Biological nitrogen fixation can be represented by the following equation, in which two moles of ammonia are produced from one mole of nitrogen gas, at the expense of 16 moles of ATP and a supply of electrons and protons (hydrogen ions):

This reaction is performed exclusively by prokaryotes (the bacteria and related organisms), using an enzyme complex termed nitrogenase. This enzyme consists of two proteins - an iron protein and a molybdenum-iron protein (see picture). 

The reactions occur while N₂ is bound to the nitrogenase enzyme complex. The Fe protein is first reduced by electrons donated by ferredoxin. Then the reduced Fe protein binds ATP and reduces the molybdenum-iron protein, which donates electrons to N₂, producing HN=NH. In two further cycles of this process (each requiring electrons donated by ferredoxin) HN=NH is reduced to H₂N-NH₂, and this in turn is reduced to 2NH₃.

Depending on the type of microorganism, the reduced ferredoxin which supplies electrons for this process is generated by photosynthesis, respiration or fermentation.

Figure 2: Nitrogen fixation (http://opbs.okstate.edu/~Blair/Bioch4113/ 1999%20Student%20Presentations/ Jacobs%20Nitrogenase%20folder/sld005.htm)

This page was based on :

Charpy-Roubaud C., Charpy L., Larkum A.W. (2001) Atmospheric dinitrogen fixation by benthic communities of Tikehau Lagoon (Tuamotu Archipelago, French Polynesia) and its contribution to benthic primary production. Mar. Biol. 139: 991-997