1cr3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:40, 22 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1cr3.png|left|200px]]
 
-
<!--
+
==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==
-
The line below this paragraph, containing "STRUCTURE_1cr3", creates the "Structure Box" on the page.
+
<StructureSection load='1cr3' size='340' side='right'caption='[[1cr3]]' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene></td></tr>
-
{{STRUCTURE_1cr3| PDB=1cr3 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [https://pdbe.org/1cr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr3 ProSAT]</span></td></tr>
 +
</table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The solution structure of the adduct derived from the covalent bonding of the fjord region (+)-(11S, 12R, 13R, 14S) stereoisomer of anti -11,12-dihydroxy-13,14-epoxy-11,12,13, 14-tetrahydrobenzo[g]chrysene, (+)- anti -B[g]CDE, to the exocyclic N(6)amino group of the adenine residue dA6, (designated (+)- trans-anti -(B[g]C)dA6), positioned opposite a thymine residue dT17 in the DNA sequence context d(C1-T2-C3-T4-C5-(B[g]C)A6-C7-T8-T9-C10-C11). d(G12-G13-A14-A15-G16-T17-G18-A19-G20++ +-A21-G22) (designated (B[g]C)dA. dT 11-mer duplex), has been studied using structural information derived from NMR data in combination with molecular dynamics (MD) calculations. The solution structure of the (+)- trans-anti -(B[g]C)dA.dT 11-mer duplex has been determined using an MD protocol where both interproton distance and dihedral angle restraints deduced from NOESY and COSY spectra are used during the refinement process, followed by additional relaxation matrix refinement to the observed NOESY intensities to account for spin diffusion effects. The results established that the covalently attached benzo[g]chrysene ring intercalates into the DNA helix directed towards the 5'-side of the modified strand and stacks predominantly with dT17 when intercalated between dC5.dG18 and (B[g]C)dA6.dT17 base-pairs. All base-pairs, including the modified (B[g]C)dA6.dT17 base-pair, are aligned through Watson-Crick pairing as in normal B -DNA. In addition, the potential strain associated with the highly sterically hindered fjord region of the aromatic portion of the benzo[g]chrysenyl ring is relieved through the adoption of a non-planar, propeller-like geometry within the chrysenyl ring system. This conformation shares common structural features with the related (+)- trans-anti -(B[c]Ph)dA adduct in the identical base sequence context, derived from the fjord region (+)-(1S,2R,3R,4S)-3, 4-dihydroxy-1,2-epoxy-1,2,3,4-tetrahydrobenzo[c]phenanthrene stereoisomer, in which intercalation is also observed towards the 5'-side of the modified dA6.dT17 base-pair.
-
===SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX===
+
Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex.,Suri AK, Mao B, Amin S, Geacintov NE, Patel DJ J Mol Biol. 1999 Sep 17;292(2):289-307. PMID:10493876<ref>PMID:10493876</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_10493876}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1cr3" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 10493876 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_10493876}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA].
+
[[Category: Amin S]]
-
 
+
[[Category: Geacintov NE]]
-
==Reference==
+
[[Category: Mao B]]
-
Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex., Suri AK, Mao B, Amin S, Geacintov NE, Patel DJ, J Mol Biol. 1999 Sep 17;292(2):289-307. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10493876 10493876]
+
[[Category: Patel DJ]]
-
[[Category: Amin, S.]]
+
[[Category: Suri AK]]
-
[[Category: Geacintov, N E.]]
+
-
[[Category: Mao, B.]]
+
-
[[Category: Patel, D J.]]
+
-
[[Category: Suri, A K.]]
+
-
[[Category: Carcinogen adduct]]
+
-
[[Category: Dna duplex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 21:11:47 2008''
+

Current revision

SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX

PDB ID 1cr3

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/1cr3"
Personal tools