Table 3.

Key residues around the active site, their analog residues across the X family, and suggested functions

pol μ	pol β	pol λ	pol X	Function in pol μ	Function in other polymerases
Asp330	Asp190	Asp427	Asp49	Coordinates with Mg2+ for chemical reaction	Coordinates with Mg2+ for chemical reaction
Asp332	Asp192	Asp429	Asp51	Coordinates with Mg2+ for chemical reaction	Coordinates with Mg2+ for chemical reaction
Asp420	Asp256	Asp490	Asp100	Coordinates with Mg2+ for chemical reaction	Coordinates with Mg2+ for chemical reaction
His329	Gly189	Gly426	Asn48	Flips to trigger the flip of Asp330
Gly435	Tyr271	Tyr505	His115		Contacts DNA bases, thereby correctly positioning the primer terminus for catalysis
Trp436	Phe272	Phe506	Phe116		Flips to initiate DNA or subdomain motion
Val422	Arg258	Ile492	Phe102		Interacts with other key residues to control their conformational change
Gln440	Asp276	Ala510	Val120	Participates in accommodating the incoming nucleotide	Weakens the binding affinity with the nucleotide (pol β)
Glu443	Asn279	Asn513	Leu123	Participate in accommodating the incoming nucleotide through water	Hydrogen-bonds to the nucleotide and is directly related to catalytic ability (pol β)
Arg444	Lys280	Arg514	Ile124	Stabilizes DNA in closed form by stacking with the template	First residue to respond to thumb motion (pol λ) stacks with template base in closed state
Arg447	Arg283	Arg517	Arg127	Stabilizes the DNA template and Loop 1 in closed form	Stabilizes DNA in closed form and helps check for correct basepairing
Arg448	Ala284	Ala518	Ala128	Stabilizes DNA to prevent insertion errors; stabilizes Loop 1 in closed form

^∗Residues in bold indicate motion detected in wild-type MD simulations.