data_7NBK
#
_entry.id 7NBK
#
_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 7NBK pdb_00007nbk 10.2210/pdb7nbk/pdb
WWPDB D_1292113667 ? ?
BMRB 34594 ? 10.13018/BMR34594
#
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 2021-04-07
2 'Structure model' 1 1 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'
#
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
#
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'
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf ?
_pdbx_database_status.status_code_mr REL
_pdbx_database_status.entry_id 7NBK
_pdbx_database_status.recvd_initial_deposition_date 2021-01-27
_pdbx_database_status.SG_entry N
_pdbx_database_status.deposit_site PDBE
_pdbx_database_status.process_site PDBE
_pdbx_database_status.status_code_cs REL
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.details
_pdbx_database_related.db_id
_pdbx_database_related.content_type
PDB 'Other structure with the same modification' 7NBL
unspecified
BMRB
;Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification
;
34594 unspecified
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Cabrero, C.' 1 ?
'Martin-Pintado, N.' 2 ?
'Mazzini, S.' 3 ?
'Gargallo, R.' 4 ?
'Eritja, R.' 5 ?
'Avino, A.' 6 ?
'Gonzalez, C.' 7 ?
#
_citation.abstract ?
_citation.abstract_id_CAS ?
_citation.book_id_ISBN ?
_citation.book_publisher ?
_citation.book_publisher_city ?
_citation.book_title ?
_citation.coordinate_linkage ?
_citation.country GE
_citation.database_id_Medline ?
_citation.details ?
_citation.id primary
_citation.journal_abbrev Chemistry
_citation.journal_id_ASTM ?
_citation.journal_id_CSD ?
_citation.journal_id_ISSN 0947-6539
_citation.journal_full ?
_citation.journal_issue ?
_citation.journal_volume ?
_citation.language ?
_citation.page_first ?
_citation.page_last ?
_citation.title
'Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.'
_citation.year 2021
_citation.database_id_CSD ?
_citation.pdbx_database_id_DOI 10.1002/chem.202100503
_citation.pdbx_database_id_PubMed 33772916
_citation.unpublished_flag ?
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Cabrero, C.' 1 ?
primary 'Martin-Pintado, N.' 2 ?
primary 'Mazzini, S.' 3 ?
primary 'Gargallo, R.' 4 ?
primary 'Eritja, R.' 5 ?
primary 'Avino, A.' 6 ?
primary 'Gonzalez, C.' 7 ?
#
_entity.id 1
_entity.type polymer
_entity.src_method syn
_entity.pdbx_description
;DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')
;
_entity.formula_weight 1845.198
_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
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer yes
_entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DA)(U7B)(DG)'
_entity_poly.pdbx_seq_one_letter_code_can CGTACG
_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 DC n
1 2 DG n
1 3 DT n
1 4 DA n
1 5 U7B n
1 6 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 1
_pdbx_entity_src_syn.pdbx_end_seq_num 6
_pdbx_entity_src_syn.organism_scientific 'synthetic construct'
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id 32630
_pdbx_entity_src_syn.details ?
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222
DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197
DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221
DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208
U7B 'DNA linking' n "2'-deoxy-2'2'-difluorodeoxycytidine"
;[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite
;
'C9 H12 F2 N3 O7 P' 343.178
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 DC 1 1 1 DC DC A . n
A 1 2 DG 2 2 2 DG DG A . n
A 1 3 DT 3 3 3 DT DT A . n
A 1 4 DA 4 4 4 DA DA A . n
A 1 5 U7B 5 5 5 U7B FFC A . n
A 1 6 DG 6 6 6 DG DG A . n
B 1 1 DC 1 7 7 DC DC B . n
B 1 2 DG 2 8 8 DG DG B . n
B 1 3 DT 3 9 9 DT DT B . n
B 1 4 DA 4 10 10 DA DA B . n
B 1 5 U7B 5 11 11 U7B FFC B . n
B 1 6 DG 6 12 12 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.entry_id 7NBK
_exptl.crystals_number ?
_exptl.details ?
_exptl.method 'SOLUTION NMR'
_exptl.method_details ?
#
_struct.entry_id 7NBK
_struct.title
;Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification
;
_struct.pdbx_model_details ?
_struct.pdbx_formula_weight ?
_struct.pdbx_formula_weight_method ?
_struct.pdbx_model_type_details ?
_struct.pdbx_CASP_flag N
#
_struct_keywords.entry_id 7NBK
_struct_keywords.text 'Fluorine modification, modified DNA, gemcitabine, DNA'
_struct_keywords.pdbx_keywords DNA
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 1 ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 7NBK
_struct_ref.pdbx_db_accession 7NBK
_struct_ref.pdbx_db_isoform ?
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin 1
#
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 7NBK A 1 ? 6 ? 7NBK 1 ? 6 ? 1 6
2 1 7NBK B 1 ? 6 ? 7NBK 7 ? 12 ? 7 12
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details dimeric
_pdbx_struct_assembly.oligomeric_count 2
#
loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
1 'ABSA (A^2)' 590 ?
