Table 5.

Normalized number densities of hydrogen bond donors around the ligands in the ion binding sites of proteins listed in table 1.^†

Biomolecule	ηH-donor/ηw × 100 (rd ∈ (6,12])	ηH-donor/ηw × 100 (rd ∈ (0,6])	ηfree-H-donor/ηw × 100 (rd ∈ (0,6])
Pyruvate Kinase (1A49)	6.90	6.17	0.00
Chaperone (1HPM)	6.58	1.30	0.47
Lysozyme (1V7T)	8.07	1.63	0.00
Neurotransmitter Transporter (2A65)	4.84	2.22	0.26
Dialkylglycine Decarboxylase (2DKB)	2.65	0.52	0.26
Thrombokinase (2BOK)	2.95	0.98	0.33

^†The normalization factor η_w is the number density of bulk water. For a given binding site, individual number densities were first estimated for all of its ligands, and then averaged. These average number densities were computed for two different spherical sub-volumes around the ligand, one limited to a region within 6 Å from the ligand, while the other extending from 6 to 12 Å from the ligand. In the estimation of η_H-donor, hydrogenbond donors from all side chain residues were considered, including Arg, Lys, His, Cys, Tyr, Thr, Trp, Ser, Gln and Asn; while in the estimation of η_free-H-donor, only thosehydrogen bond donors were considered that were not engaged in other favorable interactions, including salt-bridges and hydrogen bonds.