View source for 3iki


==5-SMe-dU containing DNA octamer==
<StructureSection load='3iki' size='340' side='right'caption='[[3iki]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3iki]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKI FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.38&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene>, <scene name='pdbligand=US2:2-DEOXY-5-(METHYLSULFANYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>US2</scene></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=3iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iki OCA], [https://pdbe.org/3iki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iki RCSB], [https://www.ebi.ac.uk/pdbsum/3iki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iki ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, &gt;76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH(3)) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH(3) and its 5'-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH(3) is replaced with a larger atom (selenium or sulfur). The 5-O-CH(3) modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH(3) modification, which might potentially rigidify the local conformation and facilitates translation.

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.,Sheng J, Zhang W, Hassan AE, Gan J, Soares AS, Geng S, Ren Y, Huang Z Nucleic Acids Res. 2012 May 28. PMID:22641848<ref>PMID:22641848</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3iki" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Gan J]]
[[Category: Hassan AEA]]
[[Category: Huang Z]]
[[Category: Sheng J]]
[[Category: Zhang W]]