data_2M8A # _entry.id 2M8A # _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 2M8A pdb_00002m8a 10.2210/pdb2m8a/pdb RCSB RCSB103334 ? ? BMRB 19226 ? 10.13018/BMR19226 WWPDB D_1000103334 ? ? # 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 2014-05-21 3 'Structure model' 1 2 2023-06-14 4 'Structure model' 1 3 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other 6 4 'Structure model' 'Data collection' 7 4 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_nmr_spectrometer 5 3 'Structure model' struct_conn 6 4 'Structure model' chem_comp_atom 7 4 'Structure model' chem_comp_bond 8 4 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_pdbx_nmr_spectrometer.model' 6 3 'Structure model' '_struct_conn.pdbx_dist_value' 7 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 9 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 10 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 4 'Structure model' '_database_2.pdbx_DOI' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2M8A _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-05-14 _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 # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 19226 BMRB unspecified . 2M84 PDB unspecified . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Martin-Pintado, N.' 1 'Deleavey, G.' 2 'Portella, G.' 3 'Campos, R.' 4 'Orozco, M.' 5 'Damha, M.' 6 'Gonzalez, C.' 7 # _citation.id primary _citation.title ;Backbone FCHO Hydrogen Bonds in 2'F-Substituted Nucleic Acids. ; _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 52 _citation.page_first 12065 _citation.page_last 12068 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1433-7851 _citation.journal_id_CSD 9999 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24115468 _citation.pdbx_database_id_DOI 10.1002/anie.201305710 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Martin-Pintado, N.' 1 ? primary 'Deleavey, G.F.' 2 ? primary 'Portella, G.' 3 ? primary 'Campos-Olivas, R.' 4 ? primary 'Orozco, M.' 5 ? primary 'Damha, M.J.' 6 ? primary 'Gonzalez, C.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;2'F-RNA/2'F-ANA chimeric duplex ; _entity.formula_weight 3865.255 _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 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(CFZ)(GF2)(CFZ)(GF2)(AF2)(AF2)(TAF)(UFT)(CFL)(GF2)(CFL)(GF2)' _entity_poly.pdbx_seq_one_letter_code_can XXXXXXTUCXCX _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 CFZ n 1 2 GF2 n 1 3 CFZ n 1 4 GF2 n 1 5 AF2 n 1 6 AF2 n 1 7 TAF n 1 8 UFT n 1 9 CFL n 1 10 GF2 n 1 11 CFL n 1 12 GF2 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 AF2 'DNA linking' n ;2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O6 P' 349.212 CFL 'DNA linking' n '4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one' "2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" 'C9 H13 F N3 O7 P' 325.188 CFZ 'DNA linking' n ;2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate) ; ? 