1 MORE -2 ?
1 'SSA (A^2)' 2520 ?
#
_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_assembly_auth_evidence.id 1
_pdbx_struct_assembly_auth_evidence.assembly_id 1
_pdbx_struct_assembly_auth_evidence.experimental_support none
_pdbx_struct_assembly_auth_evidence.details ?
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation ?
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1 covale both ? A DA 4 "O3'" ? ? ? 1_555 A U7B 5 P ? ? A DA 4 A U7B 5 1_555 ? ? ? ? ? ? ? 1.624 ? ?
covale2 covale one ? A U7B 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A U7B 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.623 ? ?
covale3 covale both ? B DA 4 "O3'" ? ? ? 1_555 B U7B 5 P ? ? B DA 10 B U7B 11 1_555 ? ? ? ? ? ? ? 1.629 ? ?
covale4 covale one ? B U7B 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B U7B 11 B DG 12 1_555 ? ? ? ? ? ? ? 1.607 ? ?
hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B U7B 5 N3 ? ? A DG 2 B U7B 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B U7B 5 O2 ? ? A DG 2 B U7B 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B U7B 5 N4 ? ? A DG 2 B U7B 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog11 hydrog ? ? A U7B 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A U7B 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog12 hydrog ? ? A U7B 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A U7B 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog13 hydrog ? ? A U7B 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A U7B 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 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 DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.14 108.30 3.84 0.30 N
2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.32 108.30 4.02 0.30 N
3 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.86 108.30 2.56 0.30 N
4 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.74 122.90 -4.16 0.60 N
5 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 111.00 108.30 2.70 0.30 N
6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.92 108.30 3.62 0.30 N
7 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 113.61 108.30 5.31 0.30 N
8 1 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.97 108.30 2.67 0.30 N
9 1 C4 B DA 10 ? ? C5 B DA 10 ? ? C6 B DA 10 ? ? 113.96 117.00 -3.04 0.50 N
10 1 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.70 118.60 -3.90 0.60 N
11 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 111.88 108.30 3.58 0.30 N
12 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.24 108.30 2.94 0.30 N
13 2 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.23 108.30 3.93 0.30 N
14 2 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.37 108.30 2.07 0.30 N
15 2 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.95 122.90 -3.95 0.60 N
16 2 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.90 117.00 -3.10 0.50 N
17 2 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 111.27 108.30 2.97 0.30 N
18 2 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.01 108.30 2.71 0.30 N
19 2 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 111.58 108.30 3.28 0.30 N
20 2 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 111.23 108.30 2.93 0.30 N
21 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.54 108.30 2.24 0.30 N
22 3 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.49 108.30 3.19 0.30 N
23 3 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.46 108.30 2.16 0.30 N
24 3 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.76 117.00 -3.24 0.50 N
25 3 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 114.59 118.60 -4.01 0.60 N
26 3 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.17 108.30 2.87 0.30 N
27 3 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.01 108.30 3.71 0.30 N
28 3 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.19 108.30 1.89 0.30 N
29 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.21 108.30 2.91 0.30 N
30 4 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 113.56 108.30 5.26 0.30 N
31 4 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.29 108.30 2.99 0.30 N
32 4 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.84 117.00 -3.16 0.50 N
33 4 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 114.67 118.60 -3.93 0.60 N
34 4 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.81 108.30 2.51 0.30 N
35 4 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.70 108.30 2.40 0.30 N
36 4 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.60 108.30 4.30 0.30 N
37 4 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 111.02 108.30 2.72 0.30 N
38 4 C6 B DT 9 ? ? C5 B DT 9 ? ? C7 B DT 9 ? ? 118.16 122.90 -4.74 0.60 N
39 4 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.94 118.60 -3.66 0.60 N
40 4 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 111.87 108.30 3.57 0.30 N
41 5 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.24 108.30 1.94 0.30 N
42 5 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.38 108.30 3.08 0.30 N
43 5 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.54 108.30 2.24 0.30 N
44 5 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 112.89 108.30 4.59 0.30 N
45 5 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.58 108.30 4.28 0.30 N
46 5 C4 B DA 10 ? ? C5 B DA 10 ? ? C6 B DA 10 ? ? 113.94 117.00 -3.06 0.50 N
