1 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_nmr_software 5 2 'Structure model' pdbx_nmr_spectrometer 6 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_nmr_software.name' 4 2 'Structure model' '_pdbx_nmr_spectrometer.model' 5 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LAR _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-03-18 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 2LB4 PDB unspecified . 17535 BMRB unspecified . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Johnson, C.N.' 1 'Spring, A.M.' 2 'Shaw, B.R.' 3 'Germann, M.W.' 4 # _citation.id primary _citation.title 'Structural basis of the RNase H1 activity on stereo regular borano phosphonate DNA/RNA hybrids.' _citation.journal_abbrev Biochemistry _citation.journal_volume 50 _citation.page_first 3903 _citation.page_last 3912 _citation.year 2011 _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 21443203 _citation.pdbx_database_id_DOI 10.1021/bi200083d # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Johnson, C.N.' 1 ? primary 'Spring, A.M.' 2 ? primary 'Sergueev, D.' 3 ? primary 'Shaw, B.R.' 4 ? primary 'Germann, M.W.' 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 "DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_" 2743.637 1 ? ? ? ? 2 polymer syn "RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_" 2854.782 1 ? ? ? ? # 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 '(DA)(DT)(DG)(DG)(DT)(BGR)(DC)(DT)(DC)' ATGGTXCTC A ? 2 polyribonucleotide no no GAGCACCAU GAGCACCAU B ? # 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 DT n 1 3 DG n 1 4 DG n 1 5 DT n 1 6 BGR n 1 7 DC n 1 8 DT n 1 9 DC n 2 1 G n 2 2 A n 2 3 G n 2 4 C n 2 5 A n 2 6 C n 2 7 C n 2 8 A n 2 9 U n # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 BGR non-polymer . '[[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]boranuide' ? 'C10 H16 B N5 O6 P -1' 344.049 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 DA A . n A 1 2 DT 2 2 2 DT DT A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 BGR 6 6 6 BGR BGR A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n B 2 1 G 1 10 10 G G B . n B 2 2 A 2 11 11 A A B . n B 2 3 G 3 12 12 G G B . n B 2 4 C 4 13 13 C C B . n B 2 5 A 5 14 14 A A B . n B 2 6 C 6 15 15 C C B . n B 2 7 C 7 16 16 C C B . n B 2 8 A 8 17 17 A A B . n B 2 9 U 9 18 18 U U B . n # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2LAR _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LAR _struct.title 'DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage' _struct.pdbx_model_details 'structure with the lowest restraint violations, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LAR _struct_keywords.pdbx_keywords DNA/RNA _struct_keywords.text 'nucleic acid heteroduplex, RNase H1 activity, DNA-RNA complex' # 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.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2LAR 2LAR 1 ? ? ? 2 PDB 2LAR 2LAR 2 ? ? ? # 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 2LAR A 1 ? 9 ? 