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Crystal structure of Z‐DNA in complex with the polyamine putrescine and potassium cations at ultra‐high resolution
Author(s) -
Drozdzal Pawel,
Gilski Miroslaw,
Jaskolski Mariusz
Publication year - 2021
Publication title -
acta crystallographica section b
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.604
H-Index - 33
ISSN - 2052-5206
DOI - 10.1107/s2052520621002663
Subject(s) - chemistry , crystallography , dication , hydrogen bond , stereochemistry , nucleobase , molecule , dna , guanine , crystal structure , cytosine , moiety , nucleotide , organic chemistry , biochemistry , gene
The X‐ray crystal structure of the d(CGCGCG) 2 /putrescine(2+)/K + complex has been determined at 0.60 Å resolution. Stereochemical restraints were used only for the putrescinium dication, and 23 bonds and 18 angles of the Z‐DNA nucleotides with dual conformation. The N atoms of the putrescine(2+) dication form three direct hydrogen bonds with the N7_G atoms of three different Z‐DNA molecules, plus three water‐mediated hydrogen bonds with cytosine, guanine and phosphate acceptors. A unique potassium cation was also unambiguously identified in the structure, albeit at a ∼0.5 occupation site shared with a water molecule, providing the first example of such a complex with Z‐DNA. The K + cation has coordination number of eight and an irregular coordination sphere, formed by four water molecules and four O atoms from two phosphate groups of the Z‐DNA, including ligands present at fractional occupancy. The structural disorder of the Z‐DNA duplex is manifested by the presence of alternate conformations along the DNA backbone. Comparison of the position and interactions of putrescine(2+) in the present structure with other ultra‐high‐resolution structures of Z‐DNA in complexes with Mn 2+ and Zn 2+ ions shows that the dicationic putrescinium moiety can effectively substitute these metal ions for stabilization of Z‐type DNA duplexes. Furthermore, this comparison also suggests that the spermine(4+) tetracation has a higher affinity for Z‐DNA than K + .