47 5 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.81 118.60 -3.79 0.60 N
48 5 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.29 108.30 1.99 0.30 N
49 6 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.73 108.30 2.43 0.30 N
50 6 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.46 108.30 3.16 0.30 N
51 6 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.23 108.30 1.93 0.30 N
52 6 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.87 117.00 -3.13 0.50 N
53 6 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 114.24 118.60 -4.36 0.60 N
54 6 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.41 108.30 3.11 0.30 N
55 6 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.36 108.30 4.06 0.30 N
56 6 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.47 108.30 2.17 0.30 N
57 6 C4 B DA 10 ? ? C5 B DA 10 ? ? C6 B DA 10 ? ? 113.78 117.00 -3.22 0.50 N
58 6 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.62 118.60 -3.98 0.60 N
59 7 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.59 108.30 2.29 0.30 N
60 7 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.46 108.30 4.16 0.30 N
61 7 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.11 108.30 2.81 0.30 N
62 7 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.92 117.00 -3.08 0.50 N
63 7 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.34 108.30 2.04 0.30 N
64 7 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.31 108.30 3.01 0.30 N
65 7 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.68 108.30 4.38 0.30 N
66 8 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.94 108.30 2.64 0.30 N
67 8 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.51 108.30 3.21 0.30 N
68 8 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.63 108.30 2.33 0.30 N
69 8 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.22 108.30 3.92 0.30 N
70 8 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.41 118.60 -4.19 0.60 N
71 8 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.19 108.30 1.89 0.30 N
72 9 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.14 108.30 1.84 0.30 N
73 9 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.22 108.30 2.92 0.30 N
74 9 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.32 108.30 2.02 0.30 N
75 9 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.81 108.30 2.51 0.30 N
76 9 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 111.66 108.30 3.36 0.30 N
77 10 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.56 108.30 3.26 0.30 N
78 10 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.86 122.90 -4.04 0.60 N
79 10 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.61 108.30 2.31 0.30 N
80 10 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 111.02 108.30 2.72 0.30 N
81 10 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.51 108.30 2.21 0.30 N
#
loop_
_pdbx_validate_planes.id
_pdbx_validate_planes.PDB_model_num
_pdbx_validate_planes.auth_comp_id
_pdbx_validate_planes.auth_asym_id
_pdbx_validate_planes.auth_seq_id
_pdbx_validate_planes.PDB_ins_code
_pdbx_validate_planes.label_alt_id
_pdbx_validate_planes.rmsd
_pdbx_validate_planes.type
1 1 DG A 2 ? ? 0.058 'SIDE CHAIN'
2 1 DC B 7 ? ? 0.065 'SIDE CHAIN'
3 1 DT B 9 ? ? 0.081 'SIDE CHAIN'
4 2 DC A 1 ? ? 0.076 'SIDE CHAIN'
5 2 DG A 6 ? ? 0.050 'SIDE CHAIN'
6 2 DC B 7 ? ? 0.067 'SIDE CHAIN'
7 3 DG B 8 ? ? 0.055 'SIDE CHAIN'
8 4 DG A 2 ? ? 0.056 'SIDE CHAIN'
9 4 DC B 7 ? ? 0.083 'SIDE CHAIN'
10 6 DC A 1 ? ? 0.078 'SIDE CHAIN'
11 7 DC B 7 ? ? 0.085 'SIDE CHAIN'
12 8 DC B 7 ? ? 0.106 'SIDE CHAIN'
13 9 DC A 1 ? ? 0.069 'SIDE CHAIN'
14 9 DC B 7 ? ? 0.064 'SIDE CHAIN'
15 10 DC A 1 ? ? 0.081 'SIDE CHAIN'
16 10 DC B 7 ? ? 0.103 'SIDE CHAIN'
#
_pdbx_entry_details.entry_id 7NBK
_pdbx_entry_details.has_ligand_of_interest Y
_pdbx_entry_details.compound_details ?
_pdbx_entry_details.source_details ?
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details ?
#
_pdbx_nmr_ensemble.entry_id 7NBK
_pdbx_nmr_ensemble.conformers_calculated_total_number 10
_pdbx_nmr_ensemble.conformers_submitted_total_number 10
_pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted'
_pdbx_nmr_ensemble.representative_conformer ?
_pdbx_nmr_ensemble.average_constraints_per_residue ?
_pdbx_nmr_ensemble.average_constraint_violations_per_residue ?
_pdbx_nmr_ensemble.maximum_distance_constraint_violation ?
_pdbx_nmr_ensemble.average_distance_constraint_violation ?
_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ?
_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ?
_pdbx_nmr_ensemble.distance_constraint_violation_method ?
_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ?
_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ?
_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ?
#
_pdbx_nmr_representative.entry_id 7NBK
_pdbx_nmr_representative.conformer_id 1
_pdbx_nmr_representative.selection_criteria 'fewest violations'
#
loop_
_pdbx_nmr_sample_details.solution_id
_pdbx_nmr_sample_details.contents
_pdbx_nmr_sample_details.solvent_system
_pdbx_nmr_sample_details.label
_pdbx_nmr_sample_details.type
_pdbx_nmr_sample_details.details
1
;0.5 M DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 90% H2O/10% D2O
;
'90% H2O/10% D2O' DiFs_Duplex solution ?
2
;0.5 mM DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 100% D2O
;
'100% D2O' DiFs_Duplex_D2O solution ?
