The reactions catalyzed by Pol with either of the ions are exoergic, with the system with Mn 2+ ion having a lower reaction energy ( E = -3.6 kcal/mol) as compared to the system with Mg 2+ (E= -1.6 kcal/mol). The energy barrier for the system with Mn 2+ ions is also lower (16.8 kcal/mol) than that of the system with Mg 2+ ions (18.0 kcal/mol). Both the systems have a pentacovalent phosphorane structure in the transtition state with the O3' … P … O3 angle being 170.36 for Mn 2+ ions and 169.24 for Mg 2+ ions, which are favorable angles for SN2 intermediate during the nucleotydil transfer. The calculated barriers are consistent with experimental results , where it was seen that in the kpol for catalytic pol A in presence of Mg 2+ ion with correct dTTP incorporation is around 3.5 s -1 . Using the formula for the pre-steady state kinetic studies for the incorporation of a single nucleotide via transition state formula ( 𝑘 𝑝𝑜𝑙 = 𝑘 𝑏 𝑇 ℎ 𝑒 -𝐺 ‡ 𝑅𝑇 ), the experimental energy barrier was found to be around 16.7 kcal/mol. EDA was also performed on the QM/MM optimized reactant, transition state and product structures to analyze the effects of the protein environment on the reaction path. When comparing the interactions in the R -> TS pathway, it is seen that 𝐸 𝑁𝐵 𝑇𝑆-𝑅𝑒𝑎𝑐𝑡𝑎𝑛𝑡 values for the system with Mn 2+ ions is -46.0 kcal/mol whereas for the system with Mg 2+ ions is -23.1 kcal/mol . This suggests that the protein environment stabilizes the active site in the transition state of both the systems, with the system with Mn 2+ ions having higher relative stabilization from the protein environment, which explains the lower energy barrier.