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1dl4

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Revision as of 22:09, 10 September 2015

THE SOLUTION STRUCTURE OF A BAY-REGION 1S-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE

Structural highlights

1dl4 is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Publication Abstract from PubMed

The (1S,2R,3S,4R)-N(6)-[1-(1,2,3,4-tetrahydro-2,3, 4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct at X6 of 5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3', incorporating codons 60, 61 (underlined), and 62 of the human N-ras protooncogene, results from trans opening of (1R,2S,3S,4R)-1,2-epoxy-1,2,3, 4-tetrahydrobenz[a]anthracenyl-3,4-diol by the exocyclic N6 of adenine. Two conformations of this adduct exist, in slow exchange on the NMR time scale. A structure for the major conformation, which represents approximately 80% of the population, is presented. In this conformation, an anti glycosidic torsion angle is observed for all nucleotides, including S,R,S,RA6. The refined structure is a right-handed duplex, with the benz[a]anthracene moiety intercalated on the 3'-face of the modified base pair, from the major groove. It is located between S,R,S,RA6.T17 and A7.T16. Intercalation is on the opposite face of the modified S,R,S,RA6.T17 base pair as compared to the (1R,2S,3R,4S)-N6-[1-(1,2,3,4-tetrahydro-2, 3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct, which intercalated 5' to the modified R,S,R,SA6.T17 base pair [Li, Z. , Mao, H., Kim, H.-Y., Tamura, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1999) Biochemistry 38, 2969-2981]. The spectroscopic data do not allow refinement of the minor conformation, but suggest that the adenyl moiety in the modified nucleoti111S,R, S,RA6 adopts a syn glycosidic torsion angle. Thus, the minor conformation may create greater distortion of the DNA duplex. The results are discussed in the context of site-specific mutagenesis studies which reveal that the S,R,S,RA6 lesion is less mutagenic than the R,S,R,SA6 lesion.

Intercalation of the (1S,2R,3S,4R)-N6-[1-(1,2,3,4-tetrahydro-2,3, 4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence.,Li Z, Kim HY, Tamura PJ, Harris CM, Harris TM, Stone MP Biochemistry. 1999 Dec 7;38(49):16045-57. PMID:10587427^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Li Z, Kim HY, Tamura PJ, Harris CM, Harris TM, Stone MP. Intercalation of the (1S,2R,3S,4R)-N6-[1-(1,2,3,4-tetrahydro-2,3, 4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence. Biochemistry. 1999 Dec 7;38(49):16045-57. PMID:10587427

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dl4"

@@ Line 4: / Line 4: @@
 <table><tr><td colspan='2'>[[1dl4]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DL4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DL4 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</scene></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=1dl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dl4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dl4 RCSB], [http://www.ebi.ac.uk/pdbsum/1dl4 PDBsum]</span></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=1dl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dl4 OCA], [http://pdbe.org/1dl4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dl4 RCSB], [http://www.ebi.ac.uk/pdbsum/1dl4 PDBsum]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 14: / Line 14: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1dl4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

1dl4

From Proteopedia

Revision as of 22:09, 10 September 2015

THE SOLUTION STRUCTURE OF A BAY-REGION 1S-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE

Structural highlights

Publication Abstract from PubMed

References

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