1ixj
From Proteopedia
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Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs
Overview
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin, structure in solution, has been crystallized in the space group I4(1)22, with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the, crystal structure has been determined at 2.5 A resolution. The four, nucleotide residues CGAA of the first half of the oligomer form a parallel, duplex with another half through the homo base pairs, C2:C2+, (singly-protonated between the Watson- Crick sites), G3:G3 (between the, minor groove sites), A4:A4 (between the major groove sites) and A5:A5, (between the Watson-Crick sites). The two strands remaining in the half of, the parallel duplex are split away in different directions, and they pair, in an anti-parallel B-form duplex with the second half extending from a, neighboring parallel duplex, so that an infinite column is formed in a, head-to-tail fashion along the c-axis. It seems that a hexa-ammine cobalt, cation supports such a branched and bent conformation of the oligomer. One, end of the parallel duplex is stacked on the corresponding end of the, adjacent parallel duplex; between them, the guanine base of the first, residue is stacked on the fourth ribose of another duplex.
About this Structure
1IXJ is a Protein complex structure of sequences from [1] with MG and NCO as ligands. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs., Sunami T, Kondo J, Kobuna T, Hirao I, Watanabe K, Miura K, Takenaka A, Nucleic Acids Res. 2002 Dec 1;30(23):5253-60. PMID:12466550
Page seeded by OCA on Sat Nov 24 22:43:36 2007
