336d: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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>
</td></tr><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>
</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>
<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>
<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>
<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>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:8977125<ref>PMID:8977125</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 336d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Boom, J H.Van]]
[[Category: Hakoshima T]]
[[Category: Hakoshima, T]]
[[Category: Nakanishi I]]
[[Category: Marel, G Van Der]]
[[Category: Ohishi H]]
[[Category: Nakanishi, I]]
[[Category: Rich A]]
[[Category: Ohishi, H]]
[[Category: Terasoma N]]
[[Category: Rich, A]]
[[Category: Tomita K-I]]
[[Category: Terasoma, N]]
[[Category: Van Boom JH]]
[[Category: Tomita, K I]]
[[Category: Van Der Marel G]]
[[Category: Wang, A H.J]]
[[Category: Wang AH-J]]
[[Category: Dna]]
[[Category: Double helix]]
[[Category: Z-dna]]

Latest revision as of 08:39, 7 February 2024

INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX

336d, resolution 1.00Å

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