178D | pdb_0000178d

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

• PDB DOI: https://doi.org/10.2210/pdb178D/pdb
• NAKB: 178D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-05-19 Released: 1994-10-04 
• Deposition Author(s): McAuley-Hecht, K.E., Leonard, G.A., Gibson, N.J., Thomson, J.B., Watson, W.P., Hunter, W.N., Brown, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.169 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

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: 8068665 
• DOI: https://doi.org/10.1021/bi00200a006
• Primary Citation Related Structures: 
  178D


• 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 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.

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Organizational Affiliation: 
• Edinburgh Centre for Molecular Recognition, Department of Chemistry, University of Edinburgh, U.K.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.41 kDa 
• Atom Count: 564 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*(8OG)P*GP*CP*G)-3')	A, B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.169 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.67	α = 90
b = 40.49	β = 90
c = 65.14	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-10-04 
Deposition Author(s): McAuley-Hecht, K.E., Leonard, G.A., Gibson, N.J., Thomson, J.B., Watson, W.P., Hunter, W.N., Brown, T.

Revision History  

• Version 1.0: 1994-10-04
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations