Nitrogenase catalyzes the biological reduction of N 2 to ammonia (nitrogen fixation) as well as the reduction of a number of alternative substrates, including acetylene (HCϵCH) to ethylene (H 2 C؍CH 2 ). It is known that the metallocluster FeMo-cofactor located within the nitrogenase MoFe protein component provides the site of substrate reduction, but the exact site where substrates bind and are reduced on the FeMo-cofactor remains unknown. We have recently shown that the ␣-70 residue of the MoFe protein plays a significant role in defining substrate access to the active site; ␣-70 approaches one face of the FeMo-cofactor, and when valine is substituted by alanine at this position, the substituted nitrogenase is able to accommodate a reduction of the larger alkyne propargyl alcohol (HCϵCCH 2 OH, propargyl-OH). During this reduction, a substrate-derived intermediate can be trapped on the FeMo-cofactor resulting in an S ؍ 1/2 spin system with a novel electron paramagnetic resonance spectrum. In the present work, trapping of the propargyl-OH-derived or propargyl amine (HCϵCCH 2 NH 2 , propargyl-NH 2 )-derived intermediates is shown to be dependent on pH and the presence of histidine at position ␣-195. It is concluded that these catalytic intermediates are stabilized and thereby trapped by H-bonding interactions between either the -OH group or the -NH 3 ؉ group and the imidazole ⑀-NH of ␣-195 His . Thus, for the first time it is possible to establish the location of a bound substrate-derived intermediate on the FeMo-cofactor. Refinement of the binding mode and site was accomplished by the use of density functional and force field calculations pointing to an 2 coordination at Fe-6 of the FeMo-cofactor.Nitrogenase is comprised of two component proteins, called the iron protein and the MoFe protein, which together catalyze the nucleotide-dependent reduction of N 2 to ammonia (Equation 1). N 2 ϩ 8e Ϫ ϩ 16MgATP ϩ 8H ϩ 3 2NH 3 ϩ H 2 ϩ 16MgADP ϩ 16P i (Eq. 1) During catalysis, electrons are delivered one at a time from the iron protein to the MoFe protein in a reaction coupled to the hydrolysis of 2 eq of MgATP for each equivalent of electrons transferred (1, 2). The MoFe protein contains two metalloclusters called the P-cluster [8Fe-7S] and the FeMo-cofactor [7Fe-9S-Mo-X-homocitrate], where X is proposed to be nitrogen, carbon, or oxygen (3). The P-clusters are thought to mediate electron transfer from the iron protein to the FeMo-cofactor, which in turn provides the site for substrate binding and reduction. The structure of the FeMo-cofactor has been elucidated from the solution of x-ray structures of MoFe proteins (3-7), yet where and how substrates interact with the FeMocofactor is still unknown. Different models for where substrates bind to the FeMo-cofactor have been developed; they were built on evidence from model compounds, theoretical calculations, and kinetic and biophysical studies on the wildtype (WT) 1 and genetically altered MoFe proteins (8). Some models propose binding and reduction of substrates at th...