. Author manuscript; available in PMC: 2018 Apr 1.

Published in final edited form as: Biochim Biophys Acta. 2017 Feb 24;1860(4):482–490. doi: 10.1016/j.bbagrm.2017.02.008

Table 2.

Secondary pore binding states.

Superstate	MSM Macrostates	ΔG [kcal/mol]	Interacting residues	Mutants
E	2, 13, 29	−3.87	R766^B ^, R1020^B ^, K752^*	R1020A
G	8, 26, 33	−3.10	K752^, R619^, K518
T	6, 19, 24, 32	−2.44	R726^, H1085^	R726H/P, H1085¹
F	0, 3, 10–12, 16, 18, 20, 22, 27, 31, 36, 40	−3.65	K1290, K1300, R731, R720, K1286, R590, K620
H	5, 14, 21, 28, 30, 39	−2.84	R19^B, K601
Bulk	1, 4, 7, 9, 15, 17, 23, 25, 34, 35, 37, 38	0.0	N/A

Superstates of UTP in the secondary pore with free energies relative to bulk solvent, contributing MSM macrostates, and key interacting secondary pore residues. Mutants with known effects on RNA elongation or misincorporation rates are listed as well.

Superscripts indicate Pol II subunits

for Rpb2;

for Rpb8

: fully conserved.

many mutations are lethal, some have altered elongation rates and/or altered phenotypes in the context of double mutants [46, 47].