2o1i: Difference between revisions

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[[Image:2o1i.gif|left|200px]]


{{Structure
==RH(BPY)2CHRYSI complexed to mismatched DNA==
|PDB= 2o1i |SIZE=350|CAPTION= <scene name='initialview01'>2o1i</scene>, resolution 1.10&Aring;
<StructureSection load='2o1i' size='340' side='right'caption='[[2o1i]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <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>, <scene name='pdbligand=R1C:BIS(2,2&#39;-BIPYRIDINE-KAPPA~2~N~1~,N~1&#39;~)[CHRYSENE-5,6-DIIMINATO(2-)-KAPPA~2~N,N&#39;]RHODIUM(4+)'>R1C</scene>
<table><tr><td colspan='2'>[[2o1i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O1I FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R1C:BIS(2,2-BIPYRIDINE-KAPPA~2~N~1~,N~1~)[CHRYSENE-5,6-DIIMINATO(2-)-KAPPA~2~N,N]RHODIUM(4+)'>R1C</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2o1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o1i OCA], [https://pdbe.org/2o1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o1i RCSB], [https://www.ebi.ac.uk/pdbsum/2o1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o1i ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o1i OCA], [http://www.ebi.ac.uk/pdbsum/2o1i PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2o1i RCSB]</span>
<div style="background-color:#fffaf0;">
}}
== Publication Abstract from PubMed ==
 
'''RH(BPY)2CHRYSI complexed to mismatched DNA'''
 
 
==Overview==
We report the 1.1-A resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5'-(dCGGAAATTCCCG)2-3'. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches.
We report the 1.1-A resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5'-(dCGGAAATTCCCG)2-3'. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches.


==About this Structure==
Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator.,Pierre VC, Kaiser JT, Barton JK Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):429-34. Epub 2006 Dec 28. PMID:17194756<ref>PMID:17194756</ref>
2O1I 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=2O1I OCA].
 
==Reference==
Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator., Pierre VC, Kaiser JT, Barton JK, Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):429-34. Epub 2006 Dec 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17194756 17194756]
[[Category: Protein complex]]
[[Category: Barton, J K.]]
[[Category: Kaiser, J T.]]
[[Category: Pierre, V C.]]
[[Category: dna mismatch]]
[[Category: dna recognition]]
[[Category: metallointercalator]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:11:21 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2o1i" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Barton JK]]
[[Category: Kaiser JT]]
[[Category: Pierre VC]]
Retrieved from "https://proteopedia.org/2o1i"