1D75

CONFORMATION OF THE GUANINE.8-OXOADENINE BASE PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(O8A)GCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformation of guanine-8-oxoadenine base pairs in the crystal structure of d(CGCGAATT(O8A)GCG).

Leonard, G.A.Guy, A.Brown, T.Teoule, R.Hunter, W.N.

(1992) Biochemistry 31: 8415-8420


  • PubMed Abstract: 
  • The structure of the synthetic deoxydodecamer d(CGCGAATT(O8A)GCG)2 (O8A = 8-oxoadenine) has been determined by single-crystal X-ray diffraction techniques. The oligonucleotide crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimen ...

    The structure of the synthetic deoxydodecamer d(CGCGAATT(O8A)GCG)2 (O8A = 8-oxoadenine) has been determined by single-crystal X-ray diffraction techniques. The oligonucleotide crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 25.48 A, b = 41.84 A, and c = 64.91 A. The refinement has converged with an R-factor of 0.151 for 1119 reflections in the resolution range 8.0-2.25 A. Sixty-seven solvent molecules were located during the course of the refinement. The B-DNA helix consists of ten Watson-Crick base pairs and two guanine-8-oxoadenine (G.O8A) base pairs. In order to achieve hydrogen-bonding complementarity between the two bases, an unusual G(anti).O8A-(syn) wobble conformation is adopted. It is proposed that the G.O8A mispairs are held together by a network of four interbase hydrogen bonds which are the result of the formation of two reverse three-center hydrogen-bonding systems. These involve one carbonyl oxygen lone pair interacting with two hydrogen atoms. In a departure from previous observations of the characteristics of purine-purine anti-syn base pairs, lambda 1 and lambda 2, the angles between the glycosidic bonds and the C1'-C1' vector, are symmetric. A reassessment of the other purine-purine mispairs suggests that similar three-center hydrogen bonds may occur and make a contribution to stabilizing other base pairings.


    Organizational Affiliation

    Department of Chemistry, University of Manchester, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(A38)P*GP*CP*G)-3')A,B12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A38
Query on A38
A, B
DNA LINKINGC10 H14 N5 O7 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.480α = 90.00
b = 41.840β = 90.00
c = 64.910γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-01-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance