Zinc in PDB 5lvd: Thermolysin in Complex with Inhibitor (JC67)

All present enzymatic activity of Thermolysin in Complex with Inhibitor (JC67):
3.4.24.27;

The structure of Thermolysin in Complex with Inhibitor (JC67), PDB code: 5lvd was solved by S.G.Krimmer, J.Cramer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.24 / 1.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.846, 92.846, 130.426, 90.00, 90.00, 120.00
R / Rfree (%)	10.5 / 12.5

The structure of Thermolysin in Complex with Inhibitor (JC67) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Thermolysin in Complex with Inhibitor (JC67) (pdb code 5lvd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Thermolysin in Complex with Inhibitor (JC67), PDB code: 5lvd:

Zinc binding site 1 out of 1 in the Thermolysin in Complex with Inhibitor (JC67)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermolysin in Complex with Inhibitor (JC67) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:6.5 occ:1.00 OE2 E:GLU166 2.0 7.1 1.0 O19 E:79F410 2.0 6.8 1.0 NE2 E:HIS142 2.0 6.8 1.0 NE2 E:HIS146 2.0 6.4 1.0 CD E:GLU166 2.8 6.7 1.0 CE1 E:HIS146 2.9 6.6 1.0 OE1 E:GLU166 3.0 7.1 1.0 CE1 E:HIS142 3.0 6.4 1.0 CD2 E:HIS142 3.0 6.4 1.0 P18 E:79F410 3.0 6.7 1.0 HE1 E:HIS146 3.0 7.9 1.0 O20 E:79F410 3.1 7.4 1.0 CD2 E:HIS146 3.1 6.3 1.0 HH E:TYR157 3.1 10.0 1.0 HD2 E:HIS142 3.2 7.7 1.0 HE1 E:HIS142 3.2 7.7 1.0 HE2 E:HIS231 3.3 9.4 1.0 HD2 E:HIS146 3.4 7.5 1.0 OH E:TYR157 3.8 8.3 1.0 HA E:GLU166 4.0 7.7 1.0 NE2 E:HIS231 4.0 7.8 1.0 N21 E:79F410 4.1 7.4 1.0 HB2 E:SER169 4.1 8.2 1.0 ND1 E:HIS146 4.1 7.0 1.0 ND1 E:HIS142 4.1 6.5 1.0 C23 E:79F410 4.1 8.1 1.0 CG E:HIS142 4.1 6.5 1.0 CG E:HIS146 4.2 6.4 1.0 CG E:GLU166 4.2 6.9 1.0 HB3 E:SER169 4.2 8.2 1.0 HE1 E:TYR157 4.3 9.6 1.0 HD2 E:HIS231 4.4 9.3 1.0 HG2 E:GLU166 4.4 8.3 1.0 C17 E:79F410 4.4 9.0 1.0 N15 E:79F410 4.5 11.6 0.5 CB E:SER169 4.5 6.9 1.0 C1 E:GOL406 4.6 14.0 1.0 CD2 E:HIS231 4.6 7.8 1.0 OG E:SER169 4.7 6.9 1.0 C24 E:79F410 4.7 7.9 1.0 N15 E:79F410 4.7 10.3 0.5 O1 E:GOL406 4.7 8.9 1.0 HG3 E:GLU166 4.8 8.3 1.0 CZ E:TYR157 4.8 7.5 1.0 HD1 E:HIS146 4.8 8.3 1.0 OE1 E:GLU143 4.8 10.1 1.0 CA E:GLU166 4.9 6.4 1.0 HD1 E:HIS142 4.9 7.8 1.0 CE1 E:TYR157 4.9 8.0 1.0 HH12 E:ARG203 4.9 8.9 1.0 O45 E:79F410 5.0 9.1 1.0

S.G.Krimmer, J.Cramer, J.Schiebel, A.Heine, G.Klebe. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. J. Am. Chem. Soc. V. 139 10419 2017.
ISSN: ESSN 1520-5126
PubMed: 28696673
DOI: 10.1021/JACS.7B05028