1oci: Difference between revisions

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[[Image:1oci.png|left|200px]]


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==[3.2.0]bcANA:DNA==
The line below this paragraph, containing "STRUCTURE_1oci", creates the "Structure Box" on the page.
<StructureSection load='1oci' size='340' side='right'caption='[[1oci]]' 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'>[[1oci]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OCI 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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLB:2-O,3-C-METHYLENE-ARABINOFURANOSYL-THYMINE-5-MONOPHOSPHATE'>TLB</scene></td></tr>
{{STRUCTURE_1oci|  PDB=1oci  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oci OCA], [https://pdbe.org/1oci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oci RCSB], [https://www.ebi.ac.uk/pdbsum/1oci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oci ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
[3.2.0]bcANA is a D-arabino-configured bicyclic nucleotide with a 2'-O,3'-C-methylene bridge. We here present the high-resolution NMR structure of a [3.2.0]bcANA modified dsDNA nonamer with one modified nucleotide incorporated. NOE restraints were obtained by analysis of NOESY cross peak intensities using a full relaxation matrix approach, and subsequently these restraints were incorporated into a simulated annealing scheme for the structure determination. In addition, the furanose ring puckers of the deoxyribose moieties were determined by analysis of COSY cross peaks. The modified duplex adopts a B-like geometry with Watson-Crick base pairing in all base pairs and all glycosidic angles in the anti range. The stacking arrangement of the nucleobases appears to be unperturbed relative to the normal B-like arrangement. The 2'-O,3'-C-methylene bridge of the modified nucleotide is located at the brim of the major groove where it fits well into the B-type duplex framework. The sugar pucker of the [3.2.0]bcANA nucleotide is O4'-endo and this sugar conformation causes a change in the delta backbone angle relative to the C2'-endo deoxyribose sugar pucker. This change is absorbed locally by slight changes in the epsilon and zeta angles of the modified nucleotide. Overall, the [3.2.0]bcANA modifications fits very well into a B-like duplex framework and only small and local perturbations are observed relative to the unmodified dsDNA of identical base sequence.


===[3.2.0]BCANA:DNA===
NMR solution structure of dsDNA containing a bicyclic D-arabino-configured nucleotide fixed in an O4'-endo sugar conformation.,Tommerholt HV, Christensen NK, Nielsen P, Wengel J, Stein PC, Jacobsen JP, Petersen M Org Biomol Chem. 2003 May 21;1(10):1790-7. PMID:12926371<ref>PMID:12926371</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_12926371}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1oci" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 12926371 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_12926371}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1OCI is a [[Single protein]] structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA].
[[Category: Synthetic construct]]
 
[[Category: Christensen NK]]
==Reference==
[[Category: Jacobsen JP]]
NMR solution structure of dsDNA containing a bicyclic D-arabino-configured nucleotide fixed in an O4'-endo sugar conformation., Tommerholt HV, Christensen NK, Nielsen P, Wengel J, Stein PC, Jacobsen JP, Petersen M, Org Biomol Chem. 2003 May 21;1(10):1790-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12926371 12926371]
[[Category: Nielsen P]]
[[Category: Single protein]]
[[Category: Petersen M]]
[[Category: Christensen, N K.]]
[[Category: Stein PC]]
[[Category: Jacobsen, J P.]]
[[Category: Tommerholt HV]]
[[Category: Nielsen, P.]]
[[Category: Wengel J]]
[[Category: Petersen, M.]]
[[Category: Stein, P C.]]
[[Category: Tommerholt, H V.]]
[[Category: Wengel, J.]]
[[Category: Arabino nucleic acid]]
[[Category: Dna]]
[[Category: Nmr]]
[[Category: Rnase h]]
 
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Retrieved from "https://proteopedia.org/1oci"