355d

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spinqualitylabelsall models 355d, resolution 1.400Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

THE B-DNA DODECAMER AT HIGH RESOLUTION

Overview

We describe a very accurate addition (called structure X here) to the, B-DNA dodecamer family of X-ray structures. Our results confirm the, observation of Drew and Dickerson [(1981) J. Mol. Biol. 151, 535-556] that, the spine of hydration in AT tract DNA is two layers deep. However, our, results suggest that the primary spine is partially occupied by sodium, ions. We suggest that many sequence-dependent features of DNA conformation, are mediated by site specific binding of cations. For example, preferential localization of cations, as described here within the minor, groove of structure X, is probably the structural origin of AT tract, bending and groove narrowing. The secondary spine, which does not interact, directly with the DNA, is as geometrically regular as the primary spine, providing a model for transmission of sequence information into solvent, regions. A fully hydrated magnesium ion located in the major groove of, structure X appears to pull cytosine bases partially out from the helical, stack, exposing pi-systems to partial positive charges of the magnesium, ion and its outer sphere. A partially ordered spermine molecule is located, within the major groove of structure X. Dodecamer structures are derived, from crystals of [d(CGCGAATTCGCG)]2 in space group P212121 (a = 25 A, b =, 40 A, and c = 66 A). On average, those crystals diffracted to around 2.5 A, resolution with 2500 unique reflections. Structure X, with the same space, group, DNA sequence, and crystal form as the "Dickerson dodecamer", is, refined against a complete, low-temperature, 1.4 A resolution data set, with over 11000 reflections. Structure X appears to be conformationally, more ordered than previous structures, suggesting that at least a portion, of the conformational heterogeneity previously attributed to DNA sequence, in fact arises from experimental error.

About this Structure

355D is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.

Reference

The B-DNA dodecamer at high resolution reveals a spine of water on sodium., Shui X, McFail-Isom L, Hu GG, Williams LD, Biochemistry. 1998 Jun 9;37(23):8341-55. PMID:9622486

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