4e1u: Difference between revisions

Latest revision as of 10:49, 13 August 2026

[Ru(bpy)2 dppz]2+ bound to DNA

Structural highlights

4e1u is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 0.92Å
Ligands:	BA, R1Z
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

DNA mismatches represent a novel target in the development of diagnostics and therapeutics for cancer, because deficiencies in DNA mismatch repair are implicated in cancers, and cells that are repair-deficient show a high frequency of mismatches. Metal complexes with bulky intercalating ligands serve as probes for DNA mismatches. Here, we report the high-resolution (0.92 A) crystal structure of the ruthenium 'light switch' complex Delta-[Ru(bpy)(2)dppz](2+) (bpy = 2,2'-bipyridine and dppz = dipyridophenazine), which is known to show luminescence on binding to duplex DNA, bound to both mismatched and well-matched sites in the oligonucleotide 5'-(dCGGAAATTACCG)(2)-3' (underline denotes AA mismatches). Two crystallographically independent views reveal that the complex binds mismatches through metalloinsertion, ejecting both mispaired adenosines. Additional ruthenium complexes are intercalated at well-matched sites, creating an array of complexes in the minor groove stabilized by stacking interactions between bpy ligands and extruded adenosines. This structure attests to the generality of metalloinsertion and metallointercalation as DNA binding modes.

Crystal structure of Delta-[Ru(bpy)(2)dppz](2)(+) bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation.,Song H, Kaiser JT, Barton JK Nat Chem. 2012 Jun 10;4(8):615-20. doi: 10.1038/nchem.1375. PMID:22824892^[1]

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

References

↑ Song H, Kaiser JT, Barton JK. Crystal structure of Delta-[Ru(bpy)(2)dppz](2)(+) bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation. Nat Chem. 2012 Jun 10;4(8):615-20. doi: 10.1038/nchem.1375. PMID:22824892 doi:10.1038/nchem.1375

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OCA

[1] Song H, Kaiser JT, Barton JK. Crystal structure of Delta-[Ru(bpy)(2)dppz](2)(+) bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation. Nat Chem. 2012 Jun 10;4(8):615-20. doi: 10.1038/nchem.1375. PMID:22824892 doi:10.1038/nchem.1375

[1]

@@ Line 1: / Line 1: @@
 ==[Ru(bpy)2 dppz]2+ bound to DNA==
-<StructureSection load='4e1u' size='340' side='right' caption='[[4e1u]], [[Resolution|resolution]] 0.92&Aring;' scene=''>
+<StructureSection load='4e1u' size='340' side='right'caption='[[4e1u]], [[Resolution|resolution]] 0.92&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4e1u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E1U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4e1u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E1U FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=R1Z:DELTA-[RU(BPY)2DPPZ]2+'>R1Z</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.92&#8491;</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=4e1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e1u RCSB], [http://www.ebi.ac.uk/pdbsum/4e1u PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=R1Z:DELTA-[RU(BPY)2DPPZ]2+'>R1Z</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=4e1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e1u OCA], [https://pdbe.org/4e1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e1u RCSB], [https://www.ebi.ac.uk/pdbsum/4e1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e1u 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 4e1u" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Barton, J K]]
+[[Category: Large Structures]]
-[[Category: Kaiser, J T]]
+[[Category: Barton JK]]
-[[Category: Song, H]]
+[[Category: Kaiser JT]]
-[[Category: Dna]]
+[[Category: Song H]]
-[[Category: Mismatch]]
-[[Category: Small molecule]]

4e1u: Difference between revisions

Latest revision as of 10:49, 13 August 2026

[Ru(bpy)2 dppz]2+ bound to DNA

Structural highlights

Publication Abstract from PubMed

References

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