'C9 H13 F N3 O7 P' 325.188 GF2 'DNA linking' n ;2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O7 P' 365.212 TAF 'DNA linking' n ;2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'-PHOSPHATE ; ? 'C10 H14 F N2 O8 P' 340.199 UFT 'DNA linking' n ;2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate) ; ? 'C9 H12 F N2 O8 P' 326.172 # 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 CFZ 1 1 1 CFZ CFZ A . n A 1 2 GF2 2 2 2 GF2 GF2 A . n A 1 3 CFZ 3 3 3 CFZ CFZ A . n A 1 4 GF2 4 4 4 GF2 GF2 A . n A 1 5 AF2 5 5 5 AF2 AF2 A . n A 1 6 AF2 6 6 6 AF2 AF2 A . n A 1 7 TAF 7 7 7 TAF TAF A . n A 1 8 UFT 8 8 8 UFT UFT A . n A 1 9 CFL 9 9 9 CFL CFL A . n A 1 10 GF2 10 10 10 GF2 GF2 A . n A 1 11 CFL 11 11 11 CFL CFL A . n A 1 12 GF2 12 12 12 GF2 GF2 A . n B 1 1 CFZ 1 13 13 CFZ CFZ B . n B 1 2 GF2 2 14 14 GF2 GF2 B . n B 1 3 CFZ 3 15 15 CFZ CFZ B . n B 1 4 GF2 4 16 16 GF2 GF2 B . n B 1 5 AF2 5 17 17 AF2 AF2 B . n B 1 6 AF2 6 18 18 AF2 AF2 B . n B 1 7 TAF 7 19 19 TAF TAF B . n B 1 8 UFT 8 20 20 UFT UFT B . n B 1 9 CFL 9 21 21 CFL CFL B . n B 1 10 GF2 10 22 22 GF2 GF2 B . n B 1 11 CFL 11 23 23 CFL CFL B . n B 1 12 GF2 12 24 24 GF2 GF2 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 2M8A _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2M8A _struct.title ;2'F-ANA/2'F-RNA alternated sequences ; _struct.pdbx_model_details 'closest to the average, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2M8A _struct_keywords.pdbx_keywords 'DNA, RNA' _struct_keywords.text 'A-form, 12-mer, Dickerson Drew dodecamer, Modified nucleotides, DNA, 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 2M8A _struct_ref.pdbx_db_accession 2M8A _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2M8A A 1 ? 12 ? 2M8A 1 ? 12 ? 1 12 2 1 2M8A B 1 ? 12 ? 2M8A 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 CFZ 1 "O3'" ? ? ? 1_555 A GF2 2 P ? ? A CFZ 1 A GF2 2 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale one ? A GF2 2 "O3'" ? ? ? 1_555 A CFZ 3 P ? ? A GF2 2 A CFZ 3 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale3 covale both ? A CFZ 3 "O3'" ? ? ? 1_555 A GF2 4 P ? ? A CFZ 3 A GF2 4 1_555 ? ? ? ? ? ? ? 1.628 ? ? covale4 covale one ? A GF2 4 "O3'" ? ? ? 1_555 A AF2 5 P ? ? A GF2 4 A AF2 5 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale5 covale one ? A AF2 5 "O3'" ? ? ? 1_555 A AF2 6 P ? ? A AF2 5 A AF2 6 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale6 covale one ? A AF2 6 "O3'" ? ? ? 1_555 A TAF 7 P ? ? A AF2 6 A TAF 7 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale7 covale one ? A TAF 7 "O3'" ? ? ? 