4HIF

Ultrahigh-resolution crystal structure of Z-DNA in complex with Zn2+ ions

Summary for 4HIF

• Entry DOI: 10.2210/pdb4hif/pdb
• Related: 1D39 1ICK 211D 3P4J 4HID
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), ZINC ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: self-complementary dna, dna, z-dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 3993.05

Authors

Drozdzal, P.,Gilski, M.,Kierzek, R.,Lomozik, L.,Jaskolski, M. (deposition date: 2012-10-11, release date: 2013-06-05, Last modification date: 2023-09-20)

Primary citation

Drozdzal, P.,Gilski, M.,Kierzek, R.,Lomozik, L.,Jaskolski, M.
Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.
Acta Crystallogr.,Sect.D, 69:1180-1190, 2013

PubMed Abstract: X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn(2+) complex. The Mn(2+) and Zn(2+) cations at the major site, designated M(2+)(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn(2+)(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn(2+)(1) and Zn(2+)(2) to the O6 atom of the guanine residues were 3.613 (6) and 3.258 (5) Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn(2+)(2). Alternate conformations were observed in the Z-DNA-Zn(2+) structure not only at internucleotide linkages but also at the terminal C3'-OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn(2+) complex is similar to the spermine(4+) conformation in analogous Z-DNA-Mg(2+) structures. In the Z-DNA-Zn(2+) complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn(2+) complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn(2+) structure it forms hydrogen bonds to both the phosphate groups and DNA bases.

PubMed: 23695262
DOI: 10.1107/S0907444913007798

Experimental method

X-RAY DIFFRACTION (0.85 Å)