355d
From Proteopedia
(New page: 200px<br /><applet load="355d" size="350" color="white" frame="true" align="right" spinBox="true" caption="355d, resolution 1.400Å" /> '''THE B-DNA DODECAMER...) |
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==Overview== | ==Overview== | ||
| - | We describe a very accurate addition (called structure X here) to the | + | 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== | ==About this Structure== | ||
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9622486 9622486] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9622486 9622486] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Hu, L | + | [[Category: Hu, L D.Williams G G.]] |
[[Category: McFail-Isom, L.]] | [[Category: McFail-Isom, L.]] | ||
[[Category: Shui, X.]] | [[Category: Shui, X.]] | ||
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[[Category: sodium form]] | [[Category: sodium form]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:17 2008'' |
Revision as of 17:02, 21 February 2008
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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
Page seeded by OCA on Thu Feb 21 19:02:17 2008
Categories: Protein complex | Hu, L D.Williams G G. | McFail-Isom, L. | Shui, X. | MG | SPM | B-dna | Double helix | Sodium form
