Abstract
This review examines the occurrence and function of water inside the protein that contains the catalytic site of the enzyme nitrogenase. The requirement of 8 protons and 8 electrons to convert N(2) to NH(3) and the opposing acid-base character of reactant and product are unique in enzymology. The active site is an unprecedented iron sulfide cluster containing one heterometal, in Mo, V, and Fe isozymes. A key component supporting the complex chemical mechanism is water, which transports multiple exogenous protons, sequentially, and assists the egress of hydrophilic ammonia. Using high-resolution crystal structures of the nitrogenase isozymes and cryoEM data, I describe and classify all intraprotein water components. A singular property is the occurrence of extensive anhydrous domains that surround the reaction zone of the cofactor. This focuses attention on the proton supply chain, a river, along which protons are transferred by a Grotthuss mechanism from protein surface to cofactor. Another river, in an opposite direction, runs along the pathway for departing NH(3). I describe mechanisms for translocation of protons and of NH(3) and their use of water and homocitrate. Other water features buried in the proteins include a mechanistically significant single water molecule and featureless water pools.