150d: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[150d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=150D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=150D FirstGlance]. <br> | <table><tr><td colspan='2'>[[150d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=150D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=150D FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=150d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=150d OCA], [https://pdbe.org/150d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=150d RCSB], [https://www.ebi.ac.uk/pdbsum/150d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=150d ProSAT]</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=150d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=150d OCA], [https://pdbe.org/150d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=150d RCSB], [https://www.ebi.ac.uk/pdbsum/150d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=150d ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Brown | [[Category: Brown T]] | ||
[[Category: Gibson | [[Category: Gibson NJ]] | ||
[[Category: Hunter | [[Category: Hunter WN]] | ||
[[Category: Leonard | [[Category: Leonard GA]] | ||
[[Category: McAuley-Hecht | [[Category: McAuley-Hecht KE]] | ||
[[Category: Watson | [[Category: Watson WP]] | ||
Revision as of 13:43, 24 November 2022
GUANINE.1,N6-ETHENOADENINE BASE-PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(EDA)GCG)GUANINE.1,N6-ETHENOADENINE BASE-PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(EDA)GCG)
Structural highlights
Publication Abstract from PubMedA single-crystal X-ray analysis of the synthetic oligomer d(CGCGAATT(epsilon dA)GCG) (epsilon dA = 1,N6-ethenoadenosine) has been carried out. The B-form duplex crystallizes in the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions a = 24.31 A, b = 39.65 A, and c = 63.05 A. Refinement has converged with R = 0.182 for 2837 reflections in the resolution range 7.0-2.25 A for a model consisting of the duplex, one Mg2+ ion, and 127 water molecules. The structure contains two G.epsilon dA base pairings which adopt a G(anti).epsilon dA(syn) conformation. The geometry of the two mispairs suggests that the G.epsilon dA pairing are held together by three interbase hydrogen bonds. These are N2(G)-H...N1(epsilon dA), N1(G)...N9(epsilon dA), and O6(G)...H-C8(epsilon dA). The last interaction serves to alleviate the destabilizing effect that would occur due to the presence of an unfulfilled hydrogen bond acceptor. A superposition of the G(4).epsilon dA-(21) base pair found in this structure and the Watson-Crick G(4).C(21) base pair observed in the native dodecamer d(CGCGAATTCGCG) indicates a significant difference in the sugar/phosphate backbone. However, the overall conformations of the two duplexes remain similar, suggesting that the modified base pairs are accommodated into the double helix mainly by alterations of the backbone conformation. Such structural rearrangement of the backbone, upon incorporation of epsilon dA, may provide a signal to the 3-methyladenine-DNA glycosylase that repairs such lesions. Guanine-1,N6-ethenoadenine base pairs in the crystal structure of d(CGCGAATT(epsilon dA)GCG).,Leonard GA, McAuley-Hecht KE, Gibson NJ, Brown T, Watson WP, Hunter WN Biochemistry. 1994 Apr 26;33(16):4755-61. PMID:8161534[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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