Understanding non-reducible N in the mechanism of Mo-nitrogenase.

In my proposed mechanism of Mo-nitrogenase there are two roles for separate N molecules. One N diffuses into the reaction zone between Fe2 and Fe6 where a strategic gallery of H atoms can capture N to form the Fe-bound HNNH intermediate which is then progressively hydrogenated through intermediates containing HNNH, NH and NH entities and then two NH in sequence. The second N can be parked in an N-pocket about 3.

The mechanism of Mo-nitrogenase: from N capture to first release of NH.

Mo-nitrogenase hydrogenates N to NH. This report continues from the previous paper [I. Dance, , 2024, , 14193-14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N, forming a key intermediate with Fe-bound HNNH.

The activating capture of N at the active site of Mo-nitrogenase.

Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N first and then add H atoms, but rather captures N ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6.

What triggers the coupling of proton transfer and electron transfer at the active site of nitrogenase?

In converting N to NH the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an FeS reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein.

The binding of reducible N in the reaction domain of nitrogenase.

The binding of N to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH, but also has a separate role in promoting the N-dependent HD reaction (D + 2H + 2e → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N, directly towards the -coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I.