The enzyme is composed of two-component metalloproteins called the iron (Fe) protein (also called dinitrogenase reductase or component II) and the molybdenum-iron (MoFe) protein (also called dinitrogenase or component I) (Figure 1). The structures of the two nitrogenase component proteins (individually and in complex with each other), have been determined by X-ray crystallography (6–25). These structures have provided detailed models of the three metal clusters contained in nitrogenase. The reduction of N2 by nitrogenase involves a complex interplay between these two protein components, electrons, MgATP, and protons (26–30). Understanding the molecular details of this multi-step and multi-component system has proven to be challenging. This review summarizes recent progress in defining aspects of this complex system, while highlighting the many remaining challenges.