1vj4
From Proteopedia
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SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)
Overview
The crystal structures of the synthetic self-complementary octamer, d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been, refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical, conformation, which is minimally affected by crystal forces. A detailed, analysis of the structure shows a considerable influence of the nucleotide, sequence on the base-pair stacking patterns. In particular, the, electrostatic stacking interactions between adjacent guanine and thymine, bases produce symmetric bending of the double helix and a major-groove, widening. The sugar-phosphate backbone appears to be only slightly, affected by the base sequence. The local variations in the base-pair, orientation are brought about by correlated adjustments in the backbone, torsion angles and the glycosidic orientation. Sequence-dependent, conformational variations of the type observed here may contribute to the, specificity of certain protein-DNA interactions.
About this Structure
1VJ4 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:6854642
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