7ATG

Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution.

(2021) Acta Crystallogr B Struct Sci Cryst Eng Mater 77: 331-338

• PubMed: 34096514 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1107/S2052520621002663
• Primary Citation of Related Structures:  
  7ATG


• PubMed Abstract: 
  

  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 ⁺ .

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Organizational Affiliation: 

Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.