In this study, we explored the effects of magnesium (Mg²⁺) and manganese (Mn²⁺) ions on the structural and catalytic properties of human polymerase gamma using molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our findings reveal that the presence of Mn²⁺ leads to increased overall flexibility in the protein, accompanied by alterations in the secondary structures of specific regions. Additionally, differences in the dynamic behavior between the two systems suggest that Mn²⁺ impacts the enzyme's conformational landscape more significantly than Mg²⁺.