Two metal ions in the catalytic domain of polymerases facilitate the forming of phosphosdiester bond

 Nucleic acid polymerases possess two metal ions such as Mg2⁺ or Mn2⁺ in their catalytic domain. One metal ion binds the 3'OH of the elongating primer terminus. The other metal ion binds the phosphates of the incoming nucleotide and positions and stabilizes it. The binding of the first metal with 3'OH facilitates a nucleophilic attack of 3'O^- on the α phosphate of the incoming nucleotide. The nucleophilic attack means the transfer of an electron containing molecule from a donor to an acceptor, which results in the forming of covalent bond between these two molecules. The 3'OH of the primer terminus (donor) attacks the α phosphate of the incoming nucleotide (acceptor), and a new phosphodiester bond between these two is formed with a release of pyrophosphate.