We employed umbrella sampling molecular dynamics simulations in explicit water to study the binding of the Mg2+ cofactor to ribonuclease H (RNase H) from three different organisms. We show that the enzyme can differentiate between different Me-binding modes that are nearly equally stable by creating a free-energy barrier between a water-rich mode and a water-depleted mode. Through a comparison with the corresponding free-energy barrier in water, this effect is shown to emanate from the enzymes's three-dimensional architecture and its associated environment. Implications of these protein medium effects in RNase H function and in structure-based drug/molecular design are discussed.