Zinc in PDB 5n3v: Thermolysin in Complex with Inhibitor JC292

All present enzymatic activity of Thermolysin in Complex with Inhibitor JC292:
3.4.24.27;

The structure of Thermolysin in Complex with Inhibitor JC292, PDB code: 5n3v was solved by J.Cramer, S.G.Krimmer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.14 / 1.12
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.694, 92.694, 130.154, 90.00, 90.00, 120.00
R / Rfree (%)	11.1 / 11.9

The structure of Thermolysin in Complex with Inhibitor JC292 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Thermolysin in Complex with Inhibitor JC292 (pdb code 5n3v). 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 JC292, PDB code: 5n3v:

Zinc binding site 1 out of 1 in the Thermolysin in Complex with Inhibitor JC292


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 JC292 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:5.8 occ:1.00 OE2 E:GLU166 2.0 6.0 1.0 O01 E:8L5406 2.0 6.0 1.0 NE2 E:HIS142 2.0 5.9 1.0 NE2 E:HIS146 2.0 5.7 1.0 CD E:GLU166 2.8 5.7 1.0 CE1 E:HIS146 2.9 5.8 1.0 O03 E:8L5406 2.9 6.4 1.0 P01 E:8L5406 3.0 6.0 1.0 OE1 E:GLU166 3.0 6.3 1.0 CE1 E:HIS142 3.0 5.5 1.0 CD2 E:HIS142 3.0 5.4 1.0 HE1 E:HIS146 3.0 7.0 1.0 CD2 E:HIS146 3.1 5.5 1.0 HH E:TYR157 3.2 8.7 1.0 HD2 E:HIS142 3.2 6.5 1.0 HE1 E:HIS142 3.2 6.6 1.0 HE2 E:HIS231 3.3 8.5 1.0 HD2 E:HIS146 3.4 6.6 1.0 H02 E:8L5406 3.4 8.5 1.0 OH E:TYR157 3.8 7.2 1.0 HA E:GLU166 4.0 7.3 1.0 NE2 E:HIS231 4.0 7.1 1.0 HB2 E:SER169 4.0 7.4 1.0 N01 E:8L5406 4.1 7.1 1.0 ND1 E:HIS146 4.1 6.0 1.0 C01 E:8L5406 4.1 7.1 1.0 ND1 E:HIS142 4.1 5.6 1.0 CG E:HIS142 4.2 5.7 1.0 CG E:HIS146 4.2 5.3 1.0 H20 E:8L5406 4.2 9.5 1.0 CG E:GLU166 4.2 6.1 1.0 HB3 E:SER169 4.2 7.4 1.0 HE1 E:TYR157 4.4 8.0 1.0 C08 E:8L5406 4.4 7.1 1.0 HG2 E:GLU166 4.4 7.3 1.0 HD2 E:HIS231 4.4 8.1 1.0 CB E:SER169 4.5 6.2 1.0 N04 E:8L5406 4.5 7.9 1.0 CD2 E:HIS231 4.6 6.7 1.0 C06 E:8L5406 4.6 7.2 1.0 H19 E:8L5406 4.6 8.5 1.0 OG E:SER169 4.7 6.2 1.0 O E:HOH678 4.7 7.5 1.0 O02 E:8L5406 4.7 7.5 1.0 HG3 E:GLU166 4.8 7.3 1.0 CZ E:TYR157 4.8 6.9 1.0 H08 E:8L5406 4.8 10.3 1.0 HD1 E:HIS146 4.8 7.1 1.0 HH12 E:ARG203 4.8 8.2 1.0 CA E:GLU166 4.9 6.0 1.0 H01 E:8L5406 4.9 8.6 1.0 OE1 E:GLU143 4.9 10.1 1.0 HD1 E:HIS142 4.9 6.7 1.0 CE1 E:TYR157 4.9 6.7 1.0

J.Cramer, S.G.Krimmer, A.Heine, G.Klebe. Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in A Series of Thermolysin Inhibitors. J. Med. Chem. V. 60 5791 2017.
ISSN: ISSN 1520-4804
PubMed: 28590130
DOI: 10.1021/ACS.JMEDCHEM.7B00490