Figure 5. Frayed Nucleotides Overlap the NTP, Closed Trigger
Loop, and the TFIIS Hairpin
(A) Frayed nucleotides overlap
the NTP bound to the insertion site (green cyan, taken from
bacterial Pol EC, PDB-code 2O5J [Vassylyev et al., 2007b]). Van
der Waals radii are represented by colored dots. All structures
were superimposed with their active site regions.
(B and C)
Frayed nucleotides overlap the closed trigger loop (cyan) at
residue F1084 (B, taken from the Pol II EC, PDB-code 2E2H [Wang
et al., 2006]) and/or at residue H1242 (C, bacterial Pol EC,
PDB-code 2O5J [Vassylyev et al., 2007b]).
nucleotides overlap the tip of the hairpin of the
cleavage-stimulatory factor TFIIS. The structures of EC III, EC
IV, and the Pol II-TFIIS complex (PDB-code 1PQV, [Kettenberger
et al., 2003]) were superimposed with their active center
regions. TFIIS is shown in orange. The canonical side view is
(E) Detailed view of the superposition in (D) around
the active site, revealing a potential clash of the TFIIS acidic
hairpin with the frayed nucleotides.