Dynamics of the CTD are influenced by Zn binding. (A) Overlay of CTDs from the indicated cryo-EM structures showing close overlap of secondary structural elements from the symmetric, holo structures: SP1, SP3sym, and SP4sym. The CTD from SP3bent also matches the configuration from the holo state, which correlates with the presence of density at Zn site C (c.f., Fig. 7 G). (B) CTDs from SP2 and SP4bent (apo) are farther apart (14.5–16 Å between C_α atoms of Arg237 and Glu281) than those from SP3sym (12.2 Å) and SP3bent (11.1 Å), suggesting that Zn binding at site C has a stabilizing influence on this domain. (C) The distance between C_α atoms from Arg237 and Glu281 was used as a collective variable to monitor CTD dynamics during the MD simulations. Data from all three simulations are plotted for apo and holo states with distributions from KDE calculations shown on the right. Time series were averaged over 20-ns intervals, with the solid line showing the average and the error bands contain 95% of the data. These data indicate that there are larger fluctuations in the CTD for the apo state.