Fig. 2. In crystallo visualization of Pol η misincorporation with Mg²⁺.

a–c Structures of Pol η during in crystallo catalysis after 1 mM Mg²⁺ soaking for 40 s (a), 80 s (b), and 140 s (c). The 2F_o-F_c map for the primer up conformation (blue) was contoured at 1.2 σ. The 2F_o-F_c map for the Me²⁺_A, Me²⁺_B, dGTP, and catalytic residues (blue) was contoured at 2 σ in (a–c). The F_o-F_c omit map for the down conformation of the primer (green) was contoured at 3.3 σ in (a–c). The F_o-F_c omit map for all the Mg²⁺_C, and newly formed bond (red) was contoured at 4 σ. d Timescale of Mg²⁺_A, Mg²⁺_C binding and reaction product in crystallo with Mg²⁺. e, f Observation of the Mg²⁺_C after 1 mM Mg²⁺ soaking for 80 s (e) and 140 s (f). g Correlation (R²) between the newly formed bond and the Mg²⁺_C binding. d, g The data points represent singular measurements for r.m.s. density values of electron density. In (e, f), the 2F_o-F_c map for the water molecules that were coordinated by the Mg²⁺_C was contoured at 0.7 σ. The F_o-F_c omit map for the Mg²⁺_C, new bond, and Mg²⁺_A and Mg²⁺_B was contoured at 4 σ. h Alternative product state of Pol η in crystallo with 1 mM Mg²⁺ at 300 s. The 2F_o-F_c map was contoured at 1 σ.