Metal ions are necessary in the mechanism of action of nuclease enzymes, allowing the substrate and water molecules to be positioned correctly in the active site. The correct positioning of water molecules is necessary for the successful inline attack on the phosphate group in the nucleic acid. If the metal ion were not present, the catalytic process would not be able to occur, as the water would not be in the correct position.
A metal ion is used as it is able to coordinate with many different molecules simultaneously. The ability to coordinate with the enzyme, substrate, and water helps ensure all molecules are in the correct position to allow catalysis to occur. The metal ion also stabilises the intermediates formed.
Two metal ions may be present, with one supporting the formation of the OH- nucleophile, and the other interacting with the leaving oxyanion.
The stabilisation effect from the metal ions cannot be too high, otherwise it would not be possible for the product to leave the active site. This would prevent the enzyme from catalysing subsequent reactions.
Magnesium ions are typically found in nuclease enzymes, due to their common occurrence. However, manganese ions are also occasionally found (but in lower numbers due to lower concentrations of Mn).
Some nucleases have a third metal ion, however this is thought to have a structural role and not to be involved in catalysis. The other two metal ions have the same function as in nucleases with only 2 ions present.