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- PDB-2mav: NMR Structure of N2-IQ-dG at the G3 position in the NarI recognit... -

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Basic information

Entry
Database: PDB / ID: 2mav
TitleNMR Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence
Components
  • DNA_(5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3')
  • DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')
KeywordsDNA / heterocyclic amine / N2-IQ / DNA adducts / NarI / oligodeoxyribonucleotides / quinolines
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsStavros, K.M. / Hawkins, E.K. / Rizzo, C.J. / Stone, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence.
Authors: Stavros, K.M. / Hawkins, E.K. / Rizzo, C.J. / Stone, M.P.
History
DepositionJul 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA_(5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3')
B: DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,5242
Polymers7,5242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-14 kcal/mol
Surface area4970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3795.551 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')


Mass: 3728.429 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.560 uM DNA (5'-D(*CP*TP*CP*GP*GP*CP*IQGP*CP*CP*AP*TP*C)-3'), 0.560 uM DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), 0.560 uM N2-2-amino-3-methylimidazo[4,5-f]quinoline-deoxyguanosine, 100% D2O100% D2O
2560 mM DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'), 560 mM DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'), 560 mM N2-2-amino-3-methylimidazo[4,5-f]quinoline-deoxyguanosine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.560 uMDNA (5'-D(*CP*TP*CP*GP*GP*CP*IQGP*CP*CP*AP*TP*C)-3')-11
0.560 uMDNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')-21
0.560 uMN2-2-amino-3-methylimidazo[4,5-f]quinoline-deoxyguanosine-31
560 mMDNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3')-42
560 mMDNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3')-52
560 mMN2-2-amino-3-methylimidazo[4,5-f]quinoline-deoxyguanosine-62
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
TopSpin3.2Bruker Biospincollection
Sparky3.115Goddardchemical shift assignment
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CORMACase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
MARDIGRASCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 10

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