3bm0: Difference between revisions

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[[~~Image~~:3bm0.~~png|left|200px~~]]

==Structure of DNA Octamer G(dUSe)G(5-SedU)ACAC==

== Structural highlights ==

<table><tr><td colspan='2'>[[3bm0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM0 FirstGlance]. <br>

</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=T5S:'>T5S</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</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=3bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm0 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm0 PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

We investigated the possibility of the interaction of 5-CH(3) of thymidine and its 5'-phosphate backbone (C-H...O(-)-PO(3) interaction) in DNA via the insertion of the atomic probe (a selenium atom) into the exo-5-position of thymidine (5-Se-T). 5-Se-T was synthesized for the first time, via Mn(OAc)(3) assisted electrophilic addition of CH(3)SeSeCH(3) to 3',5'-di-O-benzoyl-2'-deoxyuridine. The 5-Se-T phosphoramidite was subsequently synthesized and incorporated into DNA in over 99% coupling yield. Biophysical and structural investigations of the 5-Se-T DNAs revealed that the Se-modified and nonmodified DNAs are virtually identical. In addition, the crystallographic analysis of a 5-Se-T DNA strongly suggests a hydrogen-bond formation between the 5-CH(3) and 5'-phosphate groups (CH(3)...PO(4)(-) interaction).

~~{{STRUCTURE_3bm0| PDB=3bm0 | SCENE= }}~~

Synthesis and crystallographic analysis of 5-Se-thymidine DNAs.,Hassan AE, Sheng J, Jiang J, Zhang W, Huang Z Org Lett. 2009 Jun 18;11(12):2503-6. PMID:19469515<ref>PMID:19469515</ref>

~~===Structure~~ of ~~DNA Octamer G(dUSe)G(5-SedU)ACAC===~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

~~{{ABSTRACT_PUBMED_19469515}}~~

== References ==

~~==About this Structure==~~

__TOC__

~~[[3bm0]] is a 1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3BM0 OCA].~~

</StructureSection>

==~~Reference~~==

<~~ref group="xtra">PMID:019469515<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Hassan, A E.]]

[[Category: Huang, Z.]]

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@@ Line 1: / Line 1: @@
-[[Image:3bm0.png|left|200px]]
+==Structure of DNA Octamer G(dUSe)G(5-SedU)ACAC==
+<StructureSection load='3bm0' size='340' side='right' caption='[[3bm0]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3bm0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM0 FirstGlance]. <br>
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=T5S:'>T5S</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</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=3bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm0 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm0 PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We investigated the possibility of the interaction of 5-CH(3) of thymidine and its 5'-phosphate backbone (C-H...O(-)-PO(3) interaction) in DNA via the insertion of the atomic probe (a selenium atom) into the exo-5-position of thymidine (5-Se-T). 5-Se-T was synthesized for the first time, via Mn(OAc)(3) assisted electrophilic addition of CH(3)SeSeCH(3) to 3',5'-di-O-benzoyl-2'-deoxyuridine. The 5-Se-T phosphoramidite was subsequently synthesized and incorporated into DNA in over 99% coupling yield. Biophysical and structural investigations of the 5-Se-T DNAs revealed that the Se-modified and nonmodified DNAs are virtually identical. In addition, the crystallographic analysis of a 5-Se-T DNA strongly suggests a hydrogen-bond formation between the 5-CH(3) and 5'-phosphate groups (CH(3)...PO(4)(-) interaction).
-{{STRUCTURE_3bm0|  PDB=3bm0  |  SCENE=  }}
+Synthesis and crystallographic analysis of 5-Se-thymidine DNAs.,Hassan AE, Sheng J, Jiang J, Zhang W, Huang Z Org Lett. 2009 Jun 18;11(12):2503-6. PMID:19469515<ref>PMID:19469515</ref>
-===Structure of DNA Octamer G(dUSe)G(5-SedU)ACAC===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_19469515}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3bm0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM0 OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:019469515</ref><references group="xtra"/>
 [[Category: Hassan, A E.]]
 [[Category: Huang, Z.]]