Zinc in PDB 7lbr: Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89, PDB code: 7lbr 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) 46.05 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.756, 145.871, 60.15, 90, 99.64, 90
R / Rfree (%) 19.6 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89 (pdb code 7lbr). 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 XR8-89, PDB code: 7lbr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7lbr

Go back to Zinc Binding Sites List in 7lbr
Zinc binding site 1 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89


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 XR8-89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:102.4
occ:1.00
SG A:CYS189 2.4 88.2 1.0
SG A:CYS224 2.4 102.7 1.0
SG A:CYS192 2.4 90.2 1.0
SG A:CYS226 2.4 123.3 1.0
CB A:CYS189 3.3 78.6 1.0
CB A:CYS224 3.4 101.8 1.0
CB A:CYS192 3.5 84.3 1.0
CB A:CYS226 3.6 115.9 1.0
N A:CYS192 4.1 83.3 1.0
N A:CYS226 4.2 117.8 1.0
CB A:THR191 4.4 89.4 1.0
CA A:CYS192 4.4 80.7 1.0
CA A:CYS226 4.5 118.1 1.0
CG2 A:THR191 4.5 86.8 1.0
CA A:CYS189 4.8 75.0 1.0
CA A:CYS224 4.8 100.7 1.0
CB A:LYS228 4.8 96.8 1.0
OG1 A:THR225 4.9 123.4 1.0
N A:THR225 4.9 116.7 1.0

Zinc binding site 2 out of 2 in 7lbr

Go back to Zinc Binding Sites List in 7lbr
Zinc binding site 2 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-89


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 XR8-89 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:80.9
occ:1.00
SG B:CYS189 2.3 74.2 1.0
SG B:CYS224 2.3 79.1 1.0
SG B:CYS226 2.3 99.9 1.0
SG B:CYS192 2.4 73.1 1.0
CB B:CYS189 3.3 67.8 1.0
CB B:CYS226 3.4 94.9 1.0
CB B:CYS224 3.4 79.9 1.0
CB B:CYS192 3.4 70.9 1.0
N B:CYS226 3.9 87.7 1.0
N B:CYS192 4.2 70.4 1.0
CA B:CYS226 4.2 93.7 1.0
CA B:CYS192 4.4 68.8 1.0
N B:THR225 4.7 77.9 1.0
CA B:CYS224 4.7 78.0 1.0
CA B:CYS189 4.7 65.3 1.0
C B:CYS224 4.8 80.7 1.0
CB B:THR191 4.8 78.1 1.0
O B:LYS228 5.0 88.7 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 16:22:19 2021

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