Fig. 3: 8-oxodGTP insertion opposite At.
From: Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide
a Active site of the 8-oxodGTP(syn):At(anti) ground state (GS) ternary complex (PDB id 7KT3). Side-chains that interact with the incoming nucleotide or metals are shown. Ca2+ atoms are shown as orange spheres. Protein side chains are in yellow stick representation, 8-oxodGTP is shown in green, DNA in cyan. Simulated annealing omit (Fo–Fc) density is shown as a green mesh contoured at 3.0 σ, carve radius 2.0 Å. b Top down close-up view of 8-oxodGTP(syn) interactions in the active site (PDB id 7KT3). Hydrogen bonding is shown with black dashes and distances (Å) are labeled. c Active site of the 8-oxodGTP(syn):At(anti) reaction state (RS) ternary complex (PDB id 7KT4) after a 30 min soak in a Mn2+-containing cryo solution. Arrows indicate bonds broken (substrate) and formed (product). Mn2+ atoms are purple spheres. d Active site of the product state of the 8-oxodGTP(syn):At(anti) insertion after 120 min of soak (PDB id 7KT5). Glycolate was modeled into the density vacated by PPi. Water molecules are displayed as blue spheres.
