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Hypothesized interactions of serine recombinase active site residues with the scissile phosphodiester. A general base (B) deprotonates the nucleophilic hydroxyl group of the active site serine residue, and a general acid protonates the 3′-oxygen atom during strand cleavage. Negative charge on the phosphodiester non-bridging oxygens is balanced by the positively charged sidechains of arginine residues. Candidate Tn3 resolvase residues for these roles are indicated.