#
loop_
_pdbx_nmr_exptl_sample.solution_id
_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
1
;DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')
;
0.5 ? M 'natural abundance'
1 'sodium phosphate' 25 ? mM 'natural abundance'
1 'sodium chloride' 100 ? mM 'natural abundance'
1 DSS 0.5 ? '% v/v' 'natural abundance'
2
;DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')
;
0.5 ? mM 'natural abundance'
2 'sodium phosphate' 25 ? mM 'natural abundance'
2 'sodium chloride' 100 ? mM 'natural abundance'
2 DSS 0.5 ? '% v/v' 'natural abundance'
#
loop_
_pdbx_nmr_exptl_sample_conditions.conditions_id
_pdbx_nmr_exptl_sample_conditions.temperature
_pdbx_nmr_exptl_sample_conditions.pressure_units
_pdbx_nmr_exptl_sample_conditions.pressure
_pdbx_nmr_exptl_sample_conditions.pH
_pdbx_nmr_exptl_sample_conditions.ionic_strength
_pdbx_nmr_exptl_sample_conditions.details
_pdbx_nmr_exptl_sample_conditions.ionic_strength_err
_pdbx_nmr_exptl_sample_conditions.ionic_strength_units
_pdbx_nmr_exptl_sample_conditions.label
_pdbx_nmr_exptl_sample_conditions.pH_err
_pdbx_nmr_exptl_sample_conditions.pH_units
_pdbx_nmr_exptl_sample_conditions.pressure_err
_pdbx_nmr_exptl_sample_conditions.temperature_err
_pdbx_nmr_exptl_sample_conditions.temperature_units
1 278 atm 1 7 125 ? ? mM T5 ? pH ? ? K
2 298 atm 1 7 125 ? ? mM T25 ? pH ? ? K
#
loop_
_pdbx_nmr_exptl.experiment_id
_pdbx_nmr_exptl.conditions_id
_pdbx_nmr_exptl.solution_id
_pdbx_nmr_exptl.type
_pdbx_nmr_exptl.spectrometer_id
_pdbx_nmr_exptl.sample_state
1 1 1 '2D 1H-1H NOESY' 1 isotropic
2 1 1 '2D 1H-1H TOCSY' 1 isotropic
3 2 2 '2D 1H-1H COSY' 1 isotropic
4 2 2 '2D 1H-1H NOESY' 1 isotropic
5 2 2 '2D 1H-1H TOCSY' 1 isotropic
#
_pdbx_nmr_refine.entry_id 7NBK
_pdbx_nmr_refine.method 'molecular dynamics'
_pdbx_nmr_refine.details ?
_pdbx_nmr_refine.software_ordinal 5
#
loop_
_pdbx_nmr_software.ordinal
_pdbx_nmr_software.classification
_pdbx_nmr_software.name
_pdbx_nmr_software.version
_pdbx_nmr_software.authors
1 collection TopSpin ? 'Bruker Biospin'
2 processing TopSpin ? 'Bruker Biospin'
3 'chemical shift assignment' NMRFAM-SPARKY ? 'Goddard & Kneller'
4 'structure calculation' Amber 18 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman'
5 refinement Amber 18 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman'
6 'data analysis' MOLMOL ? 'Koradi, Billeter and Wuthrich'
7 'data analysis' 3DNA ? 'Lu & Olson'
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
DA OP3 O N N 1
DA P P N N 2
DA OP1 O N N 3
DA OP2 O N N 4
DA "O5'" O N N 5
DA "C5'" C N N 6
DA "C4'" C N R 7
DA "O4'" O N N 8
DA "C3'" C N S 9
DA "O3'" O N N 10
DA "C2'" C N N 11
DA "C1'" C N R 12
DA N9 N Y N 13
DA C8 C Y N 14
DA N7 N Y N 15
DA C5 C Y N 16
DA C6 C Y N 17
DA N6 N N N 18
DA N1 N Y N 19
DA C2 C Y N 20
DA N3 N Y N 21
DA C4 C Y N 22
DA HOP3 H N N 23
DA HOP2 H N N 24
DA "H5'" H N N 25
DA "H5''" H N N 26
DA "H4'" H N N 27
DA "H3'" H N N 28
DA "HO3'" H N N 29
DA "H2'" H N N 30
DA "H2''" H N N 31
DA "H1'" H N N 32
DA H8 H N N 33
DA H61 H N N 34
DA H62 H N N 35
DA H2 H N N 36
DC OP3 O N N 37
DC P P N N 38
DC OP1 O N N 39
DC OP2 O N N 40
DC "O5'" O N N 41
DC "C5'" C N N 42
DC "C4'" C N R 43
DC "O4'" O N N 44
DC "C3'" C N S 45
DC "O3'" O N N 46
DC "C2'" C N N 47
DC "C1'" C N R 48
DC N1 N N N 49
