3ltr: Difference between revisions

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[[Image:3ltr.png|left|200px]]


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==5-OMe-dU containing DNA 8mer==
The line below this paragraph, containing "STRUCTURE_3ltr", creates the "Structure Box" on the page.
<StructureSection load='3ltr' size='340' side='right'caption='[[3ltr]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3ltr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LTR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
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<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=T5O:2-DEOXY-5-METHOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>T5O</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
{{STRUCTURE_3ltr|  PDB=3ltr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ltr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ltr OCA], [https://pdbe.org/3ltr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ltr RCSB], [https://www.ebi.ac.uk/pdbsum/3ltr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ltr 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.


===5-OMe-dU containing DNA 8mer===
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>
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The line below this paragraph, {{ABSTRACT_PUBMED_22641848}}, adds the Publication Abstract to the page
<div class="pdbe-citations 3ltr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 22641848 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_22641848}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3ltr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTR OCA].
[[Category: Gan J]]
 
[[Category: Hassan AEA]]
==Reference==
[[Category: Huang Z]]
<ref group="xtra">PMID:022641848</ref><references group="xtra"/>
[[Category: Sheng J]]
[[Category: Gan, J.]]
[[Category: Zhang W]]
[[Category: Hassan, A E.A.]]
[[Category: Huang, Z.]]
[[Category: Sheng, J.]]
[[Category: Zhang, W.]]
[[Category: 2'-seme]]
[[Category: 5-methoxy-uridine]]
[[Category: 5-ome]]
[[Category: Dna]]
[[Category: Oligonucleotide]]
[[Category: Selenium]]
Retrieved from "https://proteopedia.org/3ltr"