389d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:39, 7 February 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:389d.gif|left|200px]]
 
-
<!--
+
==CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY==
-
The line below this paragraph, containing "STRUCTURE_389d", creates the "Structure Box" on the page.
+
<StructureSection load='389d' size='340' side='right'caption='[[389d]], [[Resolution|resolution]] 1.55&Aring;' 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'>[[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>
-
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">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>
-
{{STRUCTURE_389d| PDB=389d | SCENE= }}
+
<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>
-
 
+
</table>
-
'''CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Berger I]]
-
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.
+
[[Category: Egli M]]
-
 
+
[[Category: Ikeda H]]
-
==About this Structure==
+
[[Category: Marquez VE]]
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=389D OCA].
+
[[Category: Tereshko V]]
-
 
+
-
==Reference==
+
-
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://www.ncbi.nlm.nih.gov/pubmed/9580702 9580702]
+
-
[[Category: Berger, I.]]
+
-
[[Category: Egli, M.]]
+
-
[[Category: Ikeda, H.]]
+
-
[[Category: Marquez, V E.]]
+
-
[[Category: Tereshko, V.]]
+
-
[[Category: B-dna]]
+
-
[[Category: Double helix]]
+
-
[[Category: Modified]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:18:29 2008''
+

Current revision

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

PDB ID 389d

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/389d"
Personal tools