data_2M39 # _entry.id 2M39 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 2M39 pdb_00002m39 10.2210/pdb2m39/pdb RCSB RCSB103153 ? ? BMRB 18950 ? 10.13018/BMR18950 WWPDB D_1000103153 ? ? # 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 2013-11-27 2 'Structure model' 1 1 2023-06-14 3 'Structure model' 1 2 2024-05-15 # _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' 4 2 'Structure model' Other 5 3 'Structure model' 'Data collection' 6 3 'Structure model' 'Database references' # 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' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_software 4 2 'Structure model' struct_conn 5 3 'Structure model' chem_comp_atom 6 3 'Structure model' chem_comp_bond 7 3 'Structure model' database_2 # 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_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_software.name' 5 2 'Structure model' '_struct_conn.pdbx_dist_value' 6 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 2 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 2 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 2 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 2 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 2 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 2 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 2 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 2 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 2 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 3 'Structure model' '_database_2.pdbx_DOI' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2M39 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-01-15 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # _pdbx_database_related.db_id 18950 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Plevnik, M.' 1 'Cevec, M.' 2 'Plavec, J.' 3 # _citation.id primary _citation.title ;NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex. ; _citation.journal_abbrev Biochimie _citation.journal_volume 95 _citation.page_first 2385 _citation.page_last 2391 _citation.year 2013 _citation.journal_id_ASTM BICMBE _citation.country FR _citation.journal_id_ISSN 0300-9084 _citation.journal_id_CSD 0466 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24012551 _citation.pdbx_database_id_DOI 10.1016/j.biochi.2013.08.025 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Plevnik, M.' 1 ? primary 'Cevec, M.' 2 ? primary 'Plavec, J.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L)P*DG)-3') ; _entity.formula_weight 4534.364 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(C5L)(G48)(C5L)(G48)(A44)(A44)(T39)(T39)(C5L)(G48)(C5L)(DG)' _entity_poly.pdbx_seq_one_letter_code_can XGXGAATTXGXG _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 C5L n 1 2 G48 n 1 3 C5L n 1 4 G48 n 1 5 A44 n 1 6 A44 n 1 7 T39 n 1 8 T39 n 1 9 C5L n 1 10 G48 n 1 11 C5L n 1 12 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific Synthetic _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY' # 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 A44 'RNA linking' n ;2'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE ; ? 