153D image
Deposition Date 1993-12-16
Release Date 1994-01-15
Last Version Date 2024-02-07
Entry Detail
PDB ID:
153D
Keywords:
DNA
Title:
CRYSTAL STRUCTURE OF A MISPAIRED DODECAMER, D(CGAGAATTC(O6ME)GCG)2, CONTAINING A CARCINOGENIC O6-METHYLGUANINE
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.90 Å
R-Value Observed:
0.16
Space Group:
P 21 21 21
153D validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
6OG A DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
Primary Citation
Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine
Biochemistry 33 3487 3493 (1994)
PMID: 8142345 DOI: 10.1021/bi00178a004

Abstact

The crystal structure of the synthetic deoxydodecamer d(CGAGAATTC(O6Me)GCG)2 has been determined and refined to an R-factor of 16.9% with data up to 2.9-A resolution. This sequence contains two mismatched base pairs between O6-methylguanine and adenine with the arrangement A(syn).(O6-Me)G(anti) which differs from the geometry observed in solution by NMR. The intermolecular arrangement is equivalent to the other isomorphous deoxydodecamers. However, the weakening of some significant crystal packing contacts was observed and related to the effect of stacking between the mispaired adenine and the adjacent guanine in the sequence. The structure is highly hydrated, with a total of 49 solvent molecules located. The methyl group and the mismatched base-pair geometry locally disrupt the B-DNA-type solvent network with two solvent molecules found close to the N1 and N6 of the mispaired adenine.

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Primary Citation of related structures
153D
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