1_555 A UFT 8 P ? ? A TAF 7 A UFT 8 1_555 ? ? ? ? ? ? ? 1.634 ? ? covale8 covale both ? A UFT 8 "O3'" ? ? ? 1_555 A CFL 9 P ? ? A UFT 8 A CFL 9 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale9 covale one ? A CFL 9 "O3'" ? ? ? 1_555 A GF2 10 P ? ? A CFL 9 A GF2 10 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale10 covale one ? A GF2 10 "O3'" ? ? ? 1_555 A CFL 11 P ? ? A GF2 10 A CFL 11 1_555 ? ? ? ? ? ? ? 1.622 ? ? covale11 covale one ? A CFL 11 "O3'" ? ? ? 1_555 A GF2 12 P ? ? A CFL 11 A GF2 12 1_555 ? ? ? ? ? ? ? 1.626 ? ? covale12 covale both ? B CFZ 1 "O3'" ? ? ? 1_555 B GF2 2 P ? ? B CFZ 13 B GF2 14 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale13 covale one ? B GF2 2 "O3'" ? ? ? 1_555 B CFZ 3 P ? ? B GF2 14 B CFZ 15 1_555 ? ? ? ? ? ? ? 1.627 ? ? covale14 covale both ? B CFZ 3 "O3'" ? ? ? 1_555 B GF2 4 P ? ? B CFZ 15 B GF2 16 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale15 covale one ? B GF2 4 "O3'" ? ? ? 1_555 B AF2 5 P ? ? B GF2 16 B AF2 17 1_555 ? ? ? ? ? ? ? 1.628 ? ? covale16 covale one ? B AF2 5 "O3'" ? ? ? 1_555 B AF2 6 P ? ? B AF2 17 B AF2 18 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale17 covale one ? B AF2 6 "O3'" ? ? ? 1_555 B TAF 7 P ? ? B AF2 18 B TAF 19 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale18 covale one ? B TAF 7 "O3'" ? ? ? 1_555 B UFT 8 P ? ? B TAF 19 B UFT 20 1_555 ? ? ? ? ? ? ? 1.638 ? ? covale19 covale both ? B UFT 8 "O3'" ? ? ? 1_555 B CFL 9 P ? ? B UFT 20 B CFL 21 1_555 ? ? ? ? ? ? ? 1.637 ? ? covale20 covale one ? B CFL 9 "O3'" ? ? ? 1_555 B GF2 10 P ? ? B CFL 21 B GF2 22 1_555 ? ? ? ? ? ? ? 1.631 ? ? covale21 covale one ? B GF2 10 "O3'" ? ? ? 1_555 B CFL 11 P ? ? B GF2 22 B CFL 23 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale22 covale one ? B CFL 11 "O3'" ? ? ? 1_555 B GF2 12 P ? ? B CFL 23 B GF2 24 1_555 ? ? ? ? ? ? ? 1.627 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 CFZ 1 A CFZ 1 ? DC ? 2 A GF2 2 A GF2 2 ? DG ? 3 A CFZ 3 A CFZ 3 ? DC ? 4 A GF2 4 A GF2 4 ? DG ? 5 A AF2 5 A AF2 5 ? DA ? 6 A AF2 6 A AF2 6 ? DA ? 7 A TAF 7 A TAF 7 ? DT ? 8 A UFT 8 A UFT 8 ? DU ? 9 A CFL 9 A CFL 9 ? DC ? 10 A GF2 10 A GF2 10 ? DG ? 11 A CFL 11 A CFL 11 ? DC ? 12 A GF2 12 A GF2 12 ? DG ? 13 B CFZ 1 B CFZ 13 ? DC ? 14 B GF2 2 B GF2 14 ? DG ? 15 B CFZ 3 B CFZ 15 ? DC ? 16 B GF2 4 B GF2 16 ? DG ? 17 B AF2 5 B AF2 17 ? DA ? 18 B AF2 6 B AF2 18 ? DA ? 19 B TAF 7 B TAF 19 ? DT ? 20 B UFT 8 B UFT 20 ? DU ? 21 B CFL 9 B CFL 21 ? DC ? 22 B GF2 10 B GF2 22 ? DG ? 23 B CFL 11 B CFL 23 ? DC ? 24 B GF2 12 B GF2 24 ? DG ? # _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 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2M8A _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 2M8A _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.6 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(UFT)P*(CFL)P*(GFZ)P*(CFL)P*(GFZ))-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;0.6 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(UFT)P*(CFL)P*(GFZ)P*(CFL)P*(GFZ))-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 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 ;DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(UFT)P*(CFL)P*(GFZ)P*(CFL)P*(GFZ))-3')-1 ; 0.6 ? mM ? 1 'sodium chloride-2' 100 ? mM ? 1 'sodium phosphate-3' 25 ? mM ? 1 ;DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(UFT)P*(CFL)P*(GFZ)P*(CFL)P*(GFZ))-3')-4 ; 0.6 ? mM ? 2 'sodium chloride-5' 100 ? mM ? 2 'sodium phosphate-6' 25 ? 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 1 125 7.0 ambient atm 283 K 2 125 7.0 1 atm 298 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' 2 2 2 '2D 1H-1H NOESY' 2 3 2 '2D DQF-COSY' 2 4 2 '2D 1H-1H TOCSY' # _pdbx_nmr_refine.entry_id 2M8A _pdbx_nmr_refine.method 'molecular dynamics' _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 Kollman' 'geometry optimization' Amber ? 1 'Koradi, Billeter and Wuthrich' 'data analysis' MOLMOL ? 2 Goddard 'peak picking' Sparky ? 3 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' refinement Amber ? 4 # 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 AF2 F F N N 1 AF2 P P N N 2 AF2 N1 N Y N 3 AF2 C2 C Y N 4 AF2 N3 N Y N 5 AF2 C4 C Y N 6 AF2 C5 C Y N 7 AF2 C6 C Y N 8 AF2 N6 N N N 9 AF2 N7 N Y N 10 AF2 C8 C Y N 11 AF2 N9 N Y N 12 AF2 "C1'" C N R 13 AF2 OP2 O N N 14 AF2 "C2'" C N R 15 AF2 OP1 O N N 16 AF2 "C3'" C N R 17 AF2 "O3'" O N N 18 AF2 "C4'" C N R 19 AF2 "O4'" O N N 20 AF2 "C5'" C N N 21 AF2 "O5'" O N N 22 AF2 H2 H N N 23 AF2 H8 H N N 24 AF2 "H5'" H N N 25 AF2 "H5'A" H N N 26 AF2 "H1'" H N N 27 AF2 "H2'" H N N 28 AF2 "H3'" H N N 29 AF2 "H4'" H N N 30 AF2 HN6 H N N 31 AF2 HN6A H N N 32 AF2 HOP2 H N N 33 AF2 "HO3'" H N N 34 AF2 OP3 O N N 35 AF2 HOP3 H N N 36 CFL O3P O N N 37 CFL P P N N 38 CFL O1P O N N 39 CFL O2P O N N 40 CFL "O5'" O N N 41 CFL "C5'" C N N 42 CFL "C4'" C N R 43 CFL "O4'" O N N 44 CFL "C3'" C N R 45 CFL "O3'" O N N 46 CFL "C2'" C N S 47 CFL "C1'" C N R 48 CFL N1 N N N 49 CFL C2 C N N 50 CFL O2 O N N 51 CFL N3 N N N 52 CFL C4 C N N 53 CFL N4 N N N 54 CFL C5 C N N 55 CFL C6 C N N 56 CFL F F N N 57 CFL HO3P H N N 58 CFL HO1P H N N 59 CFL "H5'1" H N N 60 CFL "H5'2" H N N 61 CFL "H4'" H N N 62 CFL "H3'" H N N 63 CFL "HO3'" H N N 64 CFL "H2'" H N N 65 CFL "H1'" H N N 66 CFL HN41 H N N 67 CFL HN42 H N N 68 CFL H5 H N N 69 CFL H6 H N N 70 CFZ P P N N 71 CFZ N1 N N N 72 CFZ C2 C N N 73 CFZ O2 O N N 74 CFZ N3 N N N 75 CFZ C4 C N N 76 CFZ N4 N N N 77 CFZ C5 C N N 78 CFZ C6 C N N 79 CFZ "C1'" C N R 80 CFZ O1P O N N 81 CFZ "C2'" C N R 82 CFZ "F2'" F N N 83 CFZ O2P O N N 84 CFZ "C3'" C N R 85 CFZ "O3'" O N N 86 CFZ O3P O N N 87 CFZ "C4'" C N R 88 CFZ "O4'" O N N 89 CFZ "C5'" C N N 90 CFZ "O5'" O N N 91 CFZ HN4 H N N 92 CFZ HN4A H N N 93 CFZ H5 H N N 94 CFZ H6 H N N 95 CFZ "H1'" H N N 96 CFZ HO1P H N N 97 CFZ "H2'" H N N 98 CFZ "H3'" H N N 99 CFZ "HO3'" H N N 100 CFZ HO3P H N N 101 CFZ "H4'" H N N 102 CFZ "H5'" H N N 103 CFZ "H5'A" H N N 104 GF2 F F N N 105 GF2 P P N N 106 GF2 N1 N N N 107 GF2 C2 C N N 108 GF2 N2 N N N 109 GF2 N3 N N N 110 GF2 C4 C Y N 111 GF2 C5 C Y N 112 GF2 C6 C N N 113 GF2 O6 O N N 114 GF2 N7 N Y N 115 GF2 C8 C Y N 116 GF2 N9 N Y N 117 GF2 "C1'" C N R 118 GF2 OP2 O N N 119 GF2 "C2'" C N R 120 GF2 OP1 O N N 121 GF2 "C3'" C N R 122 GF2 "O3'" O N N 123 GF2 "C4'" C N R 124 GF2 "O4'" O N N 125 GF2 "C5'" C N N 126 GF2 "O5'" O N N 127 GF2 OP3 O N N 128 GF2 HN1 H N N 129 GF2 HN2 H N N 130 GF2 HN2A H N N 131 GF2 H8 H N N 132 GF2 "H1'" H N N 133 GF2 HOP2 H N N 134 GF2 "H2'" H N N 135 GF2 "H3'" H N N 136 GF2 "HO3'" H N N 137 GF2 "H4'" H N N 138 GF2 "H5'" H N N 139 GF2 "H5'A" H N N 140 GF2 HOP3 H N N 141 TAF P P N N 142 TAF OP1 O N N 143 TAF OP2 O N N 144 TAF OP3 O N N 145 TAF "O5'" O N N 146 TAF N1 N N N 147 TAF C6 C N N 148 TAF C2 C N N 149 TAF O2 O N N 150 TAF N3 N N N 151 TAF C4 C N N 152 TAF O4 O N N 153 TAF C5 C N N 154 TAF C5M C N N 155 TAF "F2'" F N N 156 TAF "C2'" C N S 157 TAF "C5'" C N N 158 TAF "C4'" C N R 159 TAF "O4'" O N N 160 TAF "C1'" C N R 161 TAF "C3'" C N R 162 TAF "O3'" O N N 163 TAF HOP1 H N N 164 TAF HOP2 H N N 165 TAF H6 H N N 166 TAF H3 H N N 167 TAF H71 H N N 168 TAF H72 H N N 169 TAF H73 H N N 170 TAF "H2'" H N N 171 TAF "H5'" H N N 172 TAF "H5''" H N N 173 TAF "H4'" H N N 174 TAF "H1'" H N N 175 TAF "H3'" H N N 176 TAF "HO'3" H N N 177 UFT OP3 O N N 178 UFT P P N N 179 UFT OP1 O N N 180 UFT OP2 O N N 181 UFT "O5'" O N N 182 UFT N1 N N N 183 UFT C6 C N N 184 UFT C2 C N N 185 UFT O2 O N N 186 UFT N3 N N N 187 UFT C4 C N N 188 UFT O4 O N N 189 UFT C5 C N N 190 UFT "F2'" F N N 191 UFT "C2'" C N R 192 UFT "C5'" C N N 193 UFT "C4'" C N R 194 UFT "O4'" O N N 195 UFT "C1'" C N R 196 UFT "C3'" C N R 197 UFT "O3'" O N N 198 UFT HOP3 H N N 199 UFT HOP2 H N N 200 UFT H6 H N N 201 UFT H5 H N N 202 UFT "H2'" H N N 203 UFT "H5'" H N N 204 UFT "H5'A" H N N 205 UFT "H4'" H N N 206 UFT "H1'" H N N 207 UFT "H3'" H N N 208 UFT "HO3'" H N N 209 UFT HN3 H N N 210 # 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 AF2 F "C2'" sing N N 1 AF2 P OP1 doub N N 2 AF2 P OP2 sing N N 3 AF2 N1 C6 sing Y N 4 AF2 C2 N1 doub Y N 5 AF2 C2 N3 sing Y N 6 AF2 N3 C4 doub Y N 7 AF2 C4 N9 sing Y N 8 AF2 C4 C5 sing Y N 9 AF2 C5 N7 sing Y N 10 AF2 C6 C5 doub Y N 11 AF2 C6 N6 sing N N 12 AF2 N6 HN6A sing N N 13 AF2 C8 N7 doub Y N 14 AF2 