Insights on copper coordination and reactivity of endonuclease EcoRI by ESR spectroscopy and modeling

The cleavage of DNA by restriction endonuclease EcoRI is catalyzed by metal ions such as Mg$^{2+}$. However, Cu$^{2+}$ does not catalyze the cleavage of DNA by EcoRI. In order to understand the functional difference between Cu$^{2+}$ and Mg$^{2+}$, coordination of Cu$^{2+}$ in the EcoRI--DNA complex was clarified by ESR and MD simulation. There are two Cu$^{2+}$ components in the specific EcoRI-DNA complex. Each component has one N atom from histidine imidazole and one oxygen atom from the phosphate backbone of DNA coordinate to Cu$^{2+}$ based on the ESR experimental results. MD simulation further confirmed that the N$\delta $ atom of His114 imidazole and one oxygen atom from the phosphate backbone of DNA coordinate to Cu$^{2+}$. Difference in the coordination of Cu$^{2+}$ and Mg$^{2+}$ explains their different functional behaviors.