218d: Difference between revisions

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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=218d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=218d OCA], [https://pdbe.org/218d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=218d RCSB], [https://www.ebi.ac.uk/pdbsum/218d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=218d ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=218d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=218d OCA], [https://pdbe.org/218d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=218d RCSB], [https://www.ebi.ac.uk/pdbsum/218d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=218d ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
The 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., &amp; 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<ref>PMID:8527436</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 218d" style="background-color:#fffaf0;"></div>
== References ==
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Latest revision as of 12:08, 14 February 2024

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

218d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.25Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

218d, resolution 2.25Å

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