The bacterial enzyme nitrogenase has the remarkable ability to catalyze the reduction of dinitrogen to ammonia to under physiological conditions. The mechanistic questions related to how nitrogenase overcomes the kinetic stability of the NN triple bond to fix dinitrogen under ambient conditions have intrigued chemists for the past century. We have applied a structure-based approach to examine how nitrogenase uses iron-sulfur metalloclusters and ATP-dependent electron transfer to reduce dinitrogen and other substrates. A puzzling feature of the nitrogenase mechanism has been how to reconcile the relative stability of the FeMo-cofactor with the reactivity towards dinitrogen. Our studies have established that binding of ligands to nitrogenase under turnover conditions can be accompanied by the distortions and rearrangements of the catalytic FeMo-cofactor; these rearrangements may provide clues how the active site is activated during the catalytic cycle. The complementary strengths of X-ray crystallography and electron microscopy are being used to illuminate the mechanistic foundations of this process.