2LAR 1 ? 9 ? 1 9 2 2 2LAR B 1 ? 9 ? 2LAR 10 ? 18 ? 10 18 # _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 # _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 # _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 one ? A DT 5 "O3'" ? ? ? 1_555 A BGR 6 P ? ? A DT 5 A BGR 6 1_555 ? ? ? ? ? ? ? 1.625 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B U 9 N3 ? ? A DA 1 B U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B U 9 O4 ? ? A DA 1 B U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B A 8 N1 ? ? A DT 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B A 8 N6 ? ? A DT 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B C 7 N3 ? ? A DG 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B C 7 O2 ? ? A DG 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B C 7 N4 ? ? A DG 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B C 6 N3 ? ? A DG 4 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B C 6 O2 ? ? A DG 4 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B C 6 N4 ? ? A DG 4 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B A 5 N1 ? ? A DT 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B A 5 N6 ? ? A DT 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B G 3 N1 ? ? A DC 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B G 3 O6 ? ? A DC 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B G 3 N2 ? ? A DC 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B A 2 N1 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B A 2 N6 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 9 B G 10 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 "O4'" A DA 1 ? ? "C4'" A DA 1 ? ? "C3'" A DA 1 ? ? 110.19 106.00 4.19 0.60 N 2 1 "O4'" A DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 111.90 108.30 3.60 0.30 N 3 1 C4 A DA 1 ? ? C5 A DA 1 ? ? C6 A DA 1 ? ? 113.70 117.00 -3.30 0.50 N 4 1 C5 A DA 1 ? ? C6 A DA 1 ? ? N1 A DA 1 ? ? 120.99 117.70 3.29 0.50 N 5 1 N1 A DA 1 ? ? C6 A DA 1 ? ? N6 A DA 1 ? ? 114.24 118.60 -4.36 0.60 N 6 1 C6 A DT 2 ? ? C5 A DT 2 ? ? C7 A DT 2 ? ? 119.14 122.90 -3.76 0.60 N 7 1 "O4'" A DG 3 ? ? "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 111.52 106.00 5.52 0.60 N 8 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 112.02 106.00 6.02 0.60 N 9 1 "C3'" A DG 4 ? ? "C2'" A DG 4 ? ? "C1'" A DG 4 ? ? 110.31 102.50 7.81 1.20 N 10 1 "O4'" A DT 5 ? ? "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? 112.44 106.00 6.44 0.60 N 11 1 "C3'" A DT 5 ? ? "C2'" A DT 5 ? ? "C1'" A DT 5 ? ? 110.18 102.50 7.68 1.20 N 12 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.39 108.30 2.09 0.30 N 13 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 110.66 108.30 2.36 0.30 N 14 1 "O4'" A DT 8 ? ? "C4'" A DT 8 ? ? "C3'" A DT 8 ? ? 111.19 106.00 5.19 0.60 N 15 1 C5 A DT 8 ? ? C6 A DT 8 ? ? N1 A DT 8 ? ? 120.08 123.70 -3.62 0.60 N 16 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 112.17 108.30 3.87 0.30 N 17 1 N3 A DC 9 ? ? C2 A DC 9 ? ? O2 A DC 9 ? ? 