Table 2.

C2 model systems and their simulation lengths

Model system	CuA	Heme a	BNC*	His413	Asp51	Glu242	Tyr244	Lys319	Asp364	No. of replica and simulation lengths, ns
C2-I	RED	OX	PM	D (0)	D (−1)	P (0)	D (0)	P (+1)	P (0)	2 × 200
C2-II	OX	RED	PM	D (0)	D (−1)	P (0)	D (0)	P (+1)	P (0)	2 × 200
C2-III	OX	OX	PR	D (0)	D (−1)	P (0)	D (−1)	P (+1)	P (0)	1 × 200
C2-IV	OX	RED	PM	P (+1)	D (−1)	P (0)	D (0)	P (+1)	P (0)	1 × 200
C2-V	RED	OX	PM	P (+1)	D (−1)	P (0)	D (0)	P (+1)	P (0)	1 × 100
C2-VI	RED	OX	PM	D (0)	P (0)	P (0)	D (0)	P (+1)	P (0)	1 × 100
C2-VII (MV)†	OX	OX	RED	D (0)	D (−1)	P (0)	P (0)	P (+1)	P (0)	2 × 200
C2-VIII (FR)‡	RED	RED	RED	D (0)	D (−1)	P (0)	P (0)	P (+1)	P (0)	2 × 200

Protonation state changes of key amino acid residues (D, deprotonated; P, protonated; net charge in parentheses) compared with C2-I/II/III simulations are highlighted in bold. Configurations of the BNC in different states are defined in the footnotes. MV, mixed valence; OX, oxidized; RED, reduced.

^*BNC had chemical structures of: P_M, Fe[IV] = O²⁻....HO⁻-Cu[II] TyrO^•; P_R, Fe[IV] = O²⁻....HO⁻-Cu[II] TyrO⁻; RED, Fe[II]……..Cu[I] TyrOH.

^†BNC reduced with Cu_A/heme a oxidized.

^‡BNC reduced with Cu_A/heme a reduced.