'C13 H20 N5 O8 P' 405.300 C5L 'RNA linking' n ;2'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate) ; ? 'C13 H22 N3 O9 P' 395.302 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 G48 'RNA linking' n "2'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE" ? 'C13 H20 N5 O9 P' 421.300 T39 'RNA linking' n ;2'-O-METHOXYETHYLENE THYMIDINE 5'-MONOPHOSPHATE ; ? 'C13 H21 N2 O10 P' 396.287 # 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 C5L 1 1 1 C5L C5L A . n A 1 2 G48 2 2 2 G48 G48 A . n A 1 3 C5L 3 3 3 C5L C5L A . n A 1 4 G48 4 4 4 G48 G48 A . n A 1 5 A44 5 5 5 A44 A44 A . n A 1 6 A44 6 6 6 A44 A44 A . n A 1 7 T39 7 7 7 T39 T39 A . n A 1 8 T39 8 8 8 T39 T39 A . n A 1 9 C5L 9 9 9 C5L C5L A . n A 1 10 G48 10 10 10 G48 G48 A . n A 1 11 C5L 11 11 11 C5L C5L A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 C5L 1 13 13 C5L C5L B . n B 1 2 G48 2 14 14 G48 G48 B . n B 1 3 C5L 3 15 15 C5L C5L B . n B 1 4 G48 4 16 16 G48 G48 B . n B 1 5 A44 5 17 17 A44 A44 B . n B 1 6 A44 6 18 18 A44 A44 B . n B 1 7 T39 7 19 19 T39 T39 B . n B 1 8 T39 8 20 20 T39 T39 B . n B 1 9 C5L 9 21 21 C5L C5L B . n B 1 10 G48 10 22 22 G48 G48 B . n B 1 11 C5L 11 23 23 C5L C5L B . n B 1 12 DG 12 24 24 DG DG 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 2M39 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2M39 _struct.title ;The solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX ; _struct.pdbx_model_details 'lowest energy, model7' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2M39 _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;DUPLEX, (3', 5')-RNA, 2'-O-(2-METHOXYETHYL) RIBOSE, RNA ; # 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2M39 _struct_ref.pdbx_db_accession 2M39 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code XGXGAATTXGXG _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2M39 A 1 ? 12 ? 2M39 1 ? 12 ? 1 12 2 1 2M39 B 1 ? 12 ? 2M39 13 ? 24 ? 13 24 # _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 both ? A G48 2 "O3'" ? ? ? 1_555 A C5L 3 P ? ? A G48 2 A C5L 3 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A G48 4 "O3'" ? ? ? 1_555 A A44 5 P ? ? A G48 4 A A44 5 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale3 covale both ? A A44 5 "O3'" ? ? ? 1_555 A A44 6 P ? ? A A44 5 A A44 6 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale4 covale both ? A A44 6 "O3'" ? ? ? 1_555 A T39 7 P ? ? A A44 6 A T39 7 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale5 covale both ? A T39 7 "O3'" ? ? ? 1_555 A T39 8 P ? ? A T39 7 A T39 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale6 covale both ? A T39 8 "O3'" ? ? ? 1_555 A C5L 9 P ? ? A T39 8 A C5L 9 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale7 covale both ? A G48 10 "O3'" ? ? ? 