117.43 121.90 -4.47 0.70 N 18 1 "C3'" B G 10 ? ? "C2'" B G 10 ? ? "C1'" B G 10 ? ? 107.67 101.50 6.17 0.80 N 19 1 C5 B A 11 ? ? C6 B A 11 ? ? N1 B A 11 ? ? 120.95 117.70 3.25 0.50 N 20 1 N1 B A 11 ? ? C6 B A 11 ? ? N6 B A 11 ? ? 114.04 118.60 -4.56 0.60 N 21 1 "O4'" B C 13 ? ? "C1'" B C 13 ? ? N1 B C 13 ? ? 114.15 108.50 5.65 0.70 N 22 1 "O4'" B A 14 ? ? "C1'" B A 14 ? ? N9 B A 14 ? ? 114.09 108.50 5.59 0.70 N 23 1 C5 B A 14 ? ? C6 B A 14 ? ? N1 B A 14 ? ? 121.48 117.70 3.78 0.50 N 24 1 N1 B A 14 ? ? C6 B A 14 ? ? N6 B A 14 ? ? 114.48 118.60 -4.12 0.60 N 25 1 N3 B C 16 ? ? C2 B C 16 ? ? O2 B C 16 ? ? 117.69 121.90 -4.21 0.70 N 26 1 C4 B A 17 ? ? C5 B A 17 ? ? C6 B A 17 ? ? 113.51 117.00 -3.49 0.50 N 27 1 "O4'" B U 18 ? ? "C1'" B U 18 ? ? N1 B U 18 ? ? 115.07 108.50 6.57 0.70 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 DA A 1 ? ? 0.080 'SIDE CHAIN' 2 1 DT A 2 ? ? 0.077 'SIDE CHAIN' 3 1 DG A 3 ? ? 0.073 'SIDE CHAIN' 4 1 DT A 8 ? ? 0.138 'SIDE CHAIN' 5 1 G B 10 ? ? 0.103 'SIDE CHAIN' 6 1 A B 11 ? ? 0.076 'SIDE CHAIN' 7 1 A B 14 ? ? 0.095 'SIDE CHAIN' 8 1 U B 18 ? ? 0.085 'SIDE CHAIN' # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structure with the lowest restraint violations' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LAR _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2LAR _pdbx_nmr_representative.selection_criteria 'structure with the lowest restraint violations' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS, 99.999 % D2O ; 2 '99.999 % D2O' # 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 ;DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')-1 ; 1.0 ? mM ? 1 ;RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')-2 ; 1.0 ? mM ? 1 'sodium chloride-3' 50 ? mM ? 1 'sodium phosphate-4' 10 ? mM ? 1 EDTA-5 0.5 ? mM ? 1 DSS-6 0.3 ? uM ? 1 D2O-7 10 ? % ? 1 H2O-8 90 ? % ? 1 ;DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')-9 ; 1.0 ? mM ? 2 ;RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')-10 ; 1.0 ? mM ? 2 'sodium chloride-11' 50 ? mM ? 2 'sodium phosphate-12' 10 ? mM ? 2 EDTA-13 0.5 ? mM ? 2 DSS-14 0.3 ? uM ? 2 D2O-15 99.999 ? % ? 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 50 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 2 '2D 1H-13C HSQC' 1 3 2 '2D 1H-1H TOCSY' 1 4 2 '2D DQF-COSY' 1 5 2 '2D 1H-1H NOESY' 1 6 2 '2D 1H-31P CORR' # _pdbx_nmr_refine.entry_id 2LAR _pdbx_nmr_refine.method 'molecular dynamics, matrix relaxation' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' 'structure solution' Amber 9.0 1 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' 'geometry optimization' Amber 9.0 2 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' refinement Amber 9.0 3 'Bruker Biospin' collection XwinNMR 3.5 4 'Bruker Biospin' 'data analysis' TopSpin 2.1 5 'Bruker Biospin' 'chemical shift calculation' TopSpin 2.1 6 'Bruker Biospin' processing TopSpin 2.1 7 '(CORMA) Dr. Thomas James' 'data analysis' CORMA 5.21 8 'Thomas James' refinement MARDIGRAS 5.21 9 Goddard 'data analysis' Sparky 3.98 10 Goddard 'chemical shift assignment' Sparky 3.98 11 # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 BGR P P N N 38 BGR N1 N N N 39 BGR C2 C N N 40 BGR N2 N N N 41 BGR N3 N N N 42 BGR C4 C Y N 43 BGR C5 C Y N 44 BGR C6 C N N 45 BGR O6 O N N 46 BGR N7 N Y N 47 BGR C8 C Y N 48 BGR N9 N Y N 49 BGR BP B N N 50 BGR "C1'" C N R 51 BGR "C2'" C N N 52 BGR "C3'" C N S 53 BGR "O3'" O N N 54 BGR "C4'" C N R 55 BGR "O4'" O N N 56 BGR "C5'" C N N 57 BGR "O5'" O N N 58 BGR OP1 O N N 59 BGR OP2 O N N 60 BGR HN1 H N N 61 BGR H8 H N N 62 BGR H1BP H N N 63 BGR H2BP H N N 64 BGR H3BP H N N 65 BGR "H1'" H N N 66 BGR "H2'" H N N 67 BGR "H2'A" H N N 68 BGR HN2 H N N 69 BGR HN2A H N N 70 BGR "H3'" H N N 71 BGR "H4'" H N N 72 BGR "H5'" H N N 73 BGR "H5'A" H N N 74 BGR H15 H N N 75 BGR H16 H N N 76 C OP3 O N N 77 C P P N N 78 C OP1 O N N 79 C OP2 O N N 80 C "O5'" O N N 81 C "C5'" C N N 82 C "C4'" C N R 83 C "O4'" O N N 84 C "C3'" C N S 85 C "O3'" O N N 86 C "C2'" C N R 87 C "O2'" O N N 88 C "C1'" C N R 89 C N1 N N N 90 C C2 C N N 91 C O2 O N N 92 C N3 N N N 93 C C4 C N N 94 C N4 N N N 95 C C5 C N N 96 C C6 C N N 97 C HOP3 H N N 98 C HOP2 H N N 99 C "H5'" H N N 100 C "H5''" H N N 101 C "H4'" H N N 102 C "H3'" H N N 103 C "HO3'" H N N 104 C "H2'" H N N 105 C "HO2'" H N N 106 C "H1'" H N N 107 C H41 H N N 108 C H42 H N N 109 C H5 H N N 110 C H6 H N N 111 DA OP3 O N N 112 DA P P N N 113 DA OP1 O N N 114 DA OP2 O N N 115 DA "O5'" O N N 116 DA "C5'" C N N 117 DA "C4'" C N R 118 DA "O4'" O N N 119 DA "C3'" C N S 120 DA "O3'" O N N 121 DA "C2'" C N N 122 DA "C1'" C N R 123 DA N9 N Y N 124 DA C8 C Y N 125 DA N7 N Y N 126 DA C5 C Y N 127 DA C6 C Y N 128 DA N6 N N N 129 DA N1 N Y N 130 DA C2 C Y N 131 DA N3 N Y N 132 DA C4 C Y N 133 DA HOP3 H N N 134 DA HOP2 H N N 135 DA "H5'" H N N 136 DA "H5''" H N N 137 DA "H4'" H N N 138 DA "H3'" H N N 139 DA "HO3'" H N N 140 DA "H2'" H N N 141 DA "H2''" H N N 142 DA "H1'" H N N 143 DA H8 H N N 144 DA H61 H N N 145 DA H62 H N N 146 DA H2 H N N 147 DC OP3 O N N 148 DC P P N N 149 DC OP1 O N N 150 DC OP2 O N N 151 DC "O5'" O N N 152 DC "C5'" C N N 153 DC "C4'" C N R 154 DC "O4'" O N N 155 DC "C3'" C N S 156 DC "O3'" O N N 157 DC "C2'" C N N 158 DC "C1'" C N R 159 DC N1 N N N 160 DC C2 C N N 161 DC O2 O N N 162 DC N3 N N N 163 DC C4 C N N 164 DC N4 N N N 165 DC C5 C N N 166 DC C6 C N N 167 DC HOP3 H N N 168 DC HOP2 H N N 169 DC "H5'" H N N 170 DC "H5''" H N N 171 DC "H4'" H N N 172 DC "H3'" H N N 173 DC "HO3'" H N N 174 DC "H2'" H N N 175 DC "H2''" H N N 176 DC "H1'" H N N 177 DC H41 H N N 178 DC H42 H N N 179 DC H5 H N N 180 DC H6 H N N 181 DG OP3 O N N 182 DG P P N N 183 DG OP1 O N N 184 DG OP2 O N N 185 DG "O5'" O N N 186 DG "C5'" C N N 187 DG "C4'" C N R 188 DG "O4'" O N N 189 DG "C3'" C N S 190 DG "O3'" O N N 191 DG "C2'" C N N 192 DG "C1'" C N R 193 DG N9 N Y N 194 DG C8 C Y N 195 DG N7 N Y N 196 DG C5 C Y N 197 DG C6 C N N 198 DG O6 O N N 199 DG N1 N N N 200 DG C2 C N N 201 DG N2 N N N 202 DG N3 N N N 203 DG C4 C Y N 204 DG HOP3 H N N 205 DG HOP2 H N N 206 DG "H5'" H N N 207 