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389d

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[[Image:389d.gif|left|200px]]<br /><applet load="389d" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:389d.gif|left|200px]]
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caption="389d, resolution 1.550&Aring;" />
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'''CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY'''<br />
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{{Structure
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|PDB= 389d |SIZE=350|CAPTION= <scene name='initialview01'>389d</scene>, resolution 1.550&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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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].
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389D is a [[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=389D OCA].
==Reference==
==Reference==
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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]
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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: Protein complex]]
[[Category: Protein complex]]
[[Category: Berger, I.]]
[[Category: Berger, I.]]
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[[Category: modified]]
[[Category: modified]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:32 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:55:14 2008''

Revision as of 16:55, 20 March 2008

Image:389d.gif


PDB ID 389d

Drag the structure with the mouse to rotate
, resolution 1.550Å
Ligands:
Coordinates: save as pdb, mmCIF, xml



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


Overview

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.

About this Structure

389D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

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:9580702

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