166d

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[[Image:166d.jpg|left|200px]]<br /><applet load="166d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="166d, resolution 2.200&Aring;" />
 
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'''DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2'''<br />
 
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==Overview==
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==DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2==
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The crystal structure of the complex of gamma-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. &amp; Neidle, S. (1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.
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<StructureSection load='166d' size='340' side='right'caption='[[166d]], [[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'>[[166d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=166D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=166D FirstGlance]. <br>
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166D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=PET:'>PET</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=166D 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=PET:1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE'>PET</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=166d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=166d OCA], [https://pdbe.org/166d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=166d RCSB], [https://www.ebi.ac.uk/pdbsum/166d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=166d ProSAT]</span></td></tr>
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Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition., Nunn CM, Jenkins TC, Neidle S, Eur J Biochem. 1994 Dec 15;226(3):953-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7813486 7813486]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Jenkins, T C.]]
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</StructureSection>
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[[Category: Neidle, S.]]
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[[Category: Large Structures]]
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[[Category: Nunn, C M.]]
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[[Category: Jenkins TC]]
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[[Category: PET]]
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[[Category: Neidle S]]
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[[Category: b-dna]]
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[[Category: Nunn CM]]
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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 11:38:39 2008''
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Current revision

DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2

PDB ID 166d

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