The monomer and dimer of the bacterium Serratia marcescens endonuclease (SMnase) are each catalytically active, and the two subunits of the dimer function independently of each other. Nature, however, chooses the dimer form instead of the monomer. In order to explain this, we performed molecular dynamics (MD) simulations of both model-built complexes of a subunit of SMnase and the dimer with DNA in aqueous solution, We estimated the electrostatic binding energy, analyzed the distribution and dynamics of water around the complexes, identified water clusters in the protein, and related the dynamics of water to the protein's function. We find that the dimer form has an electrostatic advantage over the monomer to associate with DNA. Although Mg2+ remains hexa-coordinated during the simulation, the binding pathway of DNA to Mg2+ changes from inner-sphere binding in the monomer to outer-sphere in the dimer, which may be more energetically favorable. In addition, two water clusters in the active site of each monomer and in the dimer complex were identified and localized in two regions, named the "stabilizing" and "working" regions. Water in the "working" region in the dimer complex has larger fluctuations than that in the monomer.