DG "H5''" H N N 208 DG "H4'" H N N 209 DG "H3'" H N N 210 DG "HO3'" H N N 211 DG "H2'" H N N 212 DG "H2''" H N N 213 DG "H1'" H N N 214 DG H8 H N N 215 DG H1 H N N 216 DG H21 H N N 217 DG H22 H N N 218 DT OP3 O N N 219 DT P P N N 220 DT OP1 O N N 221 DT OP2 O N N 222 DT "O5'" O N N 223 DT "C5'" C N N 224 DT "C4'" C N R 225 DT "O4'" O N N 226 DT "C3'" C N S 227 DT "O3'" O N N 228 DT "C2'" C N N 229 DT "C1'" C N R 230 DT N1 N N N 231 DT C2 C N N 232 DT O2 O N N 233 DT N3 N N N 234 DT C4 C N N 235 DT O4 O N N 236 DT C5 C N N 237 DT C7 C N N 238 DT C6 C N N 239 DT HOP3 H N N 240 DT HOP2 H N N 241 DT "H5'" H N N 242 DT "H5''" H N N 243 DT "H4'" H N N 244 DT "H3'" H N N 245 DT "HO3'" H N N 246 DT "H2'" H N N 247 DT "H2''" H N N 248 DT "H1'" H N N 249 DT H3 H N N 250 DT H71 H N N 251 DT H72 H N N 252 DT H73 H N N 253 DT H6 H N N 254 G OP3 O N N 255 G P P N N 256 G OP1 O N N 257 G OP2 O N N 258 G "O5'" O N N 259 G "C5'" C N N 260 G "C4'" C N R 261 G "O4'" O N N 262 G "C3'" C N S 263 G "O3'" O N N 264 G "C2'" C N R 265 G "O2'" O N N 266 G "C1'" C N R 267 G N9 N Y N 268 G C8 C Y N 269 G N7 N Y N 270 G C5 C Y N 271 G C6 C N N 272 G O6 O N N 273 G N1 N N N 274 G C2 C N N 275 G N2 N N N 276 G N3 N N N 277 G C4 C Y N 278 G HOP3 H N N 279 G HOP2 H N N 280 G "H5'" H N N 281 G "H5''" H N N 282 G "H4'" H N N 283 G "H3'" H N N 284 G "HO3'" H N N 285 G "H2'" H N N 286 G "HO2'" H N N 287 G "H1'" H N N 288 G H8 H N N 289 G H1 H N N 290 G H21 H N N 291 G H22 H N N 292 U OP3 O N N 293 U P P N N 294 U OP1 O N N 295 U OP2 O N N 296 U "O5'" O N N 297 U "C5'" C N N 298 U "C4'" C N R 299 U "O4'" O N N 300 U "C3'" C N S 301 U "O3'" O N N 302 U "C2'" C N R 303 U "O2'" O N N 304 U "C1'" C N R 305 U N1 N N N 306 U C2 C N N 307 U O2 O N N 308 U N3 N N N 309 U C4 C N N 310 U O4 O N N 311 U C5 C N N 312 U C6 C N N 313 U HOP3 H N N 314 U HOP2 H N N 315 U "H5'" H N N 316 U "H5''" H N N 317 U "H4'" H N N 318 U "H3'" H N N 319 U "HO3'" H N N 320 U "H2'" H N N 321 U "HO2'" H N N 322 U "H1'" H N N 323 U H3 H N N 324 U H5 H N N 325 U H6 H N N 326 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 BGR P BP sing N N 40 BGR P "O5'" sing N N 41 BGR P OP1 doub N N 42 BGR P OP2 sing N N 43 BGR N1 C2 sing N N 44 BGR N1 C6 sing N N 45 BGR N1 HN1 sing N N 46 BGR C2 N2 sing N N 47 BGR C2 N3 doub N N 48 BGR N2 HN2 sing N N 49 BGR N2 HN2A sing N N 50 BGR N3 C4 sing N N 51 BGR C4 C5 doub Y N 52 BGR C4 N9 sing Y N 53 BGR C5 C6 sing N N 54 BGR C5 N7 sing Y N 55 BGR C6 O6 doub N N 56 BGR N7 C8 doub Y N 57 BGR C8 N9 sing Y N 58 BGR C8 H8 sing N N 59 BGR N9 "C1'" sing N N 60 BGR BP H1BP sing N N 61 BGR BP H2BP sing N N 62 BGR BP H3BP sing N N 63 BGR "C1'" "C2'" sing N N 64 BGR "C1'" "O4'" sing N N 65 BGR "C1'" "H1'" sing N N 66 BGR "C2'" "C3'" sing N N 67 BGR "C2'" "H2'" sing N N 68 BGR "C2'" "H2'A" sing N N 69 BGR "C3'" "O3'" sing N N 70 BGR "C3'" "C4'" sing N N 71 BGR "C3'" "H3'" sing N N 72 BGR "C4'" "O4'" sing N N 73 BGR "C4'" "C5'" sing N N 74 BGR "C4'" "H4'" sing N N 75 BGR "C5'" "O5'" sing N N 76 BGR "C5'" "H5'" sing