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1mxj

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NMR solution structure of benz[a]anthracene-dG in ras codon 12,2; GGCAGXTGGTG

Structural highlights

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

Publication Abstract from PubMed

The conformation of the trans-anti-(1S,2R,3S,4R)-N(2)-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[ a]anthracenyl)]-2'-deoxyguanosyl adduct in d(G(1)G(2)C(3)A(4)G(5)X(6)T(7)G(8)G(9)T(10)G(11)).d(C(12)A(13)C(14)C(15)A( 16)C(17)C(18)T(19)G(20)C(21)C(22)), bearing codon 12 of the human N-ras protooncogene (underlined), was determined. This adduct had S stereochemistry at the benzylic carbon. Its occurrence in DNA is a consequence of trans opening by the deoxyguanosine amino group of (1R,2S,3S,4R)-1,2-epoxy-1,2,3,4-tetrahydrobenz[a]anthracenyl-3,4-diol. The resonance frequencies, relative to the unmodified DNA, of the X(6) H1' and H6 protons were shifted downfield, whereas those of the C(18) and T(19) H1', H2', H2' ', and H3' deoxyribose protons were shifted upfield. The imino and amino resonances exhibited the expected sequential connectivities, suggesting no interruption of Watson-Crick pairing. A total of 426 interproton distances, including nine uniquely assigned BA-DNA distances, were used in the restrained molecular dynamics calculations. The refined structure showed that the benz[a]anthracene moiety bound in the minor groove, in the 5'-direction from the modified site. This was similar to the (+)-trans-anti-benzo[a]pyrene-N(2)-dG adduct having S stereochemistry at the benzylic carbon [Cosman, M., De Los Santos, C., Fiala, R., Hingerty, B. E., Singh, S. B., Ibanez, V., Margulis, L. A., Live, D., Geacintov, N. E., Broyde, S., and Patel, D. J. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1914-1918]. It differed from the (-)-trans-anti-benzo[c]phenanthrene-N(2)-dG adduct having S stereochemistry at the benzylic carbon, which intercalated in the 5'-direction [Lin, C. H., Huang, X., Kolbanovskii, A., Hingerty, B. E., Amin, S., Broyde, S., Geacintov, N. E., and Patel, D. J. (2001) J. Mol. Biol. 306, 1059-1080]. The results provided insight into how PAH molecular topology modulates adduct structure in duplex DNA.

Minor groove orientation for the (1S,2R,3S,4R)-N2- [1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyguanos yl adduct in the N-ras codon 12 sequence.,Kim HY, Wilkinson AS, Harris CM, Harris TM, Stone MP Biochemistry. 2003 Mar 4;42(8):2328-38. PMID:12600200^[1]

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

References

↑ Kim HY, Wilkinson AS, Harris CM, Harris TM, Stone MP. Minor groove orientation for the (1S,2R,3S,4R)-N2- [1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyguanos yl adduct in the N-ras codon 12 sequence. Biochemistry. 2003 Mar 4;42(8):2328-38. PMID:12600200 doi:10.1021/bi020462k

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/1mxj"

@@ Line 1: / Line 1: @@
 ==NMR solution structure of benz[a]anthracene-dG in ras codon 12,2; GGCAGXTGGTG==
-<StructureSection load='1mxj' size='340' side='right' caption='[[1mxj]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1mxj' size='340' side='right'caption='[[1mxj]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1mxj]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MXJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1mxj]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MXJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZR:1S,2R,3S,4R-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZR</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1mxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mxj RCSB], [http://www.ebi.ac.uk/pdbsum/1mxj PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZR:1S,2R,3S,4R-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZR</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=1mxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mxj OCA], [https://pdbe.org/1mxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mxj RCSB], [https://www.ebi.ac.uk/pdbsum/1mxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mxj ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 14: / Line 16: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1mxj" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Harris, C M]]
+[[Category: Large Structures]]
-[[Category: Harris, T M]]
+[[Category: Harris CM]]
-[[Category: Kim, H Y.H]]
+[[Category: Harris TM]]
-[[Category: Stone, M P]]
+[[Category: Kim H-YH]]
-[[Category: Wilkinson, A S]]
+[[Category: Stone MP]]
-[[Category: B-like dna]]
+[[Category: Wilkinson AS]]
-[[Category: Dna]]
-[[Category: Dna adduct]]

1mxj

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NMR solution structure of benz[a]anthracene-dG in ras codon 12,2; GGCAGXTGGTG

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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