293d
From Proteopedia
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|PDB= 293d |SIZE=350|CAPTION= <scene name='initialview01'>293d</scene>, resolution 1.000Å | |PDB= 293d |SIZE=350|CAPTION= <scene name='initialview01'>293d</scene>, resolution 1.000Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=293d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=293d OCA], [http://www.ebi.ac.uk/pdbsum/293d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=293d RCSB]</span> | ||
}} | }} | ||
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[[Category: Tomita, K.]] | [[Category: Tomita, K.]] | ||
[[Category: Wang, A H.J.]] | [[Category: Wang, A H.J.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: SPD]] | ||
[[Category: complexed with spermidine]] | [[Category: complexed with spermidine]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:46:01 2008'' |
Revision as of 22:46, 30 March 2008
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| , resolution 1.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX
Overview
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.
About this Structure
293D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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:8706905
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