N N 77 BGR "C5'" "H5'A" sing N N 78 BGR "O3'" H15 sing N N 79 BGR OP2 H16 sing N N 80 C OP3 P sing N N 81 C OP3 HOP3 sing N N 82 C P OP1 doub N N 83 C P OP2 sing N N 84 C P "O5'" sing N N 85 C OP2 HOP2 sing N N 86 C "O5'" "C5'" sing N N 87 C "C5'" "C4'" sing N N 88 C "C5'" "H5'" sing N N 89 C "C5'" "H5''" sing N N 90 C "C4'" "O4'" sing N N 91 C "C4'" "C3'" sing N N 92 C "C4'" "H4'" sing N N 93 C "O4'" "C1'" sing N N 94 C "C3'" "O3'" sing N N 95 C "C3'" "C2'" sing N N 96 C "C3'" "H3'" sing N N 97 C "O3'" "HO3'" sing N N 98 C "C2'" "O2'" sing N N 99 C "C2'" "C1'" sing N N 100 C "C2'" "H2'" sing N N 101 C "O2'" "HO2'" sing N N 102 C "C1'" N1 sing N N 103 C "C1'" "H1'" sing N N 104 C N1 C2 sing N N 105 C N1 C6 sing N N 106 C C2 O2 doub N N 107 C C2 N3 sing N N 108 C N3 C4 doub N N 109 C C4 N4 sing N N 110 C C4 C5 sing N N 111 C N4 H41 sing N N 112 C N4 H42 sing N N 113 C C5 C6 doub N N 114 C C5 H5 sing N N 115 C C6 H6 sing N N 116 DA OP3 P sing N N 117 DA OP3 HOP3 sing N N 118 DA P OP1 doub N N 119 DA P OP2 sing N N 120 DA P "O5'" sing N N 121 DA OP2 HOP2 sing N N 122 DA "O5'" "C5'" sing N N 123 DA "C5'" "C4'" sing N N 124 DA "C5'" "H5'" sing N N 125 DA "C5'" "H5''" sing N N 126 DA "C4'" "O4'" sing N N 127 DA "C4'" "C3'" sing N N 128 DA "C4'" "H4'" sing N N 129 DA "O4'" "C1'" sing N N 130 DA "C3'" "O3'" sing N N 131 DA "C3'" "C2'" sing N N 132 DA "C3'" "H3'" sing N N 133 DA "O3'" "HO3'" sing N N 134 DA "C2'" "C1'" sing N N 135 DA "C2'" "H2'" sing N N 136 DA "C2'" "H2''" sing N N 137 DA "C1'" N9 sing N N 138 DA "C1'" "H1'" sing N N 139 DA N9 C8 sing Y N 140 DA N9 C4 sing Y N 141 DA C8 N7 doub Y N 142 DA C8 H8 sing N N 143 DA N7 C5 sing Y N 144 DA C5 C6 sing Y N 145 DA C5 C4 doub Y N 146 DA C6 N6 sing N N 147 DA C6 N1 doub Y N 148 DA N6 H61 sing N N 149 DA N6 H62 sing N N 150 DA N1 C2 sing Y N 151 DA C2 N3 doub Y N 152 DA C2 H2 sing N N 153 DA N3 C4 sing Y N 154 DC OP3 P sing N N 155 DC OP3 HOP3 sing N N 156 DC P OP1 doub N N 157 DC P OP2 sing N N 158 DC P "O5'" sing N N 159 DC OP2 HOP2 sing N N 160 DC "O5'" "C5'" sing N N 161 DC "C5'" "C4'" sing N N 162 DC "C5'" "H5'" sing N N 163 DC "C5'" "H5''" sing N N 164 DC "C4'" "O4'" sing N N 165 DC "C4'" "C3'" sing N N 166 DC "C4'" "H4'" sing N N 167 DC "O4'" "C1'" sing N N 168 DC "C3'" "O3'" sing N N 169 DC "C3'" "C2'" sing N N 170 DC "C3'" "H3'" sing N N 171 DC "O3'" "HO3'" sing N N 172 DC "C2'" "C1'" sing N N 173 DC "C2'" "H2'" sing N N 174 DC "C2'" "H2''" sing N N 175 DC "C1'" N1 sing N N 176 DC "C1'" "H1'" sing N N 177 DC N1 C2 sing N N 178 DC N1 C6 sing N N 179 DC C2 O2 doub N N 180 DC C2 N3 sing N N 181 DC N3 C4 doub N N 182 DC C4 N4 sing N N 183 DC C4 C5 sing N N 184 DC N4 H41 sing N N 185 DC N4 H42 sing N N 186 DC C5 C6 doub N N 187 DC C5 H5 sing N N 188 DC C6 H6 sing N N 189 DG OP3 P sing N N 190 DG OP3 HOP3 sing N N 191 DG P OP1 doub N N 192 DG P OP2 sing N N 193 DG P "O5'" sing N N 194 DG OP2 HOP2 sing N N 195 DG "O5'" "C5'" sing N N 196 DG "C5'" "C4'" sing N N 197 DG "C5'" "H5'" sing N N 198 DG "C5'" "H5''" sing N