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1dj6

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(New page: 200px<br /><applet load="1dj6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dj6, resolution 1.0&Aring;" /> '''COMPLEX OF A Z-DNA HE...)
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[[Image:1dj6.gif|left|200px]]<br /><applet load="1dj6" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dj6, resolution 1.0&Aring;" />
 
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'''COMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT ROOM TEMPERATURE'''<br />
 
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==Overview==
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==COMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT ROOM TEMPERATURE==
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The crystal structure of a left-handed Z-DNA hexamer, d(CG)(3) in complex, with a synthetic polyamine, N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine, NH(3)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(3)(+), [PA(222)], has been determined by the X-ray diffraction method at 1.0 A, resolution. In an orthorhombic crystal, the d(CG)(3) duplex binds two, PA(222) molecules, and this synthetic polyamine exhibits dual, conformational properties. One of the two PA(222) molecules resides on the, floor of the minor groove of a Z-DNA duplex and imino groups bridge the, two phosphate chains across a double helix, while the terminal amino, groups link the oxygen atoms O2 of four cytosine bases. This PA(222), molecule makes a U-turn like a fishhook at one of its ends to provide a, micro-environmental network previously unseen in complexes of DNA with, polyamines. The width of the minor groove does not become considerably, greater with the looped end of the polyamine, indicating conformational, rigidity of the Z-DNA backbone imposed by the high stacking energy of the, GC base pairs. While polyamine binding to the minor groove has been, postulated by theoretical studies for stabilizing the Z-DNA double helical, conformation, the finding in the crystal of the looped polyamine chain, binding the minor groove of Z-DNA is observed for the first time from the, data collected at 10 degrees C (so-called room temperature data). Another, PA(222) molecule binds on the convex outer surface of the major groove of, the Z-DNA duplex and links three d(CG)(3) duplexes which are symmetrically, related to each other. The structure of this PA(222) presents the, previously reported zig-zag type conformation [Egli et al., Biochemistry, 30 (1991) 11388-11402]. Comparison of this structure with other, polyamine-DNA cocrystals reveals structural themes and differences that, may relate to the length of the polyamine.
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<StructureSection load='1dj6' size='340' side='right'caption='[[1dj6]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1dj6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJ6 FirstGlance]. <br>
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1DJ6 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG and 104 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DJ6 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]] 1&#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=104:N,N-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE'>104</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1dj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj6 OCA], [https://pdbe.org/1dj6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dj6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dj6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dj6 ProSAT]</span></td></tr>
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The crystal structure of N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)(2), hexamer at room temperature., Ohishi H, Suzuki K, Ohtsuchi M, Hakoshima T, Rich A, FEBS Lett. 2002 Jul 17;523(1-3):29-34. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12123799 12123799]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Hakoshima, T.]]
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</StructureSection>
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[[Category: Nakanishi, I.]]
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[[Category: Large Structures]]
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[[Category: Ohishi, H.]]
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[[Category: Hakoshima T]]
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[[Category: Ohtsuchi, M.]]
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[[Category: Nakanishi I]]
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[[Category: Rich, A.]]
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[[Category: Ohishi H]]
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[[Category: Tomita, K.i.]]
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[[Category: Ohtsuchi M]]
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[[Category: 104]]
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[[Category: Rich A]]
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[[Category: MG]]
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[[Category: Tomita K-i]]
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[[Category: polyamine binding in minor groove of z-dna]]
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[[Category: x-ray crystal structure]]
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[[Category: z-dna:polyamine complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:11:07 2007''
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Current revision

COMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT ROOM TEMPERATURE

PDB ID 1dj6

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