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303d

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[[Image:303d.gif|left|200px]]<br /><applet load="303d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="303d, resolution 2.200&Aring;" />
 
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'''META-HYDROXY ANALOGUE OF HOECHST 33258 ('HYDROXYL OUT' CONFORMATION) BOUND TO D(CGCGAATTCGCG)2'''<br />
 
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==Overview==
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==META-HYDROXY ANALOGUE OF HOECHST 33258 ('HYDROXYL OUT' CONFORMATION) BOUND TO D(CGCGAATTCGCG)2==
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An analogue of the DNA binding compound Hoechst 33258, which has the para hydroxyl group altered to be at the meta position, together with the replacement of one benzimidazole group by pyridylimidazole, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The X-ray structure has been determined at 2.2 A resolution and refined to an R factor of 20.1%. The ligand binds in the minor groove at the sequence 5'-AATTC with the bulky piperazine group extending over the CxG base pair. This binding is stabilised by hydrogen bonding and numerous close van der Waals contacts to the surface of the groove walls. The meta-hydroxyl group was found in two distinct orientations, neither of which participates in direct hydrogen bonds to the exocyclic amino group of a guanine base. The conformation of the drug differs from that found previously in other X-ray structures of Hoechst 33258-DNA complexes. There is significant variation between the minor groove widths in the complexes of Hoechst 33258 and the meta-hydroxyl derivative as a result of these conformational differences. Reasons are discussed for the inability of this derivative to actively recognise guanine.
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<StructureSection load='303d' size='340' side='right'caption='[[303d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[303d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=303D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=303D FirstGlance]. <br>
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303D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=RO2:'>RO2</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=303D OCA].
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RO2:3-[5-[5-(4-METHYL-PIPERAZIN-1-YL)-1H-IMIDAZO[4,5-B]PYRIDIN-2-YL]-BENZIMIDAZOL-2-YL]-PHENOL'>RO2</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=303d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=303d OCA], [https://pdbe.org/303d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=303d RCSB], [https://www.ebi.ac.uk/pdbsum/303d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=303d ProSAT]</span></td></tr>
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Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2., Clark GR, Squire CJ, Gray EJ, Leupin W, Neidle S, Nucleic Acids Res. 1996 Dec 15;24(24):4882-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9017011 9017011]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Clark, G R.]]
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</StructureSection>
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[[Category: Gray, E J.]]
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[[Category: Large Structures]]
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[[Category: Leupin, W.]]
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[[Category: Clark GR]]
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[[Category: Neidle, S.]]
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[[Category: Gray EJ]]
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[[Category: Squire, C J.]]
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[[Category: Leupin W]]
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[[Category: MG]]
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[[Category: Neidle S]]
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[[Category: RO2]]
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[[Category: Squire CJ]]
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[[Category: b-dna]]
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[[Category: complexed with drug]]
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[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:01:47 2008''
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Current revision

META-HYDROXY ANALOGUE OF HOECHST 33258 ('HYDROXYL OUT' CONFORMATION) BOUND TO D(CGCGAATTCGCG)2

PDB ID 303d

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