Table 2.

Characteristic distances of residue pairs in the x-ray crystal structures and MD simulations of substrate-free and camphor-bound CYP101 for key salt-bridge, hydrogen-bonding, and hydrophobic interactions

Distance∗ (Å)	Camphor-bound		Substrate-free		Region(s) involved
	3L63 crystal	Simulation	3L61 crystal†	Simulation
Arg186-Asp182‡	4.56	4.56 ± 0.22	4.66	5.97 ± 1.85	F-helix, F/G loop
Arg186-Asp251‡	3.97	3.93 ± 0.07	5.63	4.44 ± 1.13	F-helix, I-helix
Arg186-Val396§	2.83	2.82 ± 0.12	9.78	6.84 ± 1.89	F-helix, β5 sheet
Asp97-Lys197‡	3.58	3.39 ± 0.55	—	4.18 ± 1.20	B′ helix, G-helix
Asp97-Tyr201§	2.83	3.25 ± 0.36	—	4.68 ± 1.94	B′ helix, G-helix
Ala95-Phe193¶	4.78	4.91 ± 0.30	—	5.86 ± 1.04	B′ helix, G-helix
Ser83-Asp104§	3.10	3.32 ± 0.88	—	9.87 ± 2.64	B/C loop
Phe87-Gln317§	2.87	2.88 ± 0.09	3.06	3.80 ± 1.76	B/C loop, β3 sheet
Arg90-Gly315§	2.91	5.58 ± 0.97	—	8.07 ± 1.48	B′ helix, β3 sheet
Arg90-Gln317§	3.37	3.60 ± 0.13	—	5.14 ± 1.12	B′ helix, β3 sheet

Distance fluctations are also given above in the simulations. Note that the individual hydrogen bonds are identified between Arg¹⁸⁶ (side chain) and Val³⁹⁶ (carbonyl oxygen), Asp⁹⁷ (side chain) and Tyr²⁰¹ (-OH group), Ser⁸³ (side chain) and Asp¹⁰⁴ (side chain), Phe⁸⁷ (carbonyl oxygen) and Gln³¹⁷ (side chain), Arg⁹⁰ (side chain) and Gly³¹⁵ (carbonyl oxygen), and Arg⁹⁰ (backbone nitrogen) and Gln³¹⁷ (side chain).

^∗The distance is calculated among the centers of the charged groups for ionic pairs (i.e., C_γ for Asp, C_δ for Glu, N_ζ for Lys, C_ζ for Arg, and N_δ or N_ε for doubly protonated His, whichever is closer to the negatively charged residue in the ionic pair), centers of side chains for hydrophobic interactions (i.e., C_β for Ala and C_γ for Phe), and donor-acceptor for hydrogen-bonding interactions.

^†Because residues 90–97 and 104 are missing in the 3L61 crystal structure, the corresponding distances are not given.

^‡Salt-bridge interactions.

^§Hydrogen-bonding interactions.

^¶Hydrophobic interactions.