1pg9

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[[Image:1pg9.gif|left|200px]]
[[Image:1pg9.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1pg9 |SIZE=350|CAPTION= <scene name='initialview01'>1pg9</scene>
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The line below this paragraph, containing "STRUCTURE_1pg9", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=1PT:CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II)'>1PT</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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{{STRUCTURE_1pg9| PDB=1pg9 | SCENE= }}
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|RELATEDENTRY=[[1pgc|1PGC]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pg9 OCA], [http://www.ebi.ac.uk/pdbsum/1pg9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pg9 RCSB]</span>
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'''NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex'''
'''NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex'''
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==About this Structure==
==About this Structure==
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1PG9 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PG9 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PG9 OCA].
==Reference==
==Reference==
NMR solution structure of an oxaliplatin 1,2-d(GG) intrastrand cross-link in a DNA dodecamer duplex., Wu Y, Pradhan P, Havener J, Boysen G, Swenberg JA, Campbell SL, Chaney SG, J Mol Biol. 2004 Aug 27;341(5):1251-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15321720 15321720]
NMR solution structure of an oxaliplatin 1,2-d(GG) intrastrand cross-link in a DNA dodecamer duplex., Wu Y, Pradhan P, Havener J, Boysen G, Swenberg JA, Campbell SL, Chaney SG, J Mol Biol. 2004 Aug 27;341(5):1251-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15321720 15321720]
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[[Category: Protein complex]]
 
[[Category: Campbel, S L.]]
[[Category: Campbel, S L.]]
[[Category: Chaney, S G.]]
[[Category: Chaney, S G.]]
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[[Category: Pradhan, P.]]
[[Category: Pradhan, P.]]
[[Category: Wu, Y.]]
[[Category: Wu, Y.]]
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[[Category: deoxyribonucleic acid]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: dna]]
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[[Category: Dna]]
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[[Category: dodecamer]]
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[[Category: Dodecamer]]
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[[Category: duplex]]
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[[Category: Duplex]]
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[[Category: nmr]]
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[[Category: Nmr]]
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[[Category: oxaliplatin]]
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[[Category: Oxaliplatin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 05:03:18 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:59:17 2008''
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Revision as of 02:03, 3 May 2008

Image:1pg9.gif

Template:STRUCTURE 1pg9

NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex


Overview

We have determined, at high resolution, the NMR solution structure of an oxaliplatin-GG DNA dodecamer in the AGGC sequence context by 2D NMR studies. Homonuclear assignment strategies resulted in unambiguous assignment of 203 out of 249 protons, which corresponds to assignment of approximately 81% of the protons. Assignments of H5' and H5" protons were tentative due to resonance overlap. The structure of the oxaliplatin duplex was calculated using the program CNS with a simulated annealing protocol. A total of 510 experimental restraints were employed in the structure calculation. Of 20 calculated structures, the 15 with the lowest energy were accepted as a family. The RMSD of the 15 lowest energy structures was 0.68 A, indicating good structural convergence. The theoretical NOESY spectrum obtained by back-calculation from the final average structure showed excellent agreement with the experimental data, indicating that the final structure was in good agreement with the experimental NMR data. Significant conformational differences were observed between the oxaliplatin-GG 12-mer DNA we studied and all previous solution structures of cisplatin-GG DNA duplexes. For example, the oxaliplatin-GG adduct shows much less distortion at the AG base-pair step than the cisplatin-GG adducts. In addition, the oxaliplatin-GG structure also has a narrow minor groove and an overall axis bend of about 31 degrees, both of which are very different from the recent NMR structures for the cisplatin-GG adducts. These structural differences may explain some of the biological differences between oxaliplatin- and cisplatin-GG adducts.

About this Structure

Full crystallographic information is available from OCA.

Reference

NMR solution structure of an oxaliplatin 1,2-d(GG) intrastrand cross-link in a DNA dodecamer duplex., Wu Y, Pradhan P, Havener J, Boysen G, Swenberg JA, Campbell SL, Chaney SG, J Mol Biol. 2004 Aug 27;341(5):1251-69. PMID:15321720 Page seeded by OCA on Sat May 3 05:03:18 2008

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