DC C2 C N N 50
DC O2 O N N 51
DC N3 N N N 52
DC C4 C N N 53
DC N4 N N N 54
DC C5 C N N 55
DC C6 C N N 56
DC HOP3 H N N 57
DC HOP2 H N N 58
DC "H5'" H N N 59
DC "H5''" H N N 60
DC "H4'" H N N 61
DC "H3'" H N N 62
DC "HO3'" H N N 63
DC "H2'" H N N 64
DC "H2''" H N N 65
DC "H1'" H N N 66
DC H41 H N N 67
DC H42 H N N 68
DC H5 H N N 69
DC H6 H N N 70
DG OP3 O N N 71
DG P P N N 72
DG OP1 O N N 73
DG OP2 O N N 74
DG "O5'" O N N 75
DG "C5'" C N N 76
DG "C4'" C N R 77
DG "O4'" O N N 78
DG "C3'" C N S 79
DG "O3'" O N N 80
DG "C2'" C N N 81
DG "C1'" C N R 82
DG N9 N Y N 83
DG C8 C Y N 84
DG N7 N Y N 85
DG C5 C Y N 86
DG C6 C N N 87
DG O6 O N N 88
DG N1 N N N 89
DG C2 C N N 90
DG N2 N N N 91
DG N3 N N N 92
DG C4 C Y N 93
DG HOP3 H N N 94
DG HOP2 H N N 95
DG "H5'" H N N 96
DG "H5''" H N N 97
DG "H4'" H N N 98
DG "H3'" H N N 99
DG "HO3'" H N N 100
DG "H2'" H N N 101
DG "H2''" H N N 102
DG "H1'" H N N 103
DG H8 H N N 104
DG H1 H N N 105
DG H21 H N N 106
DG H22 H N N 107
DT OP3 O N N 108
DT P P N N 109
DT OP1 O N N 110
DT OP2 O N N 111
DT "O5'" O N N 112
DT "C5'" C N N 113
DT "C4'" C N R 114
DT "O4'" O N N 115
DT "C3'" C N S 116
DT "O3'" O N N 117
DT "C2'" C N N 118
DT "C1'" C N R 119
DT N1 N N N 120
DT C2 C N N 121
DT O2 O N N 122
DT N3 N N N 123
DT C4 C N N 124
DT O4 O N N 125
DT C5 C N N 126
DT C7 C N N 127
DT C6 C N N 128
DT HOP3 H N N 129
DT HOP2 H N N 130
DT "H5'" H N N 131
DT "H5''" H N N 132
DT "H4'" H N N 133
DT "H3'" H N N 134
DT "HO3'" H N N 135
DT "H2'" H N N 136
DT "H2''" H N N 137
DT "H1'" H N N 138
DT H3 H N N 139
DT H71 H N N 140
DT H72 H N N 141
DT H73 H N N 142
DT H6 H N N 143
U7B P P N N 144
U7B "C5'" C N N 145
U7B "O5'" O N N 146
U7B "C4'" C N R 147
U7B "O4'" O N N 148
U7B "C3'" C N R 149
U7B "O3'" O N N 150
U7B "C2'" C N N 151
U7B "C1'" C N R 152
U7B N1 N N N 153
U7B C2 C N N 154
U7B O2 O N N 155
U7B N3 N N N 156
U7B C4 C N N 157
U7B N4 N N N 158
U7B C5 C N N 159
U7B C6 C N N 160
U7B OP1 O N N 161
U7B OP2 O N N 162
U7B F1 F N N 163
U7B F2 F N N 164
U7B "H5''" H N N 165
U7B "H5'" H N N 166
U7B "H4'" H N N 167
U7B "H3'" H N N 168
U7B H1 H N N 169
U7B "H1'" H N N 170
U7B H42 H N N 171
U7B H41 H N N 172
U7B H5 H N N 173
U7B H6 H N N 174
U7B H3 H N N 175
U7B OP3 O N N 176
U7B H2 H N N 177
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
DA OP3 P sing N N 1
DA OP3 HOP3 sing N N 2
DA P OP1 doub N N 3
DA P OP2 sing N N 4
DA P "O5'" sing N N 5
DA OP2 HOP2 sing N N 6
DA "O5'" "C5'" sing N N 7
DA "C5'" "C4'" sing N N 8
DA "C5'" "H5'" sing N N 9
DA "C5'" "H5''" sing N N 10
DA "C4'" "O4'" sing N N 11
DA "C4'" "C3'" sing N N 12
DA "C4'" "H4'" sing N N 13
DA "O4'" "C1'" sing N N 14
DA "C3'" "O3'" sing N N 15
DA "C3'" "C2'" sing N N 16
DA "C3'" "H3'" sing N N 17
DA "O3'" "HO3'" sing N N 18
DA "C2'" "C1'" sing N N 19
DA "C2'" "H2'" sing N N 20
DA "C2'" "H2''" sing N N 21
DA "C1'" N9 sing N N 22
DA "C1'" "H1'" sing N N 23
DA N9 C8 sing Y N 24
DA N9 C4 sing Y N 25
DA C8 N7 doub Y N 26
DA C8 H8 sing N N 27
DA N7 C5 sing Y N 28
DA C5 C6 sing Y N 29
DA C5 C4 doub Y N 30
DA C6 N6 sing N N 31
DA C6 N1 doub Y N 32
DA N6 H61 sing N N 33
DA N6 H62 sing N N 34
DA N1 C2 sing Y N 35
DA C2 N3 doub Y N 36
DA C2 H2 sing N N 37
DA N3 C4 sing Y N 38
DC OP3 P sing N N 39
DC OP3 HOP3 sing N N 40
DC P OP1 doub N N 41
