This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


214d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (16:31, 13 December 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:214d.png|left|200px]]
 
-
<!--
+
==THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT==
-
The line below this paragraph, containing "STRUCTURE_214d", creates the "Structure Box" on the page.
+
<StructureSection load='214d' size='340' side='right'caption='[[214d]]' 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'>[[214d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=214D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=214D 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">Solution NMR</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=T41:1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE+5-MONOPHOSPHATE'>T41</scene></td></tr>
-
{{STRUCTURE_214d| PDB=214d | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=214d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=214d OCA], [https://pdbe.org/214d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=214d RCSB], [https://www.ebi.ac.uk/pdbsum/214d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=214d ProSAT]</span></td></tr>
 +
</table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Two-dimensional 1H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3'), where X is 1-(2-O-methyl-beta-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 A. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2'-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH3O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position.
-
===THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT===
+
Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.,Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:8950487<ref>PMID:8950487</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_8950487}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 214d" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 8950487 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_8950487}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=214D OCA].
+
[[Category: Gotfredsen CH]]
-
 
+
[[Category: Jacobsen JP]]
-
==Reference==
+
[[Category: Spielmann HP]]
-
Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP, Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8950487 8950487]
+
[[Category: Wengel J]]
-
[[Category: Gotfredsen, C H.]]
+
-
[[Category: Jacobsen, J P.]]
+
-
[[Category: Spielmann, H P.]]
+
-
[[Category: Wengel, J.]]
+
-
[[Category: Dna]]
+
-
[[Category: Double helix]]
+
-
[[Category: Nmr]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:34:55 2008''
+

Current revision

THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT

PDB ID 214d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/214d"
Personal tools