293d: Difference between revisions

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[[Image:293d.gif|left|200px]]


{{Structure
==INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX==
|PDB= 293d |SIZE=350|CAPTION= <scene name='initialview01'>293d</scene>, resolution 1.000&Aring;
<StructureSection load='293d' size='340' side='right'caption='[[293d]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
<table><tr><td colspan='2'>[[293d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=293D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=293D FirstGlance]. <br>
|ACTIVITY=  
</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>
|GENE=  
<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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=293d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=293d OCA], [https://pdbe.org/293d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=293d RCSB], [https://www.ebi.ac.uk/pdbsum/293d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=293d ProSAT]</span></td></tr>
 
</table>
'''INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Hakoshima T]]
This paper deals with the crystal structure of d(CG)3-spermidine complex. The DNA fragment, d(CG)3, was crystallized with N-(2-amino-propyl)-1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many intermolecular contacts between d(CG)3 and spermidine, but the binding mode of spermidine to the d(CG)3 molecule is different from that of the d(CG)3 and N-(2-amino-ethyl)-1,4-diamino-butane [PA(24)] complex: a spermidine molecule bound to the d(CG)3 and its symmetrically related neighboring d(CG)3 molecules through the water molecules with hydrogen bonds, while one PA(24) molecule connected directly to one d(CG)3 molecule, but not to its neighboring d(CG)3 molecule. In the crystal, the d(CG)3 molecule was the left-handed Z-form, and three magnesium cations and a sodium cation were observed around the d(CG)3 moiety with different binding modes from the case of the d(CG)3-PA(24) complex.
[[Category: Inubushi K]]
 
[[Category: Nakanishi I]]
==About this Structure==
[[Category: Ohishi H]]
293D 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=293D OCA].  
[[Category: Rich A]]
 
[[Category: Tomita K]]
==Reference==
[[Category: Van Boom JH]]
Interaction between the left-handed Z-DNA and polyamine-2. The crystal structure of the d(CG)3 and spermidine complex., Ohishi H, Nakanishi I, Inubushi K, van der Marel G, van Boom JH, Rich A, Wang AH, Hakoshima T, Tomita K, FEBS Lett. 1996 Aug 5;391(1-2):153-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8706905 8706905]
[[Category: Van Der Marel GA]]
[[Category: Protein complex]]
[[Category: Wang AH-J]]
[[Category: Boom, J H.Van.]]
[[Category: Hakoshima, T.]]
[[Category: Inubushi, K.]]
[[Category: Marel, G A.Van Der.]]
[[Category: Nakanishi, I.]]
[[Category: Ohishi, H.]]
[[Category: Rich, A.]]
[[Category: Tomita, K.]]
[[Category: Wang, A H.J.]]
[[Category: MG]]
[[Category: NA]]
[[Category: SPD]]
[[Category: complexed with spermidine]]
[[Category: double helix]]
[[Category: z-dna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:43:45 2008''
Retrieved from "https://proteopedia.org/293d"