DC P OP2 sing N N 42
DC P "O5'" sing N N 43
DC OP2 HOP2 sing N N 44
DC "O5'" "C5'" sing N N 45
DC "C5'" "C4'" sing N N 46
DC "C5'" "H5'" sing N N 47
DC "C5'" "H5''" sing N N 48
DC "C4'" "O4'" sing N N 49
DC "C4'" "C3'" sing N N 50
DC "C4'" "H4'" sing N N 51
DC "O4'" "C1'" sing N N 52
DC "C3'" "O3'" sing N N 53
DC "C3'" "C2'" sing N N 54
DC "C3'" "H3'" sing N N 55
DC "O3'" "HO3'" sing N N 56
DC "C2'" "C1'" sing N N 57
DC "C2'" "H2'" sing N N 58
DC "C2'" "H2''" sing N N 59
DC "C1'" N1 sing N N 60
DC "C1'" "H1'" sing N N 61
DC N1 C2 sing N N 62
DC N1 C6 sing N N 63
DC C2 O2 doub N N 64
DC C2 N3 sing N N 65
DC N3 C4 doub N N 66
DC C4 N4 sing N N 67
DC C4 C5 sing N N 68
DC N4 H41 sing N N 69
DC N4 H42 sing N N 70
DC C5 C6 doub N N 71
DC C5 H5 sing N N 72
DC C6 H6 sing N N 73
DG OP3 P sing N N 74
DG OP3 HOP3 sing N N 75
DG P OP1 doub N N 76
DG P OP2 sing N N 77
DG P "O5'" sing N N 78
DG OP2 HOP2 sing N N 79
DG "O5'" "C5'" sing N N 80
DG "C5'" "C4'" sing N N 81
DG "C5'" "H5'" sing N N 82
DG "C5'" "H5''" sing N N 83
DG "C4'" "O4'" sing N N 84
DG "C4'" "C3'" sing N N 85
DG "C4'" "H4'" sing N N 86
DG "O4'" "C1'" sing N N 87
DG "C3'" "O3'" sing N N 88
DG "C3'" "C2'" sing N N 89
DG "C3'" "H3'" sing N N 90
DG "O3'" "HO3'" sing N N 91
DG "C2'" "C1'" sing N N 92
DG "C2'" "H2'" sing N N 93
DG "C2'" "H2''" sing N N 94
DG "C1'" N9 sing N N 95
DG "C1'" "H1'" sing N N 96
DG N9 C8 sing Y N 97
DG N9 C4 sing Y N 98
DG C8 N7 doub Y N 99
DG C8 H8 sing N N 100
DG N7 C5 sing Y N 101
DG C5 C6 sing N N 102
DG C5 C4 doub Y N 103
DG C6 O6 doub N N 104
DG C6 N1 sing N N 105
DG N1 C2 sing N N 106
DG N1 H1 sing N N 107
DG C2 N2 sing N N 108
DG C2 N3 doub N N 109
DG N2 H21 sing N N 110
DG N2 H22 sing N N 111
DG N3 C4 sing N N 112
DT OP3 P sing N N 113
DT OP3 HOP3 sing N N 114
DT P OP1 doub N N 115
DT P OP2 sing N N 116
DT P "O5'" sing N N 117
DT OP2 HOP2 sing N N 118
DT "O5'" "C5'" sing N N 119
DT "C5'" "C4'" sing N N 120
DT "C5'" "H5'" sing N N 121
DT "C5'" "H5''" sing N N 122
DT "C4'" "O4'" sing N N 123
DT "C4'" "C3'" sing N N 124
DT "C4'" "H4'" sing N N 125
DT "O4'" "C1'" sing N N 126
DT "C3'" "O3'" sing N N 127
DT "C3'" "C2'" sing N N 128
DT "C3'" "H3'" sing N N 129
DT "O3'" "HO3'" sing N N 130
DT "C2'" "C1'" sing N N 131
DT "C2'" "H2'" sing N N 132
DT "C2'" "H2''" sing N N 133
DT "C1'" N1 sing N N 134
DT "C1'" "H1'" sing N N 135
DT N1 C2 sing N N 136
DT N1 C6 sing N N 137
DT C2 O2 doub N N 138
DT C2 N3 sing N N 139
DT N3 C4 sing N N 140
DT N3 H3 sing N N 141
DT C4 O4 doub N N 142
DT C4 C5 sing N N 143
DT C5 C7 sing N N 144
DT C5 C6 doub N N 145
DT C7 H71 sing N N 146
DT C7 H72 sing N N 147
DT C7 H73 sing N N 148
DT C6 H6 sing N N 149
U7B OP1 P doub N N 150
U7B P "O5'" sing N N 151
U7B P OP2 sing N N 152
U7B "C5'" "C4'" sing N N 153
U7B "C5'" "O5'" sing N N 154
U7B "O4'" "C4'" sing N N 155
U7B "O4'" "C1'" sing N N 156
U7B "C4'" "C3'" sing N N 157
U7B "C1'" N1 sing N N 158
U7B "C1'" "C2'" sing N N 159
U7B N1 C6 sing N N 160
U7B N1 C2 sing N N 161
U7B O2 C2 doub N N 162
U7B C6 C5 doub N N 163
U7B C2 N3 sing N N 164
U7B C5 C4 sing N N 165
U7B N3 C4 doub N N 166
U7B "C3'" "O3'" sing N N 167
U7B "C3'" "C2'" sing N N 168
U7B C4 N4 sing N N 169
U7B "C2'" F1 sing N N 170
U7B "C2'" F2 sing N N 171
U7B "C5'" "H5''" sing N N 172
U7B "C5'" "H5'" sing N N 173
