Zinc in PDB 5lwd: Thermolysin in Complex with Inhibitor (JC96)

All present enzymatic activity of Thermolysin in Complex with Inhibitor (JC96):
3.4.24.27;

The structure of Thermolysin in Complex with Inhibitor (JC96), PDB code: 5lwd 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)	31.75 / 1.23
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.795, 92.795, 130.629, 90.00, 90.00, 120.00
R / Rfree (%)	10.4 / 12.3

The structure of Thermolysin in Complex with Inhibitor (JC96) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Thermolysin in Complex with Inhibitor (JC96) (pdb code 5lwd). 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 (JC96), PDB code: 5lwd:

Zinc binding site 1 out of 1 in the Thermolysin in Complex with Inhibitor (JC96)


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 (JC96) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:6.2 occ:1.00 OE2 E:GLU166 2.0 6.5 1.0 O2 E:79E411 2.0 6.2 1.0 NE2 E:HIS142 2.0 6.4 1.0 NE2 E:HIS146 2.0 5.8 1.0 CD E:GLU166 2.8 6.2 1.0 CE1 E:HIS146 2.9 6.3 1.0 OE1 E:GLU166 3.0 6.7 1.0 CE1 E:HIS142 3.0 6.2 1.0 CD2 E:HIS142 3.0 5.9 1.0 P E:79E411 3.0 6.1 1.0 HE1 E:HIS146 3.0 7.5 1.0 O1 E:79E411 3.1 7.0 1.0 HH E:TYR157 3.1 9.3 1.0 CD2 E:HIS146 3.1 5.8 1.0 HD2 E:HIS142 3.2 7.1 1.0 HE1 E:HIS142 3.2 7.5 1.0 HE2 E:HIS231 3.3 8.7 1.0 HD2 E:HIS146 3.4 7.0 1.0 OH E:TYR157 3.8 7.7 1.0 NE2 E:HIS231 4.0 7.2 1.0 HA E:GLU166 4.0 7.4 1.0 N1 E:79E411 4.0 6.6 1.0 HB2 E:SER169 4.1 7.5 1.0 ND1 E:HIS146 4.1 6.3 1.0 ND1 E:HIS142 4.1 6.2 1.0 C6 E:79E411 4.1 6.6 1.0 CG E:HIS142 4.2 5.9 1.0 CG E:HIS146 4.2 5.9 1.0 CG E:GLU166 4.2 6.3 1.0 HB3 E:SER169 4.2 7.5 1.0 HE1 E:TYR157 4.3 9.1 1.0 HD2 E:HIS231 4.4 8.7 1.0 HG2 E:GLU166 4.4 7.6 1.0 C11 E:79E411 4.4 8.0 1.0 CB E:SER169 4.5 6.3 1.0 CD2 E:HIS231 4.6 7.2 1.0 C5 E:79E411 4.6 6.6 1.0 C3 E:GOL409 4.6 12.9 1.0 N2 E:79E411 4.6 9.0 0.6 O E:79E411 4.7 7.4 1.0 OG E:SER169 4.7 6.3 1.0 N2 E:79E411 4.7 10.4 0.4 HG3 E:GLU166 4.8 7.6 1.0 OE1 E:GLU143 4.8 8.5 1.0 O3 E:GOL409 4.8 8.1 1.0 CZ E:TYR157 4.8 7.2 1.0 HD1 E:HIS146 4.8 7.6 1.0 HH12 E:ARG203 4.9 8.4 1.0 HD1 E:HIS142 4.9 7.4 1.0 CA E:GLU166 4.9 6.2 1.0 CE1 E:TYR157 4.9 7.5 1.0

J.Cramer, S.G.Krimmer, V.Fridh, T.Wulsdorf, R.Karlsson, A.Heine, G.Klebe. Elucidating the Origin of Long Residence Time Binding For Inhibitors of the Metalloprotease Thermolysin. Acs Chem. Biol. V. 12 225 2017.
ISSN: ESSN 1554-8937
PubMed: 27959500
DOI: 10.1021/ACSCHEMBIO.6B00979