Figure 6 - full size

 

Figure 6.
Figure 6. Fork Loop 2-Downstream DNA Contact
(A) Comparison of the conformation of fork loop 2 in EC III with that in previous Pol II EC structures (PDB-codes 1Y1W (Kettenberger et al., 2004) and 2E2I (Wang et al., 2006).
(B) Interaction of the side chain of fork loop 2 Rpb2 residue R504 with the guanine base at position +4 of downstream DNA. The final 2F[o]-F[c] electron density is shown in blue, contoured at 0.7 σ.
(C) Interaction of regions in EC III that may be involved in pausing, including the frayed nucleotide, βDloopII, the bridge helix, fork loop 2, and downstream DNA.
(D) Multiple sequence alignment of fork loop 2 and surrounding Rpb2 residues from S. cerevisiae, H. sapiens, P. furiosus, E. coli, and T. thermophilus (CLUSTAL W). The conserved R504 from S. cerevisiae is highlighted in blue.

The above figure is reprinted by permission from Cell Press: Mol Cell (2009, 34, 710-721) copyright 2009.