478d

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CRYSTAL STRUCTURE OF THE B-DNA DODECAMER 5'-D(CGCGAA(TAF)TCGCG), WHERE TAF IS 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE

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Retrieved from "http://52.214.119.220/wiki/index.php/478d"

Categories: Large Structures | Egli M | Minasov G | Tereshko V

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-[[Image:478d.gif|left|200px]]<br /><applet load="478d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="478d, resolution 2.20&Aring;" />
-'''CRYSTAL STRUCTURE OF THE B-DNA DODECAMER 5'-D(CGCGAA(TAF)TCGCG), WHERE TAF IS 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE B-DNA DODECAMER 5'-D(CGCGAA(TAF)TCGCG), WHERE TAF IS 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE==
-Crystal structures of B-form DNA have provided insights into the global, and local conformational properties of the double helix, the solvent, environment, drug binding and DNA packing. For example, structures of the, duplex with sequence CGCGAATTCGCG, the Dickerson-Drew dodecamer (DDD), established a unique geometry of the central A-tract and a hydration spine, in the minor groove. However, our knowledge of the various interaction, modes between metal ions and DNA is very limited and almost no information, exists concerning the origins of the different effects on DNA conformation, and packing exerted by individual metal ions.Crystallization of the DDD, duplex in the presence of Mg(2+)and Ca(2+)yields different crystal forms., The structures of the new Ca(2+)-form and isomorphous structures of, oligonucleotides with sequences GGCGAATTCGCG and GCGAATTCGCG were, determined at a maximum resolution of 1.3 A. These and the 1.1 A structure, of the DDD Mg(2+)-form have revealed the most detailed picture yet of the, ionic environment of B-DNA. In the Mg(2+)and Ca(2+)-forms, duplexes in the, crystal lattice are surrounded by 13 magnesium and 11 calcium ions, respectively.Mg(2+)and Ca(2+)generate different DNA crystal lattices and, stabilize different end-to-end overlaps and lateral contacts between, duplexes, thus using different strategies for reducing the effective, repeat length of the helix to ten base-pairs. Mg(2+)crystals allow the two, outermost base-pairs at either end to interact laterally via minor groove, H-bonds, turning the 12-mer into an effective 10-mer. Ca(2+)crystals, in, contrast, unpair the outermost base-pair at each end, converting the helix, into a 10-mer that can stack along its axis. This reduction of a 12-mer, into a functional 10-mer is followed no matter what the detailed nature of, the 5'-end of the chain: C-G-C-G-A-ellipsis, G-G-C-G-A-ellipsis, or a, truncated G-C-G-A-ellipsis Rather than merely mediating close contacts, between phosphate groups, ions are at the origin of many well-known, features of the DDD duplex structure. A Mg(2+)coordinates in the major, groove, contributing to kinking of the duplex at one end. While, Ca(2+)resides in the minor groove, coordinating to bases via its hydration, shell, two magnesium ions are located at the periphery of the minor, groove, bridging phosphate groups from opposite strands and contracting, the groove at one border of the A-tract.
+<StructureSection load='478d' size='340' side='right'caption='[[478d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[478d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=478D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=478D FirstGlance]. <br>
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=478D 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=478d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=478d OCA], [https://pdbe.org/478d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=478d RCSB], [https://www.ebi.ac.uk/pdbsum/478d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=478d ProSAT]</span></td></tr>
-Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing., Minasov G, Tereshko V, Egli M, J Mol Biol. 1999 Aug 6;291(1):83-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10438608 10438608]
+</table>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Egli, M.]]
+</StructureSection>
-[[Category: Minasov, G.]]
+[[Category: Large Structures]]
-[[Category: Tereshko, V.]]
+[[Category: Egli M]]
-[[Category: CA]]
+[[Category: Minasov G]]
-[[Category: b-dna dodecamer duplex]]
+[[Category: Tereshko V]]
-[[Category: calcium crystal form]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:45:05 2008''

478d

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CRYSTAL STRUCTURE OF THE B-DNA DODECAMER 5'-D(CGCGAA(TAF)TCGCG), WHERE TAF IS 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE

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