1_555 A C5L 11 P ? ? A G48 10 A C5L 11 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale8 covale both ? B G48 2 "O3'" ? ? ? 1_555 B C5L 3 P ? ? B G48 14 B C5L 15 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale9 covale both ? B G48 4 "O3'" ? ? ? 1_555 B A44 5 P ? ? B G48 16 B A44 17 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale10 covale both ? B A44 5 "O3'" ? ? ? 1_555 B A44 6 P ? ? B A44 17 B A44 18 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale11 covale both ? B A44 6 "O3'" ? ? ? 1_555 B T39 7 P ? ? B A44 18 B T39 19 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale12 covale both ? B T39 7 "O3'" ? ? ? 1_555 B T39 8 P ? ? B T39 19 B T39 20 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale13 covale both ? B T39 8 "O3'" ? ? ? 1_555 B C5L 9 P ? ? B T39 20 B C5L 21 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale14 covale both ? B G48 10 "O3'" ? ? ? 1_555 B C5L 11 P ? ? B G48 22 B C5L 23 1_555 ? ? ? ? ? ? ? 1.607 ? ? hydrog1 hydrog ? ? A A44 5 N1 ? ? ? 1_555 B T39 8 N3 ? ? A A44 5 B T39 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A44 5 N6 ? ? ? 1_555 B T39 8 O4 ? ? A A44 5 B T39 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A A44 6 N1 ? ? ? 1_555 B T39 7 N3 ? ? A A44 6 B T39 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A44 6 N6 ? ? ? 1_555 B T39 7 O4 ? ? A A44 6 B T39 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A T39 7 N3 ? ? ? 1_555 B A44 6 N1 ? ? A T39 7 B A44 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A T39 7 O4 ? ? ? 1_555 B A44 6 N6 ? ? A T39 7 B A44 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A T39 8 N3 ? ? ? 1_555 B A44 5 N1 ? ? A T39 8 B A44 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A T39 8 O4 ? ? ? 1_555 B A44 5 N6 ? ? A T39 8 B A44 17 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 DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.55 108.30 2.25 0.30 N 2 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.80 108.30 4.50 0.30 N 3 2 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.07 108.30 2.77 0.30 N 4 2 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.68 108.30 4.38 0.30 N 5 3 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.57 108.30 4.27 0.30 N 6 3 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.56 108.30 4.26 0.30 N 7 4 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.73 108.30 2.43 0.30 N 8 4 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.38 108.30 4.08 0.30 N 9 5 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.31 108.30 4.01 0.30 N 10 5 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 110.20 108.30 1.90 0.30 N 11 6 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.21 108.30 2.91 0.30 N 12 6 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.75 108.30 4.45 0.30 N 13 7 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.57 108.30 2.27 0.30 N 14 7 