336d: Difference between revisions

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[[Image:336d.gif|left|200px]]


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==INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX==
The line below this paragraph, containing "STRUCTURE_336d", creates the "Structure Box" on the page.
<StructureSection load='336d' size='340' side='right'caption='[[336d]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[336d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=336D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=336D FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TER:N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE'>TER</scene></td></tr>
{{STRUCTURE_336d|  PDB=336d  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=336d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=336d OCA], [https://pdbe.org/336d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=336d RCSB], [https://www.ebi.ac.uk/pdbsum/336d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=336d ProSAT]</span></td></tr>
 
</table>
'''INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Hakoshima T]]
The DNA fragment, d(CG)3, was co-crystallized with N-(3-amino-propyl)-N-(5-aminopropyl)-l,4 -diaminobutane (thermospermine; PA(334)), a polyamine metabolized from the nucleic acid. By using a good crystal with dimensions of 0.5 x 0.5 x 0.5 mm3, X-ray intensity data were collected up to 1.0 A resolution. Two thermospermine molecules and a magnesium cation were bound to the left-handed double-helical d(CG)3 molecule. The d(CG)3 molecule adopted the left-handed Z-conformation and two thermospermine molecules and a magnesium cation neutralized the negative charges of the phosphate groups of the d(CG)3 molecule. Furthermore, the binding modes between d(CG)3 and thermospermine were different from those of d(CG)3 complexes with PA(24), spermidine and spermine. This is the first case in which it was determined by X-ray crystallographic analysis that one of two thermospermine molecules bound three d(CG)3 duplexes which were symmetrically related to each other, and the other formed two hydrogen bonds at the N(5) and N(9) atoms with two adjacent nucleotide phosphate groups of a single d(CG)3 strand at the minor groove. Furthermore, no direct coordination bond was found between the d(CG)3 molecule and the magnesium cation.
[[Category: Nakanishi I]]
 
[[Category: Ohishi H]]
==About this Structure==
[[Category: Rich A]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=336D OCA].  
[[Category: Terasoma N]]
 
[[Category: Tomita K-I]]
==Reference==
[[Category: Van Boom JH]]
Interaction between left-handed Z-DNA and polyamine - 3. The crystal structure of the d(CG)3 and thermospermine complex., Ohishi H, Terasoma N, Nakanishi I, van der Marel G, van Boom JH, Rich A, Wang AH, Hakoshima T, Tomita K, FEBS Lett. 1996 Dec 2;398(2-3):291-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8977125 8977125]
[[Category: Van Der Marel G]]
[[Category: Boom, J H.Van.]]
[[Category: Wang AH-J]]
[[Category: Hakoshima, T.]]
[[Category: Marel, G Van Der.]]
[[Category: Nakanishi, I.]]
[[Category: Ohishi, H.]]
[[Category: Rich, A.]]
[[Category: Terasoma, N.]]
[[Category: Tomita, K I.]]
[[Category: Wang, A H.J.]]
[[Category: Double helix]]
[[Category: Z-dna]]
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Retrieved from "https://proteopedia.org/336d"