7ATG

Crystal structure of Z-DNA in complex with putrescinium and potassium cations at ultrahigh-resolution

Summary for 7ATG

• Entry DOI: 10.2210/pdb7atg/pdb
• Related: 4HIF 4HIG 4R15
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), POTASSIUM ION, 4-azaniumylbutylazanium, ... (4 entities in total)
• Functional Keywords: z-dna, dna, dual-conformation backbone; putrescinium cation; biogenic polyamines; potassium complex
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 3749.67

Authors

Drozdzal, P.,Gilski, M.,Jaskolski, M. (deposition date: 2020-10-30, release date: 2021-08-11, Last modification date: 2024-01-31)

Primary citation

Drozdzal, P.,Gilski, M.,Jaskolski, M.
Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution.
Acta Crystallogr.,Sect.B, 77:331-338, 2021

PubMed Abstract: The X-ray crystal structure of the d(CGCGCG)/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 and Zn 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.

PubMed: 34096514
DOI: 10.1107/S2052520621002663

Experimental method

X-RAY DIFFRACTION (0.6 Å)