Zinc in PDB 5dpf: Thermolysin in Complex with Inhibitor.

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

The structure of Thermolysin in Complex with Inhibitor., PDB code: 5dpf was solved by 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)	40.16 / 1.47
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.747, 92.747, 130.222, 90.00, 90.00, 120.00
R / Rfree (%)	11.9 / 15.2

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

Calcium

(Ca)

4 atoms

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

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


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. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:8.5 occ:1.00 O18 E:5H9401 1.9 8.2 1.0 OE2 E:GLU166 2.0 9.0 1.0 NE2 E:HIS142 2.0 8.8 1.0 NE2 E:HIS146 2.0 8.1 1.0 CD E:GLU166 2.8 9.1 1.0 CE1 E:HIS146 2.9 8.0 1.0 OE1 E:GLU166 3.0 9.2 1.0 CE1 E:HIS142 3.0 8.5 1.0 P12 E:5H9401 3.0 8.6 1.0 CD2 E:HIS142 3.0 7.9 1.0 HE1 E:HIS146 3.0 9.7 1.0 O19 E:5H9401 3.1 9.3 1.0 CD2 E:HIS146 3.1 8.5 1.0 HH E:TYR157 3.1 11.6 1.0 HE1 E:HIS142 3.2 10.2 1.0 HD2 E:HIS142 3.2 9.5 1.0 HE2 E:HIS231 3.3 11.1 1.0 HD2 E:HIS146 3.4 10.2 1.0 OH E:TYR157 3.8 9.7 1.0 NE2 E:HIS231 4.0 9.2 1.0 HA E:GLU166 4.0 9.9 1.0 N13 E:5H9401 4.0 8.3 1.0 HB2 E:SER169 4.1 10.5 1.0 ND1 E:HIS146 4.1 7.9 1.0 C14 E:5H9401 4.1 8.3 1.0 ND1 E:HIS142 4.1 8.6 1.0 CG E:HIS142 4.2 8.3 1.0 CG E:GLU166 4.2 8.6 1.0 CG E:HIS146 4.2 8.2 1.0 HB3 E:SER169 4.3 10.5 1.0 HE1 E:TYR157 4.4 10.8 1.0 HG2 E:GLU166 4.4 10.3 1.0 HD2 E:HIS231 4.4 12.1 1.0 C11 E:5H9401 4.5 11.6 1.0 CB E:SER169 4.5 8.7 1.0 CD2 E:HIS231 4.5 10.1 1.0 C3 E:GOL413 4.6 15.9 1.0 N10 E:5H9401 4.6 15.2 1.0 C15 E:5H9401 4.6 8.6 1.0 O24 E:5H9401 4.7 10.1 1.0 OG E:SER169 4.7 8.6 1.0 HG3 E:GLU166 4.7 10.3 1.0 O3 E:GOL413 4.8 10.4 1.0 OE1 E:GLU143 4.8 12.5 1.0 CZ E:TYR157 4.8 9.5 1.0 HD1 E:HIS146 4.8 9.4 1.0 HH22 E:ARG203 4.9 11.2 1.0 CA E:GLU166 4.9 8.3 1.0 HD1 E:HIS142 4.9 10.3 1.0 CE1 E:TYR157 4.9 9.0 1.0

S.G.Krimmer, G.Klebe. Thermodynamics of Protein-Ligand Interactions As A Reference For Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data. J. Comput. Aided Mol. Des. V. 29 867 2015.
ISSN: ISSN 1573-4951
PubMed: 26376645
DOI: 10.1007/S10822-015-9867-Y