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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[[Image:303d.gif|left|200px]]
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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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{{Structure
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|PDB= 303d |SIZE=350|CAPTION= <scene name='initialview01'>303d</scene>, resolution 2.200&Aring;
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|SITE=
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|LIGAND= <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> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''META-HYDROXY ANALOGUE OF HOECHST 33258 ('HYDROXYL OUT' CONFORMATION) BOUND TO D(CGCGAATTCGCG)2'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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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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303D 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=303D OCA].
==Reference==
==Reference==
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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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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://www.ncbi.nlm.nih.gov/pubmed/9017011 9017011]
[[Category: Protein complex]]
[[Category: Protein complex]]
[[Category: Clark, G R.]]
[[Category: Clark, G R.]]
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[[Category: double helix]]
[[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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:54:20 2008''

Revision as of 16:54, 20 March 2008

Image:303d.gif


PDB ID 303d

Drag the structure with the mouse to rotate
, resolution 2.200Å
Ligands: and
Coordinates: save as pdb, mmCIF, xml



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


Overview

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.

About this Structure

303D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

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:9017011

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