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- PDB-2n4m: Base-displaced intercalated structure of the N-(2'deoxyguanosin-8... -

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Basic information

Entry
Database: PDB / ID: 2n4m
TitleBase-displaced intercalated structure of the N-(2'deoxyguanosin-8-yl)-3-aminobenzanthrone DNA adduct
Components
  • DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3')
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model1
AuthorsPolitica, D.A. / Stone, M.P. / Malik, C.K. / Basu, A.K.
CitationJournal: Chem.Res.Toxicol. / Year: 2015
Title: Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct.
Authors: Politica, D.A. / Malik, C.K. / Basu, A.K. / Stone, M.P.
History
DepositionJun 23, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: 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(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3')
B: DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,5682
Polymers7,5682
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 / 85structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3')


Mass: 3958.670 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')


Mass: 3609.398 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY
2322D 1H-1H NOESY
2422D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1352 uM DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 352 uM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA, 100% D2O100% D2O
2521 uM DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 521 uM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
352 uMDNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3')-11
352 uMDNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')-21
10 mMsodium phosphate-31
100 mMsodium chloride-41
50 uMEDTA-51
521 uMDNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3')-62
521 uMDNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')-72
10 mMsodium phosphate-82
100 mMsodium chloride-92
50 uMEDTA-102
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11107ambient 298 K
21107ambient 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
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
MARDIGRASBorgias, B. A. & James, T. L.restraint calculation
CORMABorgias, B. A. & James, T. L.validation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 18 / NA beta-angle constraints total count: 18 / NA delta-angle constraints total count: 18 / NA epsilon-angle constraints total count: 18 / NA gamma-angle constraints total count: 18 / NA sugar pucker constraints total count: 75 / NOE constraints total: 330 / NOE intraresidue total count: 171 / NOE sequential total count: 125
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 85 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.083 Å / Maximum torsion angle constraint violation: 8.553 ° / Maximum upper distance constraint violation: 0.104 Å
NMR ensemble rmsDistance rms dev: 0.0125 Å

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