In addition to the selectivity for deoxyNTPs imparted to the active site by the sterochemistry of amino acid residues that interact with the incoming nucleotide, the Mg++ ions in the active site probably play a key role is this process. The top molecule is Pol B complexed with a Mn++ ion instead of a Mg++ ion. This decreases the overall steric hindrance at the 2' carbon of the ribose, perhaps allowing for incorporation of a NTP instead of a dNTP. In a normal Pol B-Mg2+ ion complex (the bottom molecule), there is too much steric hinderance to allow for the 3C' OH on a ribonucleotide. In this way the metal ions coordinated in the active site of Pol B likely confer some selectivity between nucleotide substrates.

Pol B & Mn

 

Pol B & Mg

 

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