263d: Difference between revisions

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[[Image:263d.jpg|left|200px]]<br /><applet load="263d" size="350" color="white" frame="true" align="right" spinBox="true"
caption="263d, resolution 2.200&Aring;" />
'''ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX'''<br />


==Overview==
==ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX==
The crystal structure is reported of a tris(benzimidazole) analogue of the minor-groove drug Hoechst 33258 bound to the sequence d(CGCAAATTTGCG)2. The structure has been refined to an R factor of 17.4% at a resolution of 2.2 A. The ligand covers approximately 7 1/2 base pairs, including the 5'-AAATTT central sequence. This has an exceptionally narrow minor-groove width, together with high propeller twists for individual base pairs. The ligand has a highly twisted structure, with an overall twist of 50 degrees between aromatic rings. All three benzimidazole subunits are in register with the DNA, and there is a symmetric group of six hydrogen bonds between ligand and A.T base-pair edges. By contrast, the ligand does not show an optimal isohelical fit to the DNA. The correct phasing of drug and DNA base pairs is ensured by a number of changes to the DNA such that the central 5'-AAATTT region is slightly unwound relative to the structures of other noncovalent minor-groove drug complexes.
<StructureSection load='263d' size='340' side='right'caption='[[263d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[263d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=263D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=263D FirstGlance]. <br>
263D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=TBZ:'>TBZ</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=263D OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TBZ:2-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5,2,5-TRI-BENZIMIDAZOLE'>TBZ</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=263d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=263d OCA], [https://pdbe.org/263d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=263d RCSB], [https://www.ebi.ac.uk/pdbsum/263d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=263d ProSAT]</span></td></tr>
Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex., Clark GR, Gray EJ, Neidle S, Li YH, Leupin W, Biochemistry. 1996 Oct 29;35(43):13745-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8901516 8901516]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Clark, G R.]]
</StructureSection>
[[Category: Gray, E J.]]
[[Category: Large Structures]]
[[Category: Leupin, W.]]
[[Category: Clark GR]]
[[Category: Li, Y H.]]
[[Category: Gray EJ]]
[[Category: Neidle, S.]]
[[Category: Leupin W]]
[[Category: TBZ]]
[[Category: Li Y-H]]
[[Category: b-dna]]
[[Category: Neidle S]]
[[Category: complexed with drug]]
[[Category: double helix]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:21:57 2008''

Latest revision as of 09:09, 14 February 2024

ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX

263d, resolution 2.20Å

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