U7B "C4'" "H4'" sing N N 174
U7B "C3'" "H3'" sing N N 175
U7B "O3'" H1 sing N N 176
U7B "C1'" "H1'" sing N N 177
U7B N4 H42 sing N N 178
U7B N4 H41 sing N N 179
U7B C5 H5 sing N N 180
U7B C6 H6 sing N N 181
U7B OP2 H3 sing N N 182
U7B P OP3 sing N N 183
U7B OP3 H2 sing N N 184
#
_ndb_struct_conf_na.entry_id 7NBK
_ndb_struct_conf_na.feature 'double helix'
#
loop_
_ndb_struct_na_base_pair.model_number
_ndb_struct_na_base_pair.i_label_asym_id
_ndb_struct_na_base_pair.i_label_comp_id
_ndb_struct_na_base_pair.i_label_seq_id
_ndb_struct_na_base_pair.i_symmetry
_ndb_struct_na_base_pair.j_label_asym_id
_ndb_struct_na_base_pair.j_label_comp_id
_ndb_struct_na_base_pair.j_label_seq_id
_ndb_struct_na_base_pair.j_symmetry
_ndb_struct_na_base_pair.shear
_ndb_struct_na_base_pair.stretch
_ndb_struct_na_base_pair.stagger
_ndb_struct_na_base_pair.buckle
_ndb_struct_na_base_pair.propeller
_ndb_struct_na_base_pair.opening
_ndb_struct_na_base_pair.pair_number
_ndb_struct_na_base_pair.pair_name
_ndb_struct_na_base_pair.i_auth_asym_id
_ndb_struct_na_base_pair.i_auth_seq_id
_ndb_struct_na_base_pair.i_PDB_ins_code
_ndb_struct_na_base_pair.j_auth_asym_id
_ndb_struct_na_base_pair.j_auth_seq_id
_ndb_struct_na_base_pair.j_PDB_ins_code
_ndb_struct_na_base_pair.hbond_type_28
_ndb_struct_na_base_pair.hbond_type_12
1 A DC 1 1_555 B DG 6 1_555 0.391 -0.261 0.238 -7.353 -5.922 -0.877 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1
1 A DG 2 1_555 B U7B 5 1_555 -0.310 -0.242 0.494 14.249 1.123 -0.073 2 A_DG2:U7B11_B A 2 ? B 11 ? 19 1
1 A DT 3 1_555 B DA 4 1_555 -0.056 -0.108 -0.015 18.674 1.271 2.697 3 A_DT3:DA10_B A 3 ? B 10 ? 20 1
1 A DA 4 1_555 B DT 3 1_555 0.071 -0.165 -0.264 3.685 -5.720 -0.279 4 A_DA4:DT9_B A 4 ? B 9 ? 20 1
1 A U7B 5 1_555 B DG 2 1_555 0.375 -0.261 -0.087 -6.927 -1.915 -0.404 5 A_U7B5:DG8_B A 5 ? B 8 ? 19 1
1 A DG 6 1_555 B DC 1 1_555 -0.334 -0.254 0.020 6.401 -8.494 -1.172 6 A_DG6:DC7_B A 6 ? B 7 ? 19 1
#
loop_
_ndb_struct_na_base_pair_step.model_number
_ndb_struct_na_base_pair_step.i_label_asym_id_1
_ndb_struct_na_base_pair_step.i_label_comp_id_1
_ndb_struct_na_base_pair_step.i_label_seq_id_1
_ndb_struct_na_base_pair_step.i_symmetry_1
_ndb_struct_na_base_pair_step.j_label_asym_id_1
_ndb_struct_na_base_pair_step.j_label_comp_id_1
_ndb_struct_na_base_pair_step.j_label_seq_id_1
_ndb_struct_na_base_pair_step.j_symmetry_1
_ndb_struct_na_base_pair_step.i_label_asym_id_2
_ndb_struct_na_base_pair_step.i_label_comp_id_2
_ndb_struct_na_base_pair_step.i_label_seq_id_2
_ndb_struct_na_base_pair_step.i_symmetry_2
_ndb_struct_na_base_pair_step.j_label_asym_id_2
_ndb_struct_na_base_pair_step.j_label_comp_id_2
_ndb_struct_na_base_pair_step.j_label_seq_id_2
_ndb_struct_na_base_pair_step.j_symmetry_2
_ndb_struct_na_base_pair_step.shift
_ndb_struct_na_base_pair_step.slide
_ndb_struct_na_base_pair_step.rise
_ndb_struct_na_base_pair_step.tilt
_ndb_struct_na_base_pair_step.roll
_ndb_struct_na_base_pair_step.twist
_ndb_struct_na_base_pair_step.x_displacement
_ndb_struct_na_base_pair_step.y_displacement
_ndb_struct_na_base_pair_step.helical_rise
_ndb_struct_na_base_pair_step.inclination
_ndb_struct_na_base_pair_step.tip
_ndb_struct_na_base_pair_step.helical_twist
_ndb_struct_na_base_pair_step.step_number
