A Z-DNA binding protein (ZBP)-containing protein kinase (PKZ) in fish species has an important role in the innate immune response. Previous structural studies of the Z alpha domain of the Pia from Carassius auratus (caZ alpha(PKZ)) showed that the protein initially binds to B-DNA and induces B-Z transition of double stranded DNA in a salt concentration-dependent manner. However, the significantly reduced B-Z transition activity of caZ alpha(PKZ) at high salt concentration was not fully understood. In this study, we present the binding affinity of the protein for B-DNA and Z-DNA and characterize its extremely low B-Z transition activity at 250 mM NaCI. Our results emphasize that the B-DNA-bound form of caZ alpha(PKZ) can be used as molecular ruler to measure the degree of B-Z transition. (C) 2016 Elsevier Inc. All rights reserved.