FIGURE 3.

Z-DNA binding modes of viral Zα domains from ORF112 (Cyprinid herpesvirus 3) and E3L (Yaba-like disease virus). a, binding interface between CyHV-3 ORF112-Zα and a reconstructed Z-DNA 7-bp duplex. The protein is represented as a light blue cartoon and with ball and stick key residues (wheat color) involved in the interaction with Z-DNA. Phosphate backbone and sugars are colored in red, and bases are in gray. Waters are depicted as the blue spheres. b, Z-DNA recognition by Yaba-like disease virus E3L-Zα (6 bp, PDB code 1SFU). The protein is shown as green cartoon; all other depictions are represented as in a. c and d, schematic representation of the interactions between ORF112-Zα (c) and Yaba-like disease virus E3L-Zα (d) with Z-DNA. The phosphate backbone and sugars are depicted in red, and bases are in gray. Direct hydrogen bonds are represented as black dashed lines, and water-mediated bonds shown as light blue dashed lines. Nonbonded contacts are drawn as solid light gray lines. The characteristic CH-π interaction between tyrosine and guanosine in syn conformation is shown as dotted black line. Blue ovals represent water molecules. e, close view of Arg-258A and Tyr-257B interactions with G4 (green) in syn conformation. The dotted lines indicate hydrogen bonds, whereas the filled line distinguishes the CH-π-bond of Tyr-257 to the G4 ring.