Transition metal ions are an indispensable component of numerous cellular processes of living organisms. However, excessive cellular concentration of metal ions can be toxic to the cell, so sensitive mechanisms of regulation of their cellular concentration are necessary. The MntR protein is a transcription factor that participates in the mechanism of regulation of the cellular concentration of manganese(II) ions in the bacterium Halalkalibacterium halodurans. In the solution, it is present as a homodimer which, by binding two manganese(II) ions, is activated to bind to DNA and prevents the transcription of genes for the intake of manganese(II) ions. Molecular dynamics (MD) simulations were used to investigate the differences in the structural and dynamic properties of the MntR protein in the apoprotein (without bound manganese(II) ions) and holoprotein (with bound manganese(II) ions) form. The analysis of MD simulations identified conformational features that facilitate the binding of the holoprotein in two adjacent large grooves of the DNA molecule. Noncovalent interactions were found that potentially play an important role in the molecular mechanism that leads to an increase in the affinity of the MntR protein to DNA due to the binding of manganese(II) ions. The simulation results suggest that the presence of manganese(II) ions in the binding site of the protein leads to the replacement of the hydrogen bond between Arg72 and Asp111 with a cation–π interaction between Arg72 and Trp107, which is reflected in the bending of the α4 helix and the distance between the DNA binding domains. The computational results were compared with experimental data available in the literature