Modeling of molybdoenzymes began even before the knowledge of the three-dimensional structure of these enzymes. The theoretical and experimental knowledge on these enzymes is vast and newer investigation is regularly pursued to understand the electronic aspect of these proteins using computational means. The present review deals with some unique observation regarding the structure, function and reactivity of some models and native proteins in rationalizing the choice of diverse substrates in seemingly similar enzymes such as Nap (nitrate reductase) and Fdh (formate dehydrogenase) and the dual form of a specific substrate of an enzyme like trimethylamine N-oxide reductase (TAMOR) and providing the electronic reason for the inhibition in the oxypurinol-inhibited xanthine oxidase (XO).