336d: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:336d.gif|left|200px]]


{{Structure
==INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX==
|PDB= 336d |SIZE=350|CAPTION= <scene name='initialview01'>336d</scene>, resolution 1.000&Aring;
<StructureSection load='336d' size='340' side='right'caption='[[336d]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=TER:N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE'>TER</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
<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>
|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=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>
 
</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]]
336D 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=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: Protein complex]]
[[Category: Wang AH-J]]
[[Category: Boom, J H.Van.]]
[[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: MG]]
[[Category: TER]]
[[Category: double helix]]
[[Category: z-dna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:54:42 2008''

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

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=336d&oldid=4047370"