Table 3.

Geometrical parameters and estimation of protonation state after His-only unrestrained refinement. The PROPKA predicted pKa values for these histidine residues are also given in the last column. These pKa values denotes the transition of the His imidazole ring from doubly protonated, positively charged state to singly protonated neutral form. The grey boxes represent values of his1 or his2 between +1 and −1, and thus with low confidence in predicting the protonation states. For each structure, the first two (or one in some cases) represent the active site His residues and the last residue represents the 2nd coordination sphere His.

	Nδ1-Cε1 (X1) (Å)	Cε1-Nε2 (X2) (Å)	-Nδ1- (X3) (deg)	-Nε2- (X4) deg)	his1	his2	Protonated Group	Predicted pKa
LsAA9A_Ec_1
1	1.37	1.33	105.04	108.92	2.3922	−0.9368	Nε2	5.65
78	1.34	1.31	107.76	106.57	−0.3255	−0.2142	Nδ1	3.70
147	1.35	1.37	107.88	110.02	2.7804	0.9156	Nδ1 + Nε2	5.07
LsAA9A_Ec_2
1	1.36	1.33	105.33	107.53	1.5237	−1.3366	Nε2	5.53
78	1.33	1.37	110.10	106.26	−0.751	0.6228	Nδ1	3.49
147	1.34	1.43	107.53	107.20	2.1689	−0.808	Nε2	4.95
TaAA9A_A chain
86	1.39	1.33	105.37	105.03	−1.5224	−2.429	Nδ1	2.78
164	1.32	1.33	105.30	109.14	4.2605	−0.5908	Nε2	4.80
TaAA9A_B chain
86	1.40	1.31	104.16	106.83	−0.0649	−2.2506	Nδ1	2.83
164	1.31	1.33	106.09	107.37	2.7832	−0.8702	Nε2	4.82
5O2X
86	1.36	1.30	105.81	103.08	−2.6326	−2.7544	Nδ1	2.45
163	1.34	1.34	105.72	107.36	2.0476	−1.2072	Nε2	4.63
4EIR_A chain
84	1.35	1.30	107.34	106.85	−0.3731	−0.2926	Nδ1	2.21
157	1.30	1.32	106.39	108.31	3.5234	−0.225	Nε2	4.68
4EIR_B chain
84	1.33	1.32	108.83	105.27	−1.4691	−0.2002	Nδ1	2.24
157	1.31	1.33	106.17	107.73	3.0056	−0.6742	Nε2	4.67
5OPF
37	1.33	1.32	105.02	103.23	−0.5811	−3.1906	Nδ1	3.44
144	1.32	1.30	106.03	103.60	−0.8842	−2.3264	Nδ1	2.18
216	1.30	1.34	103.87	104.49	2.5444	−3.3622	Nε2	4.83
4QI8_A chain
1	1.36	1.28	105.25	110.2	2.8256	0.044	Nδ1 + Nε2	4.29
72	1.34	1.30	107.14	104.41	−1.7260	−1.4078	Nδ1	2.19
146	1.33	1.36	105.18	105.13	1.3833	−2.5462	Nε2	4.75
4QI8_B chain
1	1.37	1.32	106.58	107.07	−0.1551	−0.7906	Nδ1	4.23
72	1.36	1.32	107.96	105.84	−1.5996	−0.5128	Nδ1	2.11
146	1.32	1.32	105.02	106.52	2.2928	−1.7872	Nε2	4.64