C8 H8 sing N N 15 AF2 N9 C8 sing Y N 16 AF2 "C1'" N9 sing N N 17 AF2 "C1'" "C2'" sing N N 18 AF2 OP2 HOP2 sing N N 19 AF2 "C2'" "H2'" sing N N 20 AF2 "C2'" "C3'" sing N N 21 AF2 "C3'" "H3'" sing N N 22 AF2 "C3'" "O3'" sing N N 23 AF2 "O3'" "HO3'" sing N N 24 AF2 "C4'" "C3'" sing N N 25 AF2 "C4'" "C5'" sing N N 26 AF2 "O4'" "C1'" sing N N 27 AF2 "O4'" "C4'" sing N N 28 AF2 "C5'" "O5'" sing N N 29 AF2 "C5'" "H5'A" sing N N 30 AF2 "O5'" P sing N N 31 AF2 H2 C2 sing N N 32 AF2 "H5'" "C5'" sing N N 33 AF2 "H1'" "C1'" sing N N 34 AF2 "H4'" "C4'" sing N N 35 AF2 HN6 N6 sing N N 36 AF2 P OP3 sing N N 37 AF2 OP3 HOP3 sing N N 38 CFL O3P P sing N N 39 CFL O3P HO3P sing N N 40 CFL P O1P sing N N 41 CFL P O2P doub N N 42 CFL P "O5'" sing N N 43 CFL O1P HO1P sing N N 44 CFL "O5'" "C5'" sing N N 45 CFL "C5'" "C4'" sing N N 46 CFL "C5'" "H5'1" sing N N 47 CFL "C5'" "H5'2" sing N N 48 CFL "C4'" "O4'" sing N N 49 CFL "C4'" "C3'" sing N N 50 CFL "C4'" "H4'" sing N N 51 CFL "O4'" "C1'" sing N N 52 CFL "C3'" "O3'" sing N N 53 CFL "C3'" "C2'" sing N N 54 CFL "C3'" "H3'" sing N N 55 CFL "O3'" "HO3'" sing N N 56 CFL "C2'" "C1'" sing N N 57 CFL "C2'" F sing N N 58 CFL "C2'" "H2'" sing N N 59 CFL "C1'" N1 sing N N 60 CFL "C1'" "H1'" sing N N 61 CFL N1 C2 sing N N 62 CFL N1 C6 sing N N 63 CFL C2 O2 doub N N 64 CFL C2 N3 sing N N 65 CFL N3 C4 doub N N 66 CFL C4 N4 sing N N 67 CFL C4 C5 sing N N 68 CFL N4 HN41 sing N N 69 CFL N4 HN42 sing N N 70 CFL C5 C6 doub N N 71 CFL C5 H5 sing N N 72 CFL C6 H6 sing N N 73 CFZ O2P P doub N N 74 CFZ P "O5'" sing N N 75 CFZ P O1P sing N N 76 CFZ P O3P sing N N 77 CFZ C6 N1 sing N N 78 CFZ C2 N1 sing N N 79 CFZ N1 "C1'" sing N N 80 CFZ N3 C2 sing N N 81 CFZ C2 O2 doub N N 82 CFZ C4 N3 doub N N 83 CFZ N4 C4 sing N N 84 CFZ C4 C5 sing N N 85 CFZ N4 HN4 sing N N 86 CFZ N4 HN4A sing N N 87 CFZ C5 C6 doub N N 88 CFZ C5 H5 sing N N 89 CFZ C6 H6 sing N N 90 CFZ "C2'" "C1'" sing N N 91 CFZ "C1'" "O4'" sing N N 92 CFZ "C1'" "H1'" sing N N 93 CFZ O1P HO1P sing N N 94 CFZ "C3'" "C2'" sing N N 95 CFZ "C2'" "F2'" sing N N 96 CFZ "C2'" "H2'" sing N N 97 CFZ "C3'" "O3'" sing N N 98 CFZ "C3'" "C4'" sing N N 99 CFZ "C3'" "H3'" sing N N 100 CFZ "O3'" "HO3'" sing N N 101 CFZ O3P HO3P sing N N 102 CFZ "O4'" "C4'" sing N N 103 CFZ "C5'" "C4'" sing N N 104 CFZ "C4'" "H4'" sing N N 105 CFZ "O5'" "C5'" sing N N 106 CFZ "C5'" "H5'" sing N N 107 CFZ "C5'" "H5'A" sing N N 108 GF2 P "O5'" sing N N 109 GF2 N1 C2 sing N N 110 GF2 C2 N3 doub N N 111 GF2 C2 N2 sing N N 112 GF2 C4 N3 sing N N 113 GF2 C5 C4 doub Y N 114 GF2 C6 N1 sing N N 115 GF2 C6 C5 sing N N 116 GF2 O6 C6 doub N N 117 GF2 N7 C5 sing Y N 118 GF2 N7 C8 doub Y N 119 GF2 C8 N9 sing Y N 120 GF2 N9 C4 sing Y N 121 GF2 N9 "C1'" sing N N 122 GF2 "C1'" "O4'" sing N N 123 GF2 OP2 