1d75: Difference between revisions

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 ==CONFORMATION OF THE GUANINE.8-OXOADENINE BASE PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(O8A)GCG)==
-<StructureSection load='1d75' size='340' side='right' caption='[[1d75]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1d75' size='340' side='right'caption='[[1d75]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1d75]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D75 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D75 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1d75]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D75 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d75 OCA], [http://pdbe.org/1d75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d75 RCSB], [http://www.ebi.ac.uk/pdbsum/1d75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d75 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5-MONOPHOSPHATE'>A38</scene></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=1d75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d75 OCA], [https://pdbe.org/1d75 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d75 RCSB], [https://www.ebi.ac.uk/pdbsum/1d75 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d75 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of the synthetic deoxydodecamer d(CGCGAATT(O8A)GCG)2 (O8A = 8-oxoadenine) has been determined by single-crystal X-ray diffraction techniques. The oligonucleotide crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 25.48 A, b = 41.84 A, and c = 64.91 A. The refinement has converged with an R-factor of 0.151 for 1119 reflections in the resolution range 8.0-2.25 A. Sixty-seven solvent molecules were located during the course of the refinement. The B-DNA helix consists of ten Watson-Crick base pairs and two guanine-8-oxoadenine (G.O8A) base pairs. In order to achieve hydrogen-bonding complementarity between the two bases, an unusual G(anti).O8A-(syn) wobble conformation is adopted. It is proposed that the G.O8A mispairs are held together by a network of four interbase hydrogen bonds which are the result of the formation of two reverse three-center hydrogen-bonding systems. These involve one carbonyl oxygen lone pair interacting with two hydrogen atoms. In a departure from previous observations of the characteristics of purine-purine anti-syn base pairs, lambda 1 and lambda 2, the angles between the glycosidic bonds and the C1'-C1' vector, are symmetric. A reassessment of the other purine-purine mispairs suggests that similar three-center hydrogen bonds may occur and make a contribution to stabilizing other base pairings.
-Conformation of guanine-8-oxoadenine base pairs in the crystal structure of d(CGCGAATT(O8A)GCG).,Leonard GA, Guy A, Brown T, Teoule R, Hunter WN Biochemistry. 1992 Sep 15;31(36):8415-20. PMID:1390625<ref>PMID:1390625</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1d75" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Brown, T]]
+[[Category: Large Structures]]
-[[Category: Guy, A]]
+[[Category: Brown T]]
-[[Category: Hunter, W N]]
+[[Category: Guy A]]
-[[Category: Leonard, G A]]
+[[Category: Hunter WN]]
-[[Category: Teoule, R]]
+[[Category: Leonard GA]]
-[[Category: B-dna]]
+[[Category: Teoule R]]
-[[Category: Dna]]
-[[Category: Double helix]]
-[[Category: Mismatched]]
-[[Category: Modified]]