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. 2010 Mar 31;38(14):4559–4569. doi: 10.1093/nar/gkq201

Figure 5.

Figure 5.

NTP loading and organization of the switch 2 domain in yeast RNAP II. (A) NTP loading. The left and right panel correspond to the NTP entry and addition configurations, respectively, and are based on the PDB 1R9T and 1R9S coordinates (8). The invariant Rpb1-R446 (light blue), the Rpb2-K979 and Rpb2-K987 of the basic loop (dark blue), and the Rpb1-K752 and Rpb2-R1020 of the funnel domain (orange and green) are shown as space-filled spheres. The red and magenta spheres denote the catalytic MgA and MgB, respectively. The incoming NTP is shown in yellow. Thin black lines indicate the last two nucleotides of the RNA transcript. A blue arrow symbolises the rotation of the NTP toward the 3′-OH end of the transcript. (B) View of the entry site showing the surface of the RNAP II molecule at the end of the secondary channel (NTP entry pore). Same colour code as above, with additional indication of the DFDGD MgA loop. (C) Switch 2 domain: the switch 2 motif (Rpb1327–351) is shown in magenta. Space-filled spheres denote positively charged residues. Crystallographic coordinates were taken from PDB 1R9T (8).