This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


478d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:40, 1 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==CRYSTAL STRUCTURE OF THE B-DNA DODECAMER 5'-D(CGCGAA(TAF)TCGCG), WHERE TAF IS 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE==
==CRYSTAL STRUCTURE OF THE B-DNA DODECAMER 5'-D(CGCGAA(TAF)TCGCG), WHERE TAF IS 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE==
-
<StructureSection load='478d' size='340' side='right' caption='[[478d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+
<StructureSection load='478d' size='340' side='right'caption='[[478d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=478D FirstGlance]. <br>
+
<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>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
+
</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><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TAF:2-DEOXY-2-FLUORO-ARABINO-FURANOSYL+THYMINE-5-PHOSPHATE'>TAF</scene></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>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=478d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=478d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=478d RCSB], [http://www.ebi.ac.uk/pdbsum/478d PDBsum]</span></td></tr>
+
<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>
-
<table>
+
</table>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
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.
+
-
 
+
-
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:10438608<ref>PMID:10438608</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Egli, M.]]
+
[[Category: Large Structures]]
-
[[Category: Minasov, G.]]
+
[[Category: Egli M]]
-
[[Category: Tereshko, V.]]
+
[[Category: Minasov G]]
-
[[Category: B-dna dodecamer duplex]]
+
[[Category: Tereshko V]]
-
[[Category: Calcium crystal form]]
+
-
[[Category: Dna]]
+

Current revision

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

PDB ID 478d

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/478d"
Personal tools