Fig. 4.

Adjunct metal binding sites in the pol β active site. (A) The post-insertion product state of the pol β active site is shown following insertion of the incoming dNTP (DNA_n+1). The catalytic (M_c), nucleotide (M_n), and product (M_p) metal binding sites are shown as red circles with dashed lines to coordinating groups. Four M_p coordinating water molecules are in blue. Active site aspartic acid residues, the remaining bound pyrophosphate (PP_i) group, and a coordinating water molecule (blue) are indicated. The groups corresponding to Pα, Pβ, and Pγ of the inserted dNTP triphosphate are labeled for clarity. The M_c binding site has only five coordinating ligands due to the missing 3′-OH. This results in the catalytic Mg²⁺ vacating the active site and being replaced by a Na²⁺ for pol β. (B) The pre-insertion state of the pol β active site is shown with an incoming dNTP and a primer terminus with a 3′-OH (i.e., 2′-deoxyribose). The black arrow corresponds to deprotonation of the 3′-OH to Asp256. The green arrow indicates the resulting O3′ anion attack on Pα. The catalytic (M_c), nucleotide (M_n), and ground (M_g) metal binding sites are shown as red circles with dashed lines to coordinating groups. Active site aspartic acid residues and coordinating waters (blue) are shown.