218d: Difference between revisions
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<table><tr><td colspan='2'>[[218d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=218D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=218D FirstGlance]. <br> | <table><tr><td colspan='2'>[[218d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=218D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=218D FirstGlance]. <br> | ||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=218d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=218d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=218d RCSB], [http://www.ebi.ac.uk/pdbsum/218d PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=218d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=218d OCA], [http://pdbe.org/218d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=218d RCSB], [http://www.ebi.ac.uk/pdbsum/218d PDBsum]</span></td></tr> | ||
</table> | </table> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 218d" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 05:29, 11 September 2015
THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRSTHE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS
Structural highlights
Publication Abstract from PubMedThe structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been determined to a resolution of 2.25 A and refined to a final R factor of 16.7%. The volume of the unit cell is significantly smaller by 16% than the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is in a different position in the unit cell, rotated by -85.9 degrees, and translated by 9.9 A around the helical axis with respect to the parent structure. The intermolecular arrangement of helices, characterized by double hydrogen bonded guanine-guanine minor groove interactions, remains conserved. The molecular geometry exhibits several significant changes that are related to the changed position of the helix and the presence of two mismatched base pairs with O6-methylguanine. Both mispairs are found in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups are in proximal orientation. The hydration pattern of the structure is different and can be related to changes in the minor groove geometry. An incorrect model that was isomorphous to the parent dodecamer could be refined to a low R factor. Characteristics of the refinement and of the geometry that are indicative of incorrect structures have been analyzed. Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs.,Vojtechovsky J, Eaton MD, Gaffney B, Jones R, Berman HM Biochemistry. 1995 Dec 26;34(51):16632-40. PMID:8527436[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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