By using molecular dynamics (MD) simulations and crystallographic data for rat liver arginase, the substrate positions in the active sites of native and mutant forms of the enzyme, were compared and correlated with known kinetic consequences of mutations. The mutants compared were His 141Phe and His 141Asn. The simulations show that mutation His141Asn gives the greatest divergence from the atomic coordinates, when compared with the control native enzyme. The mutant Asp128Asn does not show a change in atomic coordinates in the substrate, in agreement with the concept that a change in the metal coordination is responsible for the loss of catalytic activity in this mutant. Results obtained agree with reported kinetic consequences of mutations in arginase.