Fig. 5: Active site dynamics.
From: Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide
a Base-pair hydrogen bonding is retained post-catalysis. Hydrogen bonding with the template base in the 960 min Mn2+ soaks of the 8-oxodGMP(syn):At(anti) (PDB id 7KT6), 8-oxodGMP(anti):Ct(anti) (PDB id 7KTD), dGMP(anti):Ct(anti) (PDB id 7KSV), and the dGMP(anti):At(syn) (PDB id 7KT2) product complexes are shown with black dashes and distances (Å) labeled. DNA is shown in cyan stick representation. Fo–Fc density (green mesh) shown is contoured at 3.0 σ, carve radius 2.0 Å. b Product metal supports catalysis at sub-physiological Mn2+ concentrations (PDB id 7KTI). Ground state Ca2+:8-oxodGTP(anti):Ct(anti) ternary complex crystals were soaked in a cryo solution containing 20 μM Mn2+ for 120 min. Full product formation has occurred. Anomalous map (purple mesh, contoured at 4 σ) displays density for Mnp. Distances between metal atoms are shown with dashes and distances (Å) are indicated.
