1omk
From Proteopedia
(New page: 200px<br /><applet load="1omk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1omk, resolution 1.30Å" /> '''The Crystal Structur...) |
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| - | [[Image:1omk.gif|left|200px]]<br /><applet load="1omk" size=" | + | [[Image:1omk.gif|left|200px]]<br /><applet load="1omk" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1omk, resolution 1.30Å" /> | caption="1omk, resolution 1.30Å" /> | ||
'''The Crystal Structure of d(CACG(5IU)G)'''<br /> | '''The Crystal Structure of d(CACG(5IU)G)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes | + | The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal X-ray diffraction techniques. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c = 41.99 A. Refinement in the resolution range 20-1.3 A converged with a final R1 = 0.167, including 43 water molecules and two cobalt hexammine complexes. The incorporation of a large I atom has only minor consequences for the overall structure as is noticed in the IDU.A base pairs, which are of the common Watson-Crick type. To contribute to the still puzzling mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of cobalt hexammine-binding modes in Z-DNA is provided, revealing similar binding modes for the reported structure. |
==About this Structure== | ==About this Structure== | ||
| - | 1OMK 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]. Full crystallographic information is available from [http:// | + | 1OMK 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMK OCA]. |
==Reference== | ==Reference== | ||
Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G]., Schuerman G, Van Hecke K, Van Meervelt L, Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1525-8. Epub 2003, Jul 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12876373 12876373] | Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G]., Schuerman G, Van Hecke K, Van Meervelt L, Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1525-8. Epub 2003, Jul 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12876373 12876373] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Hecke, K | + | [[Category: Hecke, K Van.]] |
| - | [[Category: Meervelt, L | + | [[Category: Meervelt, L Van.]] |
[[Category: Schuerman, G.]] | [[Category: Schuerman, G.]] | ||
[[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 14:19:22 2008'' |
Revision as of 12:19, 21 February 2008
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The Crystal Structure of d(CACG(5IU)G)
Overview
The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal X-ray diffraction techniques. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c = 41.99 A. Refinement in the resolution range 20-1.3 A converged with a final R1 = 0.167, including 43 water molecules and two cobalt hexammine complexes. The incorporation of a large I atom has only minor consequences for the overall structure as is noticed in the IDU.A base pairs, which are of the common Watson-Crick type. To contribute to the still puzzling mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of cobalt hexammine-binding modes in Z-DNA is provided, revealing similar binding modes for the reported structure.
About this Structure
1OMK is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G]., Schuerman G, Van Hecke K, Van Meervelt L, Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1525-8. Epub 2003, Jul 23. PMID:12876373
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