Zinc in PDB 7lbs: Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24, PDB code: 7lbs 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) 45.96 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.6, 145.94, 60.05, 90, 99.78, 90
R / Rfree (%) 20.2 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24 (pdb code 7lbs). 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 XR8-24, PDB code: 7lbs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7lbs

Go back to Zinc Binding Sites List in 7lbs
Zinc binding site 1 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24


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 XR8-24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:76.6
occ:1.00
SG A:CYS224 2.3 72.7 1.0
SG A:CYS192 2.3 66.1 1.0
SG A:CYS226 2.3 78.8 1.0
SG A:CYS189 2.4 74.9 1.0
CB A:CYS192 3.1 65.2 1.0
CB A:CYS189 3.3 62.3 1.0
CB A:CYS224 3.4 66.9 1.0
CB A:CYS226 3.8 78.0 1.0
N A:CYS192 3.9 61.8 1.0
CA A:CYS192 4.1 59.8 1.0
N A:CYS226 4.1 70.8 1.0
CA A:CYS226 4.5 75.7 1.0
N A:THR225 4.6 58.9 1.0
CA A:CYS224 4.7 62.7 1.0
CB A:THR191 4.7 61.1 1.0
CA A:CYS189 4.7 56.0 1.0
C A:CYS224 4.8 60.8 1.0
C A:THR191 4.9 63.9 1.0

Zinc binding site 2 out of 2 in 7lbs

Go back to Zinc Binding Sites List in 7lbs
Zinc binding site 2 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) Bound to Inhibitor XR8-24


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 XR8-24 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:105.3
occ:1.00
SG B:CYS192 2.4 70.2 1.0
SG B:CYS189 2.4 84.1 1.0
SG B:CYS224 2.4 98.3 1.0
CB B:CYS192 3.3 67.1 1.0
CB B:CYS189 3.4 70.3 1.0
CB B:CYS224 3.4 88.2 1.0
CB B:CYS226 4.0 96.4 1.0
SG B:CYS226 4.3 93.4 1.0
O B:LYS228 4.5 79.7 1.0
CA B:CYS192 4.6 63.6 1.0
N B:CYS192 4.6 66.0 1.0
N B:CYS226 4.6 102.9 1.0
CA B:CYS189 4.8 61.4 1.0
CA B:CYS224 4.8 85.3 1.0
CB B:ALA230 5.0 43.3 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 16:22:20 2021

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