_ndb_struct_na_base_pair_step.step_name
_ndb_struct_na_base_pair_step.i_auth_asym_id_1
_ndb_struct_na_base_pair_step.i_auth_seq_id_1
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1
_ndb_struct_na_base_pair_step.j_auth_asym_id_1
_ndb_struct_na_base_pair_step.j_auth_seq_id_1
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1
_ndb_struct_na_base_pair_step.i_auth_asym_id_2
_ndb_struct_na_base_pair_step.i_auth_seq_id_2
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2
_ndb_struct_na_base_pair_step.j_auth_asym_id_2
_ndb_struct_na_base_pair_step.j_auth_seq_id_2
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2
1 A DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B U7B 5 1_555 1.094 0.716 3.295 -3.340 14.249 26.544 -1.650 -2.805 3.112 28.450
6.669 30.248 1 AA_DC1DG2:U7B11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ?
1 A DG 2 1_555 B U7B 5 1_555 A DT 3 1_555 B DA 4 1_555 -0.384 -1.132 3.342 2.023 1.335 27.056 -2.749 1.332 3.247 2.847
-4.313 27.162 2 AA_DG2DT3:DA10U7B11_BB A 2 ? B 11 ? A 3 ? B 10 ?
1 A DT 3 1_555 B DA 4 1_555 A DA 4 1_555 B DT 3 1_555 -0.433 -0.720 3.495 -0.017 9.026 43.108 -1.854 0.576 3.287 12.126
0.022 43.999 3 AA_DT3DA4:DT9DA10_BB A 3 ? B 10 ? A 4 ? B 9 ?
1 A DA 4 1_555 B DT 3 1_555 A U7B 5 1_555 B DG 2 1_555 0.490 -1.687 3.742 -0.962 -3.218 30.108 -2.470 -1.165 3.880 -6.171
1.846 30.290 4 AA_DA4U7B5:DG8DT9_BB A 4 ? B 9 ? A 5 ? B 8 ?
1 A U7B 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -1.003 -0.219 3.262 1.766 11.043 30.384 -2.308 2.107 2.944 20.229
-3.234 32.331 5 AA_U7B5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ?
#
loop_
_pdbx_audit_support.funding_organization
_pdbx_audit_support.country
_pdbx_audit_support.grant_number
_pdbx_audit_support.ordinal
'Spanish Ministry of Science, Innovation, and Universities' Spain BFU2017-89707-P 1
'Spanish Ministry of Science, Innovation, and Universities' Spain PRE2018-083173 2
#
_pdbx_entity_instance_feature.ordinal 1
_pdbx_entity_instance_feature.comp_id U7B
_pdbx_entity_instance_feature.asym_id ?
_pdbx_entity_instance_feature.seq_num ?
_pdbx_entity_instance_feature.auth_comp_id U7B
_pdbx_entity_instance_feature.auth_asym_id ?
_pdbx_entity_instance_feature.auth_seq_num ?
_pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION'
_pdbx_entity_instance_feature.details ?
#
_pdbx_nmr_spectrometer.spectrometer_id 1
_pdbx_nmr_spectrometer.model AVANCE
_pdbx_nmr_spectrometer.type ?
_pdbx_nmr_spectrometer.manufacturer Bruker
_pdbx_nmr_spectrometer.field_strength 600
_pdbx_nmr_spectrometer.details ?
#
_atom_sites.entry_id 7NBK
_atom_sites.Cartn_transf_matrix[1][1] ?
_atom_sites.Cartn_transf_matrix[1][2] ?
_atom_sites.Cartn_transf_matrix[1][3] ?
_atom_sites.Cartn_transf_matrix[2][1] ?
_atom_sites.Cartn_transf_matrix[2][2] ?
_atom_sites.Cartn_transf_matrix[2][3] ?
_atom_sites.Cartn_transf_matrix[3][1] ?
_atom_sites.Cartn_transf_matrix[3][2] ?
_atom_sites.Cartn_transf_matrix[3][3] ?
_atom_sites.Cartn_transf_vector[1] ?
_atom_sites.Cartn_transf_vector[2] ?
_atom_sites.Cartn_transf_vector[3] ?
_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
_atom_sites.solution_primary ?
_atom_sites.solution_secondary ?
_atom_sites.solution_hydrogens ?
_atom_sites.special_details ?
#
loop_
_atom_type.symbol
C
F
H
N
O
P
#
loop_