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 113.41 108.30 5.11 0.30 N 15 8 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.10 108.30 3.80 0.30 N 16 8 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.54 108.30 4.24 0.30 N 17 9 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.18 108.30 3.88 0.30 N 18 9 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 110.49 108.30 2.19 0.30 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A C5L 1 A C5L 1 ? C ? 2 A G48 2 A G48 2 ? G ? 3 A C5L 3 A C5L 3 ? C ? 4 A G48 4 A G48 4 ? G ? 5 A A44 5 A A44 5 ? A ? 6 A A44 6 A A44 6 ? A ? 7 A T39 7 A T39 7 ? DT ? 8 A T39 8 A T39 8 ? DT ? 9 A C5L 9 A C5L 9 ? C ? 10 A G48 10 A G48 10 ? G ? 11 A C5L 11 A C5L 11 ? C ? 12 B C5L 1 B C5L 13 ? C ? 13 B G48 2 B G48 14 ? G ? 14 B C5L 3 B C5L 15 ? C ? 15 B G48 4 B G48 16 ? G ? 16 B A44 5 B A44 17 ? A ? 17 B A44 6 B A44 18 ? A ? 18 B T39 7 B T39 19 ? DT ? 19 B T39 8 B T39 20 ? DT ? 20 B C5L 9 B C5L 21 ? C ? 21 B G48 10 B G48 22 ? G ? 22 B C5L 11 B C5L 23 ? C ? # _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 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 9 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2M39 _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 2M39 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;2.5 mM 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', 100 mM potassium chloride, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;2.5 mM 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', 100 mM potassium chloride, 100% D2O ; 2 '100% 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 "5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3'-1" 2.5 ? mM ? 1 'potassium chloride-2' 100 ? mM ? 1 "5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3'-3" 2.5 ? mM ? 2 'potassium chloride-4' 100 ? mM ? 2 # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 100 7.0 ambient ? 303 K 2 100 7.0 ambient ? 278 K # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 2 1 1 '2D NOESY' 1 2 2 '2D NOESY' 1 3 2 '2D DQF-COSY' # _pdbx_nmr_details.entry_id 2M39 _pdbx_nmr_details.text 'STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND HETERONUCLEAR TECHNIQUES.' # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2M39 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 394 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # _pdbx_nmr_refine.entry_id 2M39 _pdbx_nmr_refine.method 'simulated annealing, energy minimization' _pdbx_nmr_refine.details ;STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. 