P sing N N 124 GF2 "C2'" F sing N N 125 GF2 "C2'" "C1'" sing N N 126 GF2 OP1 P doub N N 127 GF2 "C3'" "C2'" sing N N 128 GF2 "C3'" "C4'" sing N N 129 GF2 "O3'" "C3'" sing N N 130 GF2 "C4'" "O4'" sing N N 131 GF2 "C5'" "C4'" sing N N 132 GF2 "O5'" "C5'" sing N N 133 GF2 P OP3 sing N N 134 GF2 N1 HN1 sing N N 135 GF2 N2 HN2 sing N N 136 GF2 N2 HN2A sing N N 137 GF2 C8 H8 sing N N 138 GF2 "C1'" "H1'" sing N N 139 GF2 OP2 HOP2 sing N N 140 GF2 "C2'" "H2'" sing N N 141 GF2 "C3'" "H3'" sing N N 142 GF2 "O3'" "HO3'" sing N N 143 GF2 "C4'" "H4'" sing N N 144 GF2 "C5'" "H5'" sing N N 145 GF2 "C5'" "H5'A" sing N N 146 GF2 OP3 HOP3 sing N N 147 TAF P OP1 sing N N 148 TAF P OP2 sing N N 149 TAF P OP3 doub N N 150 TAF P "O5'" sing N N 151 TAF OP1 HOP1 sing N N 152 TAF OP2 HOP2 sing N N 153 TAF "O5'" "C5'" sing N N 154 TAF N1 C6 sing N N 155 TAF N1 C2 sing N N 156 TAF N1 "C1'" sing N N 157 TAF C6 C5 doub N N 158 TAF C6 H6 sing N N 159 TAF C2 O2 doub N N 160 TAF C2 N3 sing N N 161 TAF N3 C4 sing N N 162 TAF N3 H3 sing N N 163 TAF C4 O4 doub N N 164 TAF C4 C5 sing N N 165 TAF C5 C5M sing N N 166 TAF C5M H71 sing N N 167 TAF C5M H72 sing N N 168 TAF C5M H73 sing N N 169 TAF "F2'" "C2'" sing N N 170 TAF "C2'" "C1'" sing N N 171 TAF "C2'" "C3'" sing N N 172 TAF "C2'" "H2'" sing N N 173 TAF "C5'" "C4'" sing N N 174 TAF "C5'" "H5'" sing N N 175 TAF "C5'" "H5''" sing N N 176 TAF "C4'" "O4'" sing N N 177 TAF "C4'" "C3'" sing N N 178 TAF "C4'" "H4'" sing N N 179 TAF "O4'" "C1'" sing N N 180 TAF "C1'" "H1'" sing N N 181 TAF "C3'" "O3'" sing N N 182 TAF "C3'" "H3'" sing N N 183 TAF "O3'" "HO'3" sing N N 184 UFT OP3 P sing N N 185 UFT OP1 P doub N N 186 UFT P OP2 sing N N 187 UFT P "O5'" sing N N 188 UFT OP3 HOP3 sing N N 189 UFT OP2 HOP2 sing N N 190 UFT "O5'" "C5'" sing N N 191 UFT C6 N1 sing N N 192 UFT N1 C2 sing N N 193 UFT N1 "C1'" sing N N 194 UFT C5 C6 doub N N 195 UFT C6 H6 sing N N 196 UFT N3 C2 sing N N 197 UFT C2 O2 doub N N 198 UFT C4 N3 sing N N 199 UFT O4 C4 doub N N 200 UFT C5 C4 sing N N 201 UFT C5 H5 sing N N 202 UFT "C2'" "F2'" sing N N 203 UFT "C3'" "C2'" sing N N 204 UFT "C2'" "C1'" sing N N 205 UFT "C2'" "H2'" sing N N 206 UFT "C5'" "C4'" sing N N 207 UFT "C5'" "H5'" sing N N 208 UFT "C5'" "H5'A" sing N N 209 UFT "C3'" "C4'" sing N N 210 UFT "C4'" "O4'" sing N N 211 UFT "C4'" "H4'" sing N N 212 UFT "O4'" "C1'" sing N N 213 UFT "C1'" "H1'" sing N N 214 UFT "C3'" "O3'" sing N N 215 UFT "C3'" "H3'" sing N N 216 UFT "O3'" "HO3'" sing N N 217 UFT N3 HN3 sing N N 218 # 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' 800 Bruker AVANCE 2 'Bruker Avance' 800 Varian INOVA 3 'Varian INOVA' 700 Bruker AVANCE 4 'Bruker Avance' # _atom_sites.entry_id 2M8A _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 F H N O P # loop_