233d: Difference between revisions

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[[Image:233d.gif|left|200px]]<br /><applet load="233d" size="350" color="white" frame="true" align="right" spinBox="true"
caption="233d, resolution 2.400&Aring;" />
'''THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDES'''<br />


==Overview==
==THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDES==
The crystal structure refinement of the synthetic dodecamer d(CGCGAASSCGCG), where S = 4'-thio-2'-deoxythymidine, has converged at R=0.201 for 2605 reflections with F &gt; 2sigma(F) in the resolution range 8.0-2.4 A for a model consisting of the dodecamer duplex and 66 water molecules. A comparison of its structure with that of the native dodecamer d(CGCGAATTCGCG) has revealed that the major differences between the two structures is a change in the conformation of the sugar-phosphate backbone in the regions at and adjacent to the positions of the modified nucleosides. Examination of the fine structural parameters for each of the structures reveals that the thiosugars adopt a C3'-exo conformation in d(CGCGAASSCGCG), rather than the approximate C1'-exo conformation found for the analogous sugars in the structure of d(CGCGAATTCGCG). The observed differences in structure between the two duplexes may help to explain the enhanced resistance to nuclease digestion of synthetic oligonucleotides containing 4'-thio-2'-deoxynucleotides.
<StructureSection load='233d' size='340' side='right'caption='[[233d]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[233d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=233D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=233D FirstGlance]. <br>
233D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=233D OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=T49:S4-2DEOXYTHYMIDINE+5-MONOPHOSPHATE'>T49</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=233d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=233d OCA], [https://pdbe.org/233d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=233d RCSB], [https://www.ebi.ac.uk/pdbsum/233d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=233d ProSAT]</span></td></tr>
The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides., Boggon TJ, Hancox EL, McAuley-Hecht KE, Connolly BA, Hunter WN, Brown T, Walker RT, Leonard GA, Nucleic Acids Res. 1996 Mar 1;24(5):951-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8600465 8600465]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Boggon, T J.]]
</StructureSection>
[[Category: Brown, T.]]
[[Category: Large Structures]]
[[Category: Connolly, B A.]]
[[Category: Boggon TJ]]
[[Category: Hancox, E L.]]
[[Category: Brown T]]
[[Category: Hunter, W N.]]
[[Category: Connolly BA]]
[[Category: Leonard, G A.]]
[[Category: Hancox EL]]
[[Category: McAuley-Hecht, K E.]]
[[Category: Hunter WN]]
[[Category: Walker, R T.]]
[[Category: Leonard GA]]
[[Category: b-dna]]
[[Category: McAuley-Hecht KE]]
[[Category: double helix]]
[[Category: Walker RT]]
[[Category: modified]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:21:23 2008''

Latest revision as of 12:08, 14 February 2024

THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDESTHE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDES

Structural highlights

233d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

233d, resolution 2.40Å

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