Zinc in PDB 8uuv: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197, PDB code: 8uuv was solved by A.Ansari, B.Tan, E.Arnold, F.X.Ruiz, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.05 / 3.01
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.212, 114.212, 218.533, 90, 90, 90
R / Rfree (%) 20.2 / 22.4

Other elements in 8uuv:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197 (pdb code 8uuv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197, PDB code: 8uuv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8uuv

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Zinc binding site 1 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197


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) with Inhibitor JUN12197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:155.5
occ:1.00
 ND1 A:HIS89 2.3 74.0 1.0
ZN A:ZN404 2.3 82.9 1.0
O A:HOH551 2.5 49.2 1.0
NZ A:LYS92 2.7 99.8 1.0
CE1 A:HIS89 2.9 78.6 1.0
CE A:LYS92 3.1 97.6 1.0
CG A:HIS89 3.4 68.2 1.0
NE2 A:HIS89 4.0 58.3 1.0
CB A:HIS89 4.0 74.3 1.0
CA A:HIS89 4.1 61.8 1.0
OD2 A:ASP108 4.3 67.1 1.0
CD2 A:HIS89 4.3 62.1 1.0
O A:HOH508 4.5 80.0 1.0
CD A:LYS92 4.6 90.4 1.0
