336d | pdb_0000336d
INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX
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Overview
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.
About this Structure
336D is a Protein complex structure of sequences from [1] with TER and MG as ligands. Full crystallographic information is available from OCA.
Reference
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
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