Zinc in PDB 7los: Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65, PDB code: 7los was solved by K.M.Ratia, R.Xiong, G.R.Thatcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.85 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.564, 146.184, 60.321, 90, 99.53, 90
R / Rfree (%) 20.9 / 29.3

Other elements in 7los:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65 (pdb code 7los). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65, PDB code: 7los:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7los

Go back to Zinc Binding Sites List in 7los
Zinc binding site 1 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:135.7
occ:1.00
SG A:CYS224 1.9 127.2 1.0
SG A:CYS189 2.3 102.6 1.0
SG A:CYS192 2.4 109.5 1.0
SG A:CYS226 2.6 150.5 1.0
CB A:CYS224 3.1 117.6 1.0
CB A:CYS192 3.5 100.5 1.0
CB A:CYS189 3.5 89.2 1.0
CB A:CYS226 3.6 132.3 1.0
N A:CYS226 4.2 127.7 1.0
O A:LYS228 4.2 90.8 1.0
CA A:CYS224 4.4 110.0 1.0
CA A:CYS226 4.5 126.1 1.0
N A:CYS192 4.5 95.7 1.0
N A:THR225 4.6 116.9 1.0
CA A:CYS192 4.6 93.6 1.0
C A:CYS224 4.7 116.0 1.0
CB A:THR191 4.8 103.9 1.0
CA A:CYS189 4.9 79.6 1.0
CB A:ALA230 4.9 72.2 1.0

Zinc binding site 2 out of 2 in 7los

Go back to Zinc Binding Sites List in 7los
Zinc binding site 2 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-65 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:92.2
occ:1.00
SG B:CYS189 2.3 91.5 1.0
SG B:CYS226 2.3 121.3 1.0
SG B:CYS224 2.3 86.4 1.0
SG B:CYS192 2.4 85.0 1.0
CB B:CYS189 3.2 82.1 1.0
CB B:CYS192 3.5 85.4 1.0
CB B:CYS224 3.7 85.2 1.0
CB B:CYS226 3.7 116.9 1.0
N B:CYS192 4.2 80.9 1.0
N B:CYS226 4.3 106.2 1.0
CA B:CYS192 4.5 82.3 1.0
CA B:CYS226 4.6 113.3 1.0
CB B:THR191 4.7 80.8 1.0
CA B:CYS189 4.7 76.0 1.0
N B:THR225 4.9 85.1 1.0
CA B:CYS224 4.9 84.1 1.0

Reference:

K.M.Ratia, R.Xiong, G.R.Thatcher. Potent, Novel Sars-Cov-2 Plpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures Biorxiv 2021.
Page generated: Wed Mar 3 16:22:15 2021

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