This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1omk
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:1omk.gif|left|200px]] | [[Image:1omk.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_1omk", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_1omk| PDB=1omk | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''The Crystal Structure of d(CACG(5IU)G)''' | '''The Crystal Structure of d(CACG(5IU)G)''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | 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://www.ncbi.nlm.nih.gov/pubmed/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://www.ncbi.nlm.nih.gov/pubmed/12876373 12876373] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Hecke, K Van.]] | [[Category: Hecke, K Van.]] | ||
[[Category: Meervelt, L Van.]] | [[Category: Meervelt, L Van.]] | ||
[[Category: Schuerman, G.]] | [[Category: Schuerman, G.]] | ||
[[Category: 5-iodo-2'-deoxyuridine]] | [[Category: 5-iodo-2'-deoxyuridine]] | ||
| - | [[Category: | + | [[Category: Z-dna]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:02:01 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 01:02, 3 May 2008
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
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 Page seeded by OCA on Sat May 3 04:02:01 2008
