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- PDB-2n0q: N2-dG-IQ modified DNA at the G1 position of the NarI recognition ... -

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Basic information

Entry
Database: PDB / ID: 2n0q
TitleN2-dG-IQ modified DNA at the G1 position of the NarI recognition sequence
Components
  • DNA_(5'-D(*CP*TP*CP*(IQG)P*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 / base-displaced intercated
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsStavros, K. / Hawkins, E. / Rizzo, C. / Stone, M.
CitationJournal: Chem.Res.Toxicol. / Year: 2015
Title: Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site.
Authors: Stavros, K.M. / Hawkins, E.K. / Rizzo, C.J. / Stone, M.P.
History
DepositionMar 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: 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 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA_(5'-D(*CP*TP*CP*(IQG)P*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
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA_(5'-D(*CP*TP*CP*(IQG)P*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

DetailsContents: 430 uM IQ, 430 mM DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3'), 430 mM DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
430 uMIQ-11
430 mMDNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3')-21
430 mMDNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')-31
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
MARDIGRASCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanchemical shift calculation
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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