431d
From Proteopedia
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5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'
Overview
Despite the importance of hydration around DNA in the understanding of its, conformation and interactions with other molecules in many biological, processes, only limited atomic resolution information is available., Crystal-engineering techniques, which were originally developed to mimic, DNA base triplets in a crystal lattice, also eliminate the rotational, disorder of oligonucleotides around their helical axis and thereby enhance, the resolution of the structure analysis. We have determined the, low-temperature crystal structure of the synthetic DNA decamer, d(GGCCAATTGG) at atomic resolution (1. 15 A) using 17700 reflections and, have characterized the highly organized hydration patterns in both, grooves. The narrow d(AATT) minor groove is occupied by an 'extended, hydration spine' alternately bridging base pairs and phosphate O1P atoms, of opposite strands, while a distinctive pattern of parallel water ribbons, is observed in the major groove. This analysis provides structural insight, into the correlation found between narrow minor-groove width and, occurrence of the B(I) conformation and can be used to design new, minor-groove binders. By their location between adjacent helices, two, fully hydrated magnesium ions further stabilize the crystal packing. The, structure also provides details of the hydration and conformation of G.GC, triple helices.
About this Structure
431D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
B-DNA at atomic resolution reveals extended hydration patterns., Vlieghe D, Turkenburg JP, Van Meervelt L, Acta Crystallogr D Biol Crystallogr. 1999 Sep;55(Pt 9):1495-502. PMID:10489444
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