3',5'-PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O2' OF EACH RIBOSE MODIFIED BY METHOXYETHYL. ; _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 Varian collection VNMR 6.1B 1 Varian processing VNMR 6.1B 2 'Accelrys Software Inc.' processing Felix 2000 3 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollman' 'structure solution' Amber 7 4 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollman' refinement Amber 7 5 # 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 A44 P P N N 1 A44 OP2 O N N 2 A44 OP1 O N N 3 A44 "O5'" O N N 4 A44 "C5'" C N N 5 A44 "C4'" C N R 6 A44 "O4'" O N N 7 A44 "C3'" C N R 8 A44 "O3'" O N N 9 A44 "C2'" C N R 10 A44 "O2'" O N N 11 A44 "C1'" C N R 12 A44 N9 N Y N 13 A44 C8 C Y N 14 A44 N7 N Y N 15 A44 C5 C Y N 16 A44 C6 C Y N 17 A44 N6 N N N 18 A44 N1 N Y N 19 A44 C2 C Y N 20 A44 N3 N Y N 21 A44 C4 C Y N 22 A44 "CA'" C N N 23 A44 "CD'" C N N 24 A44 "OC'" O N N 25 A44 "CB'" C N N 26 A44 OP3 O N N 27 A44 HOP2 H N N 28 A44 "H5'" H N N 29 A44 "H5''" H N N 30 A44 "H4'" H N N 31 A44 "H3'" H N N 32 A44 "HO3'" H N N 33 A44 "H2'" H N N 34 A44 "H1'" H N N 35 A44 H8 H N N 36 A44 H61 H N N 37 A44 H62 H N N 38 A44 H2 H N N 39 A44 HCA2 H N N 40 A44 HCA1 H N N 41 A44 HCD1 H N N 42 A44 HCD2 H N N 43 A44 HCD3 H N N 44 A44 HCB1 H N N 45 A44 HCB2 H N N 46 A44 HOP3 H N N 47 C5L P P N N 48 C5L N1 N N N 49 C5L C2 C N N 50 C5L O2 O N N 51 C5L N3 N N N 52 C5L C4 C N N 53 C5L N4 N N N 54 C5L C5 C N N 55 C5L C6 C N N 56 C5L C7 C N N 57 C5L "C1'" C N R 58 C5L "C2'" C N R 59 C5L "O2'" O N N 60 C5L "C3'" C N R 61 C5L "O3'" O N N 62 C5L "C4'" C N R 63 C5L "O4'" O N N 64 C5L "C5'" C N N 65 C5L "O5'" O N N 66 C5L "CA'" C N N 67 C5L "CB'" C N N 68 C5L "OC'" O N N 69 C5L "CD'" C N N 70 C5L OP1 O N N 71 C5L OP2 O N N 72 C5L OP3 O N N 73 C5L H6 H N N 74 C5L "H5'" H N N 75 C5L "H1'" H N N 76 C5L "H2'" H N N 77 C5L "H3'" H N N 78 C5L "H4'" H N N 79 C5L H41 H N N 80 C5L H42 H N N 81 C5L "H5''" H N N 82 C5L H71 H N N 83 C5L H72 H N N 84 C5L H73 H N N 85 C5L HCA1 H N N 86 C5L HCA2 H N N 87 C5L HCB1 H N N 88 C5L HCB2 H N N 89 C5L HCD1 H N N 90 C5L HCD2 H N N 91 C5L HCD3 H N N 92 C5L "HO3'" H N N 93 C5L HOP1 H N N 94 C5L HOP3 H N N 95 DG OP3 O N N 96 DG P P N N 97 DG OP1 O N N 98 DG OP2 O N N 99 DG "O5'" O N N 100 DG "C5'" C N N 101 DG "C4'" C N R 102 DG "O4'" O N N 103 DG "C3'" C N S 104 DG "O3'" O N N 105 DG "C2'" C N N 106 DG "C1'" C N R 107 DG N9 N Y N 108 DG C8 C Y N 109 DG N7 N Y N 110 DG C5 C Y N 111 DG C6 C N N 112 DG O6 O N N 113 DG N1 N N N 114 DG C2 C N N 115 DG N2 N N N 116 DG N3 N N N 117 DG C4 C Y N 118 DG HOP3 H N N 119 DG HOP2 H N N 120 DG "H5'" H N N 121 DG "H5''" H N N 122 DG "H4'" H N N 123 DG "H3'" H N N 124 DG "HO3'" H N N 125 DG "H2'" H N N 126 DG "H2''" H N N 127 DG "H1'" H N N 128 DG H8 H N N 129 DG H1 H N N 130 DG H21 H N N 131 DG H22 H N N 132 G48 P P N N 133 G48 OP1 O N N 134 G48 OP3 O N N 135 G48 "O5'" O N N 136 G48 "C5'" C N N 137 G48 "C4'" C N R 138 G48 "O4'" O N N 139 G48 "C3'" C N R 140 G48 "O3'" O N N 141 G48 "C2'" C N R 142 G48 "O2'" O N N 143 G48 "C1'" C N R 144 G48 N9 N Y N 145 G48 C8 C Y N 146 G48 N7 N Y N 147 G48 C5 C Y N 148 G48 C6 C N N 149 G48 O6 O N N 150 G48 N1 N N N 151 G48 C2 C N N 152 G48 N2 N N N 153 G48 N3 N N N 154 G48 C4 C Y N 155 G48 "CA'" C N N 156 G48 "CB'" C N N 157 G48 "OC'" O N N 158 G48 "CD'" C N N 159 G48 OP2 O N N 160 G48 HOP3 H N N 161 G48 "H5'" H N N 162 G48 "H5''" H N N 163 G48 "H4'" H N N 164 G48 "H3'" H N N 165 G48 "HO3'" H N N 166 G48 "H2'" H N N 167 G48 "H1'" H N N 168 G48 H8 H N N 169 G48 H1 H N N 170 G48 H21 H N N 171 G48 H22 H N N 172 G48 HCA2 H N N 173 G48 HCA1 H N N 174 G48 HCB1 H N N 175 G48 HCB2 H N N 176 G48 HCD1 H N N 177 G48 HCD2 H N N 178 G48 HCD3 H N N 179 G48 HOP2 H N N 180 T39 P P N N 181 T39 OP1 O N N 182 T39 OP2 O N N 183 T39 "O5'" O N N 184 T39 "C5'" C N N 185 T39 "C4'" C N R 186 T39 "O4'" O N N 187 T39 "C3'" C N R 188 T39 "O3'" O N N 189 T39 "C2'" C N R 190 T39 "O2'" O N N 191 T39 "C1'" C N R 192 T39 N1 N N N 193 T39 C2 C N N 194 T39 O2 O N N 195 T39 N3 N N N 196 T39 C4 C N N 197 T39 O4 O N N 198 T39 C5 C N N 199 T39 C7 C N N 200 T39 C6 C N N 201 T39 "CA'" C N N 202 T39 "CD'" C N N 203 T39 "CB'" C N N 204 T39 "OC'" O N N 205 T39 OP3 O N N 206 T39 HOP2 H N N 207 T39 "H5'" H N N 208 T39 "H5''" H N N 209 T39 "H4'" H N N 210 T39 "H3'" H N N 211 T39 "HO3'" H N N 212 T39 H7 H N N 213 T39 "H1'" H N N 214 T39 H3 H N N 215 T39 H71 H N N 216 T39 H72 H N N 217 T39 H73 H N N 218 T39 H6 H N N 219 T39 HCA2 H N N 220 T39 HCA1 H N N 221 T39 HCD1 H N N 222 T39 HCD2 H N N 223 T39 HCD3 H N N 224 T39 HCB1 H N N 225 T39 HCB2 H N N 226 T39 HOP3 H N N 227 # 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 A44 C2 N1 doub Y N 1 A44 C2 N3 sing Y N 2 A44 N1 C6 sing Y N 3 A44 "CB'" "CA'" sing N N 4 A44 "CB'" "OC'" sing N N 5 A44 N3 C4 doub Y N 6 A44 C6 N6 sing N N 7 A44 C6 C5 doub Y N 8 A44 "CD'" "OC'" sing N N 9 A44 "CA'" "O2'" sing N N 10 A44 C4 C5 sing Y N 11 A44 C4 N9 sing Y N 12 A44 C5 N7 sing Y N 13 A44 "O2'" "C2'" sing N N 14 A44 "C2'" "C1'" sing N N 15 A44 "C2'" "C3'" sing N N 16 A44 N9 "C1'" sing N N 17 A44 N9 C8 sing Y N 18 A44 N7 C8 doub Y N 19 A44 "C1'" "O4'" sing N N 20 A44 "O3'" "C3'" sing N N 21 A44 "C3'" "C4'" sing N N 22 A44 "O4'" "C4'" sing N N 23 A44 "C4'" "C5'" sing N N 24 A44 "O5'" "C5'" sing N N 25 A44 "O5'" P sing N N 26 A44 OP1 P doub N N 27 A44 P OP2 sing N N 28 A44 P OP3 sing N N 29 A44 OP2 HOP2 sing N N 30 A44 "C5'" "H5'" sing N N 31 A44 "C5'" "H5''" sing N N 32 A44 "C4'" "H4'" sing N N 33 A44 "C3'" "H3'" sing N N 34 A44 "O3'" "HO3'" sing N N 35 A44 "C2'" "H2'" sing N N 36 A44 "C1'" "H1'" sing N N 37 A44 C8 H8 sing N N 38 A44 N6 H61 sing N N 39 A44 N6 H62 sing N N 40 A44 C2 H2 sing N N 41 A44 "CA'" HCA2 sing N N 42 A44 "CA'" HCA1 sing N N 43 A44 "CD'" HCD1 sing N N 44 A44 "CD'" HCD2 sing N N 45 A44 "CD'" HCD3 sing N N 46 A44 "CB'" HCB1 sing N N 47 A44 "CB'" HCB2 sing N N 48 A44 OP3 HOP3 sing N N 49 C5L OP2 P doub N N 50 C5L "O5'" P sing N N 51 C5L P OP3 sing N N 52 C5L P OP1 sing N N 53 C5L C2 N1 sing N N 54 C5L C6 N1 sing N N 55 C5L N1 "C1'" sing N N 56 C5L N3 C2 sing N N 57 C5L C2 O2 doub N N 58 C5L C4 N3 doub N N 59 C5L N4 C4 sing N N 60 C5L C4 C5 sing N N 61 C5L H41 N4 sing N N 62 C5L H42 N4 sing N N 63 C5L C7 C5 sing N N 64 C5L C5 C6 doub N N 65 C5L C6 H6 sing N N 66 C5L H72 