Two novel P450 heme iron ligand sets were generated by directed mutagenesis of the flavocytochrome P450 BM3 heme domain. The A264H and A264K variants produce Cys-Fe-His and Cys-Fe-Lys axial ligand sets, which were validated structurally and characterized by spectroscopic analysis. Electron Paramagnetic Resonance (EPR) and Magnetic Circular Dichroism (MCD) provided fingerprints defining these P450 ligand sets. Near infrared (NIR) MCD spectra identified ferric low-spin charge transfer bands diagnostic of the novel ligands. For the A264K mutant, this is the first report of a Cys-Fe-Lys NIR MCD band. Crystal structure determination showed substrate-free A264H and A264K proteins crystallize in distinct conformations, observed previously in substrate-free (SF) and fatty acid-bound (SB) P450 forms, respectively. This, in turn, likely reflects the positioning of the I alpha helix section of the protein that is required for optimal configuration of the ligands to the heme iron. One of the monomers in the asymmetric unit of the A264H crystals was in a novel conformation with a more open substrate access route to the active site. The same species was isolated for the wild-type heme domain and represents a novel conformational state of BM3 (termed SF2). The “locking” of these distinct conformations is evident from the fact that the endogenous ligands cannot be displaced by substrate or exogenous ligands. The consequent reduction of heme domain conformational heterogeneity will be important in attempts to determine atomic structure of the full length, multidomain flavocytochrome, and thus to understand in atomic detail interactions between its heme and reductase domains.