I wish I had more time tonight at least write a little bit about haem–copper oxidases, but it is late and I have other things to do. I may write about them as a separate post later.
I know a little bit about the preference that is mention in the title, and read some papers trying to explain the choice of copper (I remember a PNAS paper for example). Anyway, I think this paper finally explains the nature's choice without any doubt. Here they modified a haem–copper oxidase in myoglobin and were able to fully characterize a Cu, Fe and Zn bound haem–copper oxidase. The detailed studies show that copper is superior owing to its more electron rich character and higher reduction potential (activates O2 better). A fantastic paper by Yi Lu.