C7 sing N N 67 C5L H73 C7 sing N N 68 C5L C7 H71 sing N N 69 C5L "H1'" "C1'" sing N N 70 C5L "C1'" "C2'" sing N N 71 C5L "C1'" "O4'" sing N N 72 C5L "H2'" "C2'" sing N N 73 C5L "C2'" "O2'" sing N N 74 C5L "C2'" "C3'" sing N N 75 C5L "CA'" "O2'" sing N N 76 C5L "H3'" "C3'" sing N N 77 C5L "C3'" "C4'" sing N N 78 C5L "C3'" "O3'" sing N N 79 C5L "O3'" "HO3'" sing N N 80 C5L "O4'" "C4'" sing N N 81 C5L "C4'" "C5'" sing N N 82 C5L "C4'" "H4'" sing N N 83 C5L "O5'" "C5'" sing N N 84 C5L "C5'" "H5'" sing N N 85 C5L "C5'" "H5''" sing N N 86 C5L HCA1 "CA'" sing N N 87 C5L HCA2 "CA'" sing N N 88 C5L "CA'" "CB'" sing N N 89 C5L "OC'" "CB'" sing N N 90 C5L "CB'" HCB2 sing N N 91 C5L "CB'" HCB1 sing N N 92 C5L "CD'" "OC'" sing N N 93 C5L HCD1 "CD'" sing N N 94 C5L HCD2 "CD'" sing N N 95 C5L "CD'" HCD3 sing N N 96 C5L OP1 HOP1 sing N N 97 C5L OP3 HOP3 sing N N 98 DG OP3 P sing N N 99 DG OP3 HOP3 sing N N 100 DG P OP1 doub N N 101 DG P OP2 sing N N 102 DG P "O5'" sing N N 103 DG OP2 HOP2 sing N N 104 DG "O5'" "C5'" sing N N 105 DG "C5'" "C4'" sing N N 106 DG "C5'" "H5'" sing N N 107 DG "C5'" "H5''" sing N N 108 DG "C4'" "O4'" sing N N 109 DG "C4'" "C3'" sing N N 110 DG "C4'" "H4'" sing N N 111 DG "O4'" "C1'" sing N N 112 DG "C3'" "O3'" sing N N 113 DG "C3'" "C2'" sing N N 114 DG "C3'" "H3'" sing N N 115 DG "O3'" "HO3'" sing N N 116 DG "C2'" "C1'" sing N N 117 DG "C2'" "H2'" sing N N 118 DG "C2'" "H2''" sing N N 119 DG "C1'" N9 sing N N 120 DG "C1'" "H1'" sing N N 121 DG N9 C8 sing Y N 122 DG N9 C4 sing Y N 123 DG C8 N7 doub Y N 124 DG C8 H8 sing N N 125 DG N7 C5 sing Y N 126 DG C5 C6 sing N N 127 DG C5 C4 doub Y N 128 DG C6 O6 doub N N 129 DG C6 N1 sing N N 130 DG N1 C2 sing N N 131 DG N1 H1 sing N N 132 DG C2 N2 sing N N 133 DG C2 N3 doub N N 134 DG N2 H21 sing N N 135 DG N2 H22 sing N N 136 DG N3 C4 sing N N 137 G48 OP1 P doub N N 138 G48 P "O5'" sing N N 139 G48 P OP3 sing N N 140 G48 "C5'" "O5'" sing N N 141 G48 "C5'" "C4'" sing N N 142 G48 "C4'" "O4'" sing N N 143 G48 "C4'" "C3'" sing N N 144 G48 "O4'" "C1'" sing N N 145 G48 "O3'" "C3'" sing N N 146 G48 "C3'" "C2'" sing N N 147 G48 "C1'" "C2'" sing N N 148 G48 "C1'" N9 sing N N 149 G48 "O2'" "C2'" sing N N 150 G48 "O2'" "CA'" sing N N 151 G48 "CD'" "OC'" sing N N 152 G48 C8 N9 sing Y N 153 G48 C8 N7 doub Y N 154 G48 "CB'" "OC'" sing N N 155 G48 "CB'" "CA'" sing N N 156 G48 N9 C4 sing Y N 157 G48 N7 C5 sing Y N 158 G48 C4 C5 doub Y N 159 G48 C4 N3 sing N N 160 G48 C5 C6 sing N N 161 G48 N3 C2 doub N N 162 G48 C6 O6 doub N N 163 G48 C6 N1 sing N N 164 G48 C2 N1 sing N N 165 G48 C2 N2 sing N N 166 G48 P OP2 sing N N 167 G48 OP3 HOP3 sing N N 168 G48 "C5'" "H5'" sing N N 169 G48 "C5'" "H5''" sing N N 170 G48 "C4'" "H4'" sing N N 171 G48 "C3'" "H3'" sing N N 172 G48 "O3'" "HO3'" sing N N 173 G48 "C2'" "H2'" sing N N 174 G48 "C1'" "H1'" sing N N 175 G48 C8 H8 sing N N 176 G48 N1 H1 sing N N 177 G48 N2 H21 sing N N 178 G48 N2 H22 sing N N 179 G48 "CA'" HCA2 sing N N 180 G48 "CA'" HCA1 sing N N 181 G48 "CB'" HCB1 sing N N 182 G48 "CB'" HCB2 sing N N 183 G48 "CD'" HCD1 sing N N 184 G48 "CD'" HCD2 sing N N 185 G48 "CD'" HCD3 sing N N 186 G48 OP2 HOP2 sing N N 187 T39 "CD'" "OC'" sing N N 188 T39 "OC'" "CB'" sing N N 189 T39 "CB'" "CA'" sing N N 190 T39 "CA'" "O2'" sing N N 191 T39 "O2'" "C2'" sing N N 192 T39 "O3'" "C3'" sing N N 193 T39 "C2'" "C3'" sing N N 194 T39 "C2'" "C1'" sing N N 195 T39 "C3'" "C4'" sing N N 196 T39 O2 C2 doub N N 197 T39 "C4'" "O4'" sing N N 198 T39 "C4'" "C5'" sing N N 199 T39 "C1'" "O4'" sing N N 200 T39 "C1'" N1 sing N N 201 T39 C2 N1 sing N N 202 T39 C2 N3 sing N N 203 T39 N1 C6 sing N N 204 T39 "C5'" "O5'" sing N N 205 T39 N3 C4 sing N N 206 T39 "O5'" P sing N N 207 T39 C6 C5 doub N N 208 T39 C4 C5 sing N N 209 T39 C4 O4 doub N N 210 T39 C5 C7 sing N N 211 T39 OP1 P doub N N 212 T39 P OP2 sing N N 213 T39 P OP3 sing N N 214 T39 OP2 HOP2 sing N N 215 T39 "C5'" "H5'" sing N N 216 T39 "C5'" "H5''" sing N N 217 T39 "C4'" "H4'" sing N N 218 T39 "C3'" "H3'" sing N N 219 T39 "O3'" "HO3'" sing N N 220 T39 "C2'" H7 sing N N 221 T39 "C1'" "H1'" sing N N 222 T39 N3 H3 sing N N 223 T39 C7 H71 sing N N 224 T39 C7 H72 sing N N 225 T39 C7 H73 sing N N 226 T39 C6 H6 sing N N 227 T39 "CA'" HCA2 sing N N 228 T39 "CA'" HCA1 sing N N 229 T39 "CD'" HCD1 sing N N 230 T39 "CD'" HCD2 sing N N 231 T39 "CD'" HCD3 sing N N 232 T39 "CB'" HCB1 sing N N 233 T39 "CB'" HCB2 sing N N 234 T39 OP3 HOP3 sing N N 235 # _ndb_struct_conf_na.entry_id 2M39 _ndb_struct_conf_na.feature 'a-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 A44 5 1_555 B T39 8 1_555 -0.006 -0.075 -0.316 -9.894 -15.860 -5.992 1 A_A445:T3920_B A 5 ? B 20 ? 20 1 1 A A44 6 1_555 B T39 7 1_555 -0.554 -0.170 0.796 8.068 -7.899 8.582 2 A_A446:T3919_B A 6 ? B 19 ? 20 1 1 A T39 7 1_555 B A44 6 1_555 0.501 -0.127 0.729 -10.581 -8.856 8.548 3 A_T397:A4418_B A 7 ? B 18 ? 20 1 1 A T39 8 1_555 B A44 5 1_555 0.060 -0.140 -0.202 3.833 -19.200 0.611 4 A_T398:A4417_B A 8 ? B 17 ? 20 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 A44 5 1_555 B T39 8 1_555 A A44 6 1_555 B T39 7 1_555 0.555 -1.712 2.490 -5.779 1.519 28.623 -3.633 -2.016 2.245 3.030 11.530 29.227 1 AA_A445A446:T3919T3920_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A A44 6 1_555 B T39 7 1_555 A T39 7 1_555 B A44 6 1_555 0.032 -1.007 3.780 0.498 12.060 33.079 -3.658 0.029 3.228 20.356 -0.841 35.155 2 AA_A446T397:A4418T3919_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A T39 7 1_555 B A44 6 1_555 A T39 8 1_555 B A44 5 1_555 -0.340 -1.769 2.574 4.933 3.762 27.935 -4.216 1.519 2.230 7.673 -10.062 28.602 3 AA_T397T398:A4417A4418_BB A 7 ? B 18 ? A 8 ? B 17 ? # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model 'Unity Inova' _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian Unity Inova' # _atom_sites.entry_id 2M39 _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 HO N O P # loop_