. Author manuscript; available in PMC: 2017 Sep 1.

Published in final edited form as: Biochim Biophys Acta. 2016 Jun 16;1857(9):1594–1606. doi: 10.1016/j.bbabio.2016.06.005

Table 1.

Molecular dynamics simulations performed in this work. Protonation state D is the lowest energy protonation state for the investigated true peroxo state of CcO (state 6 in the catalytic cycle of Ref [45]; hydroperoxo-bridged DNC with Fe_a3³⁺, Cu_B²⁺, Fe_b²⁺, Cu_A⁺-Cu_A⁺). See also Figure 1.

Simulation No.	Protonation states
Simulation No.	PRAa₃ protonated	Asp372 protonated	His376 protonated^a	Glu126^II protonated
A	no	yes	ε	no
B	yes	no	ε	no
C	yes	yes	ε	no
D	no	yes	ε,δ	no
E	no	yes	δ	yes
F	no	yes	δ	no

^a:

ε=epsilon-protonated histidine; δ=delta-protonated histidine; ε,δ=doubly protonated histidine.