178D

CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 8-HYDROXYDEOXYGUANINE.ADENINE BASE-PAIRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs.

McAuley-Hecht, K.E.Leonard, G.A.Gibson, N.J.Thomson, J.B.Watson, W.P.Hunter, W.N.Brown, T.

(1994) Biochemistry 33: 10266-10270


  • PubMed Abstract: 
  • The crystal structure of the oligonucleotide d(CGCAAATTO8GGCG), containing the chemically modified base 8-hydroxydeoxyguanine (O8G), has been determined at 2.5-A resolution and refined to a crystallographic R-factor of 16.8%. The B-type DNA helix con ...

    The crystal structure of the oligonucleotide d(CGCAAATTO8GGCG), containing the chemically modified base 8-hydroxydeoxyguanine (O8G), has been determined at 2.5-A resolution and refined to a crystallographic R-factor of 16.8%. The B-type DNA helix contains standard Watson-Crick base pairs except at the mismatch sites, where O8G adopts a syn conformation and forms hydrogen bonds to adenine in the anti conformation. The thermodynamic stability of the duplex was found by UV melting techniques to be intermediate between the native oligonucleotide d(CGCAAATTTGCG) and an oligonucleotide containing A.G mispairs d(CGCAAATTGGCG). Comparison of the structure of the O8G(syn).A(anti) base pair with those of Watson-Crick base pairs has given a reason why O8G.A base pairs are not well repaired by DNA proofreading enzymes.


    Organizational Affiliation

    Edinburgh Centre for Molecular Recognition, Department of Chemistry, University of Edinburgh, U.K.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*(8OG)P*GP*CP*G)-3')A,B12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
A, B
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.670α = 90.00
b = 40.490β = 90.00
c = 65.140γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-10-04
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance