Chloroperoxidase (CPO) is the most versatile of the knownheme enzymes [1]. This enzyme has a manganese ions in its structure [2]. We have carried out molecular dynamics (MD) simulation studies on the removal of manganese(Mn2+) and studied its effect on the CPO. In this study protein secondary structure, root-mean-square deviation of atomic positions(RMSD), root mean square fluctuation (RMSF) and contact map were studied before and after the removal of manganese and corresponding graphs were drawn. The study of secondary structure of protein showed that with manganese removal, three of amino acids were rearranged in 3.1 Helix, and the percent of alpha helix, extended and isolated bridge in the protein secondary structure are decreased, while the percent of coil and turn are increased. The results of the RMSD diagram showed that the presence of manganese does not have a large impact on the on the stability of the tertiary structure of the CPO. The results of the RMSF diagram showed that the removal of manganese very effective on amino acid binding site and C-terminal.

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