328d

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[[Image:328d.jpg|left|200px]]
 
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{{Structure
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==STRUCTURE OF A D(CGCGAATTCGCG)2-SN7167 COMPLEX==
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|PDB= 328d |SIZE=350|CAPTION= <scene name='initialview01'>328d</scene>, resolution 2.600&Aring;
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<StructureSection load='328d' size='340' side='right'caption='[[328d]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SN7:4-[4-[2-AMINO-4-[4,6-(N-METHYLQUINOLINIUM)AMINO]BENZAMIDO]ANILINO]-N-METHYLPYRIDINIUM MESYLATE'>SN7</scene>
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<table><tr><td colspan='2'>[[328d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=328D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=328D FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.6&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SN7:4-[4-[2-AMINO-4-[4,6-(N-METHYLQUINOLINIUM)AMINO]BENZAMIDO]ANILINO]-N-METHYLPYRIDINIUM+MESYLATE'>SN7</scene></td></tr>
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}}
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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=328d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=328d OCA], [https://pdbe.org/328d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=328d RCSB], [https://www.ebi.ac.uk/pdbsum/328d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=328d ProSAT]</span></td></tr>
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</table>
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'''STRUCTURE OF A D(CGCGAATTCGCG)2-SN7167 COMPLEX'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Clark GR]]
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The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridinium ring extending as far as the C9-G16 base pair and the 1-methylquinolinium ring lying between the G4-C21 and A5-T20 base pairs. The ligand interacts only weakly with the DNA, as evidenced by long range contacts and shallow penetration into the groove. This structure is compared with that of the complex between the parent compound SN 6999 and the alkylated DNA sequence d(CGC[e6G]AATTCGCG)2. There are significant differences between the two structures in the extent of DNA bending, ligand conformation and groove binding.
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[[Category: Denny WA]]
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[[Category: Squire CJ]]
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==About this Structure==
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328D 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=328D OCA].
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==Reference==
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Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2., Squire CJ, Clark GR, Denny WA, Nucleic Acids Res. 1997 Oct 15;25(20):4072-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9321660 9321660]
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[[Category: Protein complex]]
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[[Category: Clark, G R.]]
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[[Category: Denny, W A.]]
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[[Category: Squire, C J.]]
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[[Category: SN7]]
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[[Category: b-dna]]
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[[Category: complexed with drug]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:54:39 2008''
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Current revision

STRUCTURE OF A D(CGCGAATTCGCG)2-SN7167 COMPLEX

PDB ID 328d

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