2KE8

NMR solution structure of metal-modified DNA

> Summary

Summary for 2KE8

Related2K67 2K68 2K69
Descriptor5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3'
Functional Keywordsdna, artificial nucleobase, imidazole nucleoside, ag+
Total number of polymer chains2
Total molecular weight10354.31
Authors
Johannsen, S.,Duepre, N.,Boehme, D.,Mueller, J.,Sigel, R.K.O. (deposition date: 2009-01-27, release date: 2010-02-09, modification date: 2011-01-05)
Primary citation
Johannsen, S.,Megger, N.,Bohme, D.,Sigel, R.K.,Muller, J.
Solution structure of a DNA double helix with consecutive metal-mediated base pairs.
Nat.Chem., 2:229-234, 2010
PubMed: 21124482
DOI: 10.1038/nchem.512
MImport into Mendeley
Experimental method
SOLUTION NMR
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Structure validation

Clashscore6MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all NMR structures

More Asymmetric unit images

Molmil generated image of 2ke8
no rotation
Molmil generated image of 2ke8
rotated about x axis by 90°
Molmil generated image of 2ke8
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BDNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3')polymer175015.42
SILVER IONnon-polymer107.93

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight10030.7
Non-Polymers*Number of molecules3
Total molecular weight323.6
All*Total molecular weight10354.3
*Water molecules are not included.

> Experimental details

Spectrometer

Experimental method:SOLUTION NMR

Spectrometer IDSpectrometer makerSpectrometer modelSpectrometer typeSpectrometer field strength
1BrukerAvanceBruker Avance700
2BrukerAV-2Bruker AV-2400

Experiment

experiment idconditions idsolution idExperiment type
1112D 1H-1H NOESY
2112D 1H-1H TOCSY
3112D 1H-13C HSQC
4112D 1H-15N HSQC
5111D 31P
6222D 1H-1H NOESY

NMR Sample

conditions idNMR sample pHNMR sample pressureNMR sample temperature
17.2ambient298
27.2ambient278

Conformers

Conformers Calculated Total Number200
Conformers Submitted Total Number20

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC12BINDING SITE FOR RESIDUE AG A 35
ChainResidue
AD338
BD3310

AC22BINDING SITE FOR RESIDUE AG A 36
ChainResidue
AD339
BD339

AC32BINDING SITE FOR RESIDUE AG A 37
ChainResidue
AD3310
BD338

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
AG_2ke8_A_356SILVER ION binding site
ChainResidueligand
ADT7-D339AG: SILVER ION
BD3326-DA28AG: SILVER ION

AG_2ke8_A_366SILVER ION binding site
ChainResidueligand
AD338-D3310AG: SILVER ION
BD3325-D3327AG: SILVER ION

AG_2ke8_A_376SILVER ION binding site
ChainResidueligand
AD339-DA11AG: SILVER ION
BDT24-D3326AG: SILVER ION

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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