Zinc in PDB 7sdr: Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor

Enzymatic activity of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor

All present enzymatic activity of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor, PDB code: 7sdr was solved by J.Osipiuk, C.Tesar, M.Endres, J.Wang, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.49 / 2.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.074, 112.605, 127.677, 90, 90, 90
R / Rfree (%) 17.3 / 21.2

Other elements in 7sdr:

The structure of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor (pdb code 7sdr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor, PDB code: 7sdr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7sdr

Go back to Zinc Binding Sites List in 7sdr
Zinc binding site 1 out of 3 in the Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:55.9
occ:1.00
SG A:CYS224 2.3 54.1 1.0
SG A:CYS189 2.3 56.8 1.0
SG A:CYS226 2.4 56.6 1.0
SG A:CYS192 2.4 54.5 1.0
CB A:CYS224 3.2 57.8 1.0
CB A:CYS226 3.3 58.4 1.0
CB A:CYS192 3.3 53.2 1.0
CB A:CYS189 3.4 54.6 1.0
N A:CYS192 3.8 56.4 1.0
CB A:THR191 4.1 63.2 1.0
CA A:CYS192 4.2 54.5 1.0
N A:CYS226 4.2 57.1 1.0
CA A:CYS226 4.3 60.2 1.0
O A:HOH665 4.6 45.0 1.0
CA A:CYS224 4.6 59.0 1.0
OG1 A:THR191 4.7 64.6 1.0
CG2 A:THR191 4.7 64.0 1.0
C A:THR191 4.8 57.9 1.0
CA A:CYS189 4.8 54.2 1.0
N A:THR225 4.9 58.5 1.0
CA A:THR191 4.9 60.0 1.0

Zinc binding site 2 out of 3 in 7sdr

Go back to Zinc Binding Sites List in 7sdr
Zinc binding site 2 out of 3 in the Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:128.0
occ:1.00
SG B:CYS189 2.3 110.3 1.0
SG B:CYS226 2.3 130.7 1.0
SG B:CYS192 2.4 121.3 1.0
SG B:CYS224 2.4 120.3 1.0
CB B:CYS226 3.3 128.2 1.0
CB B:CYS189 3.4 105.4 1.0
CB B:CYS224 3.4 114.9 1.0
CB B:CYS192 3.4 117.3 1.0
N B:CYS192 4.0 117.9 1.0
CB B:THR191 4.2 118.9 1.0
CA B:CYS192 4.4 115.8 1.0
CA B:CYS226 4.5 127.3 1.0
N B:CYS226 4.5 124.3 1.0
CA B:CYS189 4.8 101.0 1.0
OG1 B:THR191 4.8 116.3 1.0
CA B:CYS224 4.8 115.3 1.0
CB B:LYS228 4.9 124.8 1.0
CG2 B:THR191 4.9 119.6 1.0
C B:THR191 4.9 117.5 1.0

Zinc binding site 3 out of 3 in 7sdr

Go back to Zinc Binding Sites List in 7sdr
Zinc binding site 3 out of 3 in the Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:85.4
occ:1.00
SG C:CYS226 2.3 92.3 1.0
SG C:CYS192 2.4 92.6 1.0
SG C:CYS189 2.4 73.7 1.0
SG C:CYS224 2.4 82.9 1.0
CB C:CYS226 3.3 86.4 1.0
CB C:CYS192 3.3 94.9 1.0
CB C:CYS189 3.3 79.0 1.0
CB C:CYS224 3.4 83.2 1.0
N C:CYS226 4.0 77.6 1.0
N C:CYS192 4.0 95.2 1.0
CA C:CYS226 4.2 79.9 1.0
CA C:CYS192 4.3 94.0 1.0
CB C:THR191 4.6 103.4 1.0
CA C:CYS189 4.7 81.8 1.0
CA C:CYS224 4.8 80.6 1.0
N C:THR225 4.8 76.9 1.0
C C:CYS224 4.9 76.7 1.0
C C:CYS226 5.0 78.1 1.0

Reference:

J.Osipiuk, C.Tesar, M.Endres, J.Wang, A.Joachimiak. Papain-Like Protease of Sars Cov-2 in Complex with JUN9-72-2 Inhibitor To Be Published.
Page generated: Fri Nov 5 17:00:17 2021

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