Skip to main content
. 2010 Aug 23;107(36):15745–15750. doi: 10.1073/pnas.1009898107

Fig. 1.

Fig. 1.

A schematic view of the locations of His1085 and Leu1081 in the RNA pol II active site. RNA is shown in red, template DNA in cyan, and the trigger loop in magenta. Three different protonation states for His1085 are investigated in our simulations: HIP (the protonated form); HID (one of the unprotonated forms with a hydrogen bonded to Nδ); and HIE (the other unprotonated form with a hydrogen bonded to Nε). An artificial state with an extra positive charge placed on Nε (HID+) is also studied in order to investigate the role of the charge–charge interactions for the stabilization of His1085 in the active site. Two single mutants (PHE and TYR) for His1085 and two single mutants (GLY and ALA) for Leu1081 are also studied. The nucleotide on the DNA template forming the base paring with GTP is eliminated (Abasic) in order to investigate the role of base-pairing interactions in stabilizing the active site configuration. Finally, the 3′ terminal base of the RNA is eliminated (Abasic 3′ RNA) to investigate the role of base stacking in stabilizing the active site configuration.