N 199 DG "C4'" "O4'" sing N N 200 DG "C4'" "C3'" sing N N 201 DG "C4'" "H4'" sing N N 202 DG "O4'" "C1'" sing N N 203 DG "C3'" "O3'" sing N N 204 DG "C3'" "C2'" sing N N 205 DG "C3'" "H3'" sing N N 206 DG "O3'" "HO3'" sing N N 207 DG "C2'" "C1'" sing N N 208 DG "C2'" "H2'" sing N N 209 DG "C2'" "H2''" sing N N 210 DG "C1'" N9 sing N N 211 DG "C1'" "H1'" sing N N 212 DG N9 C8 sing Y N 213 DG N9 C4 sing Y N 214 DG C8 N7 doub Y N 215 DG C8 H8 sing N N 216 DG N7 C5 sing Y N 217 DG C5 C6 sing N N 218 DG C5 C4 doub Y N 219 DG C6 O6 doub N N 220 DG C6 N1 sing N N 221 DG N1 C2 sing N N 222 DG N1 H1 sing N N 223 DG C2 N2 sing N N 224 DG C2 N3 doub N N 225 DG N2 H21 sing N N 226 DG N2 H22 sing N N 227 DG N3 C4 sing N N 228 DT OP3 P sing N N 229 DT OP3 HOP3 sing N N 230 DT P OP1 doub N N 231 DT P OP2 sing N N 232 DT P "O5'" sing N N 233 DT OP2 HOP2 sing N N 234 DT "O5'" "C5'" sing N N 235 DT "C5'" "C4'" sing N N 236 DT "C5'" "H5'" sing N N 237 DT "C5'" "H5''" sing N N 238 DT "C4'" "O4'" sing N N 239 DT "C4'" "C3'" sing N N 240 DT "C4'" "H4'" sing N N 241 DT "O4'" "C1'" sing N N 242 DT "C3'" "O3'" sing N N 243 DT "C3'" "C2'" sing N N 244 DT "C3'" "H3'" sing N N 245 DT "O3'" "HO3'" sing N N 246 DT "C2'" "C1'" sing N N 247 DT "C2'" "H2'" sing N N 248 DT "C2'" "H2''" sing N N 249 DT "C1'" N1 sing N N 250 DT "C1'" "H1'" sing N N 251 DT N1 C2 sing N N 252 DT N1 C6 sing N N 253 DT C2 O2 doub N N 254 DT C2 N3 sing N N 255 DT N3 C4 sing N N 256 DT N3 H3 sing N N 257 DT C4 O4 doub N N 258 DT C4 C5 sing N N 259 DT C5 C7 sing N N 260 DT C5 C6 doub N N 261 DT C7 H71 sing N N 262 DT C7 H72 sing N N 263 DT C7 H73 sing N N 264 DT C6 H6 sing N N 265 G OP3 P sing N N 266 G OP3 HOP3 sing N N 267 G P OP1 doub N N 268 G P OP2 sing N N 269 G P "O5'" sing N N 270 G OP2 HOP2 sing N N 271 G "O5'" "C5'" sing N N 272 G "C5'" "C4'" sing N N 273 G "C5'" "H5'" sing N N 274 G "C5'" "H5''" sing N N 275 G "C4'" "O4'" sing N N 276 G "C4'" "C3'" sing N N 277 G "C4'" "H4'" sing N N 278 G "O4'" "C1'" sing N N 279 G "C3'" "O3'" sing N N 280 G "C3'" "C2'" sing N N 281 G "C3'" "H3'" sing N N 282 G "O3'" "HO3'" sing N N 283 G "C2'" "O2'" sing N N 284 G "C2'" "C1'" sing N N 285 G "C2'" "H2'" sing N N 286 G "O2'" "HO2'" sing N N 287 G "C1'" N9 sing N N 288 G "C1'" "H1'" sing N N 289 G N9 C8 sing Y N 290 G N9 C4 sing Y N 291 G C8 N7 doub Y N 292 G C8 H8 sing N N 293 G N7 C5 sing Y N 294 G C5 C6 sing N N 295 G C5 C4 doub Y N 296 G C6 O6 doub N N 297 G C6 N1 sing N N 298 G N1 C2 sing N N 299 G N1 H1 sing N N 300 G C2 N2 sing N N 301 G C2 N3 doub N N 302 G N2 H21 sing N N 303 G N2 H22 sing N N 304 G N3 C4 sing N N 305 U OP3 P sing N N 306 U OP3 HOP3 sing N N 307 U P OP1 doub N N 308 U P OP2 sing N N 309 U P "O5'" sing N N 310 U OP2 HOP2 sing N N 311 U "O5'" "C5'" sing N N 312 U "C5'" "C4'" sing N N 313 U "C5'" "H5'" sing N N 314 U "C5'" "H5''" sing N N 315 U "C4'" "O4'" sing N N 316 U "C4'" "C3'" sing N N 317 U "C4'" "H4'" sing N N 318 U "O4'" "C1'" sing N N 319 U "C3'" "O3'" sing N N 320 U "C3'" "C2'" sing N N 321 U "C3'" "H3'" sing N N 322 U "O3'" "HO3'" sing N N 323 U "C2'" "O2'" sing N N 324 U "C2'" "C1'" sing N N 325 U "C2'" "H2'" sing N N 326 U "O2'" "HO2'" sing N N 327 U "C1'" N1 sing N N 328 U "C1'" "H1'" sing N N 329 U N1 C2 sing N N 330 U N1 C6 sing N N 331 U C2 O2 doub N N 332 U C2 N3 sing N N 333 U N3 C4 sing N N 334 U N3 H3 sing N N 335 U C4 O4 doub N N 336 U C4 C5 sing N N 337 U C5 C6 doub N N 338 U C5 H5 sing N N 339 U C6 H6 sing N N 340 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LAR 'double helix' 2LAR 'a-form double helix' 2LAR 'mismatched base pair' # 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 U 9 1_555 -0.253 -0.051 0.225 -17.295 15.349 5.586 1 A_DA1:U18_B A 1 ? B 18 ? 20 1 1 A DT 2 1_555 B A 8 1_555 0.216 -0.106 0.143 8.753 4.890 -0.881 2 A_DT2:A17_B A 2 ? B 17 ? 20 1 1 A DG 3 1_555 B C 7 1_555 -0.194 -0.039 -0.217 1.968 9.081 -1.220 3 A_DG3:C16_B A 3 ? B 16 ? 19 1 1 A DG 4 1_555 B C 6 1_555 -0.335 -0.068 0.105 19.403 -4.362 0.494 4 A_DG4:C15_B A 4 ? B 15 ? 19 1 1 A DT 5 1_555 B A 5 1_555 -0.197 0.180 -0.311 25.931 -24.748 -8.947 5 A_DT5:A14_B A 5 ? B 14 ? 20 1 1 A DC 7 1_555 B G 3 1_555 0.393 -0.172 0.019 9.659 -29.110 -2.018 6 A_DC7:G12_B A 7 ? B 12 ? 19 1 1 A DT 8 1_555 B A 2 1_555 0.282 -0.024 0.142 4.023 -20.317 -2.816 7 A_DT8:A11_B A 8 ? B 11 ? 20 1 1 A DC 9 1_555 B G 1 1_555 -0.178 -0.058 0.484 -10.722 -23.723 -3.268 8 A_DC9:G10_B A 9 ? B 10 ? 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 DA 1 1_555 B U 9 1_555 A DT 2 1_555 B A 8 1_555 -0.611 -1.765 3.010 5.854 2.789 25.535 -4.527 2.709 2.603 6.185 -12.978 26.332 1 AA_DA1DT2:A17U18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A DT 2 1_555 B A 8 1_555 A DG 3 1_555 B C 7 1_555 -1.285 -0.675 3.277 -3.332 17.614 35.876 -2.969 1.504 2.769 26.645 5.040 39.973 2 AA_DT2DG3:C16A17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A DG 3 1_555 B C 7 1_555 A DG 4 1_555 B C 6 1_555 0.207 -1.232 3.022 -1.152 4.154 27.784 -3.411 -0.669 2.801 8.584 2.380 28.110 3 AA_DG3DG4:C15C16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A DG 4 1_555 B C 6 1_555 A DT 5 1_555 B A 5 1_555 -0.450 -0.446 3.271 4.916 1.504 33.670 -0.999 1.541 3.153 2.578 -8.425 34.049 4 AA_DG4DT5:A14C15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A DT 5 1_555 B A 5 1_555 A DC 7 1_555 B G 3 1_555 0.625 -2.589 6.691 6.638 19.828 67.470 -3.630 -0.081 5.865 17.429 -5.835 70.268 5 AA_DT5DC7:G12A14_BB A 5 ? B 14 ? A 7 ? B 12 ? 1 A DC 7 1_555 B G 3 1_555 A DT 8 1_555 B A 2 1_555 -0.294 -0.871 3.374 3.768 6.206 36.480 -2.198 0.967 3.144 9.795 -5.947 37.171 6 AA_DC7DT8:A11G12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DT 8 1_555 B A 2 1_555 A DC 9 1_555 B G 1 1_555 0.650 -0.477 3.345 -0.528 4.323 35.453 -1.411 -1.137 3.256 7.067 0.862 35.711 7 AA_DT8DC9:G10A11_BB A 8 ? B 11 ? A 9 ? B 10 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Bruker AVANCE 1 'Bruker Avance' 500 Bruker AVANCE 2 'Bruker Avance' # _atom_sites.entry_id 2LAR _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 B C H N O P # loop_