389d: Difference between revisions

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New page: left|200px<br /><applet load="389d" size="350" color="white" frame="true" align="right" spinBox="true" caption="389d, resolution 1.550Å" /> '''CRYSTAL STRUCTURE O...
 
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[[Image:389d.gif|left|200px]]<br /><applet load="389d" size="350" color="white" frame="true" align="right" spinBox="true"
caption="389d, resolution 1.550&Aring;" />
'''CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY'''<br />


==Overview==
==CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY==
The fundamental conformational states of right-handed double helical DNA, the A- and B-forms, are associated with distinct puckers of the sugar, moieties. The furanose conformation itself is affected by the steric and, electronic nature of the ring substituents. For example, a strongly, electronegative substituent at the C2' position, such as in the, 2'-deoxy-2'-fluoro ribo furanosyl analogue, will drive the conformational, equilibrium towards the C3'- endo type (north). Conversely, the, 2'-deoxy-2'-fluoro arabino furanosyl modification with opposite, stereochemistry at C2' appears to have a preference for a C2'- endo type, pucker (south). Incorporation of 2'-fluoroarabinofuranosyl thymines was, previously shown to enhance the thermodynamic stability of B-DNA duplexes., We have determined the crystal structures of the B-DNA dodecamer duplexes, [d(CGCGAASSCGCG)]2and [d(CGCGAASTCGCG)]2with incorporated, 2'-deoxy-2'-fluoroarabinofuranosyl thymines S (south) at 1.55 A, resolution. In the crystal structures, all S residues adopt an O4'- endo, conformation (east), well compatible with an overall B-form duplex, geometry. In addition to the increased rigidity of S nucleosides, a, clathrate-like ordered water structure around the 2'-fluorines may account, for the observed larger thermodynamic stability of DNA duplexes containing, 2'-deoxy-2'-fluoroarabino thymidines.
<StructureSection load='389d' size='340' side='right'caption='[[389d]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[389d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=389D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=389D FirstGlance]. <br>
389D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=389D 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]] 1.55&#8491;</td></tr>
 
<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=TAF:2-DEOXY-2-FLUORO-ARABINO-FURANOSYL+THYMINE-5-PHOSPHATE'>TAF</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=389d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=389d OCA], [https://pdbe.org/389d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=389d RCSB], [https://www.ebi.ac.uk/pdbsum/389d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=389d ProSAT]</span></td></tr>
Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability., Berger I, Tereshko V, Ikeda H, Marquez VE, Egli M, Nucleic Acids Res. 1998 May 15;26(10):2473-80. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9580702 9580702]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Berger, I.]]
</StructureSection>
[[Category: Egli, M.]]
[[Category: Large Structures]]
[[Category: Ikeda, H.]]
[[Category: Berger I]]
[[Category: Marquez, V.E.]]
[[Category: Egli M]]
[[Category: Tereshko, V.]]
[[Category: Ikeda H]]
[[Category: MG]]
[[Category: Marquez VE]]
[[Category: b-dna]]
[[Category: Tereshko V]]
[[Category: double helix]]
[[Category: modified]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:37:41 2008''

Latest revision as of 11:39, 7 February 2024

CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITYCRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY

Structural highlights

389d 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 1.55Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

389d, resolution 1.55Å

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