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- PDB-1c0y: SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED OPPOSITE D... -

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Basic information

Entry
Database: PDB / ID: 1c0y
TitleSOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED OPPOSITE DA AT A TEMPLATE-PRIMER JUNCTION
Components
  • DNA (5'-D(*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*TP*GP*GP*TP*AP*GP*C)-3')
KeywordsDNA / DNA DUPLEX / AMINOFLUORENE ADDUCT / CARCINOGEN ADDUCT / TEMPLATE-PRIMER JUNCTION
Function / homology2-AMINOFLUORENE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RELAXATION MATRIX REFINEMENT
AuthorsGu, Z. / Gorin, A. / Hingerty, B.E. / Broyde, S. / Patel, D.J.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structures of aminofluorene [AF]-stacked conformers of the syn [AF]-C8-dG adduct positioned opposite dC or dA at a template-primer junction.
Authors: Gu, Z. / Gorin, A. / Hingerty, B.E. / Broyde, S. / Patel, D.J.
History
DepositionJul 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*TP*GP*GP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1873
Polymers7,0062
Non-polymers1811
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 6ALL CONFORMERS PRESENTED
Representative

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Components

#1: DNA chain DNA (5'-D(*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*C)-3')


Mass: 3880.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N ATOM OF AF-GROUP LINKED TO C8 ATOM OF G 4
#2: DNA chain DNA (5'-D(*GP*GP*AP*TP*GP*GP*TP*AP*GP*C)-3')


Mass: 3125.052 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-AF / 2-AMINOFLUORENE / 2-Aminofluorene


Mass: 181.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11N

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
NMR detailsText: IONIC STRENGTH: 100MM NACL, 10MM PHOSPHATE PRESSURE: 1 ATM

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Sample preparation

DetailsContents: H2O, D2O
Sample conditionsIonic strength: 100 mM NACL, 10mM PHOSPHATE / pH: 7.0 / Pressure: 1 atm / Temperature: 322 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
DUPLEXstructure solution
X-PLORstructure solution
RefinementMethod: RELAXATION MATRIX REFINEMENT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: ALL CONFORMERS PRESENTED / Conformers calculated total number: 6 / Conformers submitted total number: 6

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