Metal ions play an integral role in enzymatic reactions and about third of the enzyme mediated processes are controlled by metal ions. DNA polymerases that are critical for genome integrity and stability are assisted by divalent metal ions in carrying out their functions of repair or replication. In DNA repair, two magnesium ions are required at the active site of the repair enzymes, DNA polymerases. One metal ion is bound to the incoming nucleotide triphosphate (the nucleotide binding metal) whereas the second metal ion helps prepare the O3'  of the primer terminal for nucleophilic attach (the catalytic metal). The final event before the chemical step is speculated to be the occupation of the catalytic metal ion  at the catalytic metal site. We have carried out a series of molecular dynamics simulations to study the assembly of two divalent metal ions at the active site of the DNA polymerase beta. The results are discussed in terms of the ion hydration under various conditions.

Metal ion binding at the active site of DNA plymerases

248th National Meeting (2014)

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