362d
From Proteopedia
(New page: 200px<br /><applet load="362d" size="450" color="white" frame="true" align="right" spinBox="true" caption="362d, resolution 1.300Å" /> '''THE STRUCTURE OF D(...) |
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| - | [[Image:362d.gif|left|200px]]<br /><applet load="362d" size=" | + | [[Image:362d.gif|left|200px]]<br /><applet load="362d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="362d, resolution 1.300Å" /> | caption="362d, resolution 1.300Å" /> | ||
'''THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS'''<br /> | '''THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to | + | The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure. |
==About this Structure== | ==About this Structure== | ||
| - | 362D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NCO as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | + | 362D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 347D. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=362D OCA]. |
==Reference== | ==Reference== | ||
Structure of d(TGCGCA)2 and a comparison to other DNA hexamers., Harper A, Brannigan JA, Buck M, Hewitt L, Lewis RJ, Moore MH, Schneider B, Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1273-84. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10089504 10089504] | Structure of d(TGCGCA)2 and a comparison to other DNA hexamers., Harper A, Brannigan JA, Buck M, Hewitt L, Lewis RJ, Moore MH, Schneider B, Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1273-84. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10089504 10089504] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Brannigan, J | + | [[Category: Brannigan, J A.]] |
[[Category: Buck, M.]] | [[Category: Buck, M.]] | ||
| - | [[Category: Harper, N | + | [[Category: Harper, N A.]] |
| - | [[Category: Lewis, R | + | [[Category: Lewis, R J.]] |
| - | [[Category: Moore, M | + | [[Category: Moore, M H.]] |
[[Category: Schneider, B.]] | [[Category: Schneider, B.]] | ||
[[Category: NCO]] | [[Category: NCO]] | ||
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[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:18 2008'' |
Revision as of 17:02, 21 February 2008
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THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS
Overview
The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.
About this Structure
362D is a Protein complex structure of sequences from [1] with as ligand. This structure supersedes the now removed PDB entry 347D. Full crystallographic information is available from OCA.
Reference
Structure of d(TGCGCA)2 and a comparison to other DNA hexamers., Harper A, Brannigan JA, Buck M, Hewitt L, Lewis RJ, Moore MH, Schneider B, Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1273-84. PMID:10089504
Page seeded by OCA on Thu Feb 21 19:02:18 2008
Categories: Protein complex | Brannigan, J A. | Buck, M. | Harper, N A. | Lewis, R J. | Moore, M H. | Schneider, B. | NCO | Double helix | Z-dna
