Fig. 4: Ground state 8-oxo-rGTP(syn):At ternary complex.
From: Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair
a Active site of the Ca2+-bound pre-catalytic ground state 8-oxo-dGTP(syn):At ternary complex. Protein sidechains (yellow), DNA (cyan), and nucleotide (green) are shown in stick representation, Helix N is the yellow cartoon. Ca2+ atoms are the orange spheres, water molecules are blue spheres. Simulated annealing omit density (green mesh) is contoured at 3 σ. b Comparison of active site nucleotide interactions in the Ca2+-ground state 8-oxo-rGTP(syn):At (green and yellow) and 8-oxo-dGTP(syn):At (magenta) ternary complexes. Hydrogen bonding (Å) and key distances (Å) are shown with black and red dashes, respectively. Green spheres indicate (favorable) stabilizing interactions. The inset shows that the distance between O3´ and O2B is altered due to the rigid sugar pucker induced by the ribose (O2´) oxygen. c Mn2+-ground state 8-oxo-dGTP(syn):At ternary complex (15 min soak). An additional metal (MnD) coordinates Pγ, His329 and 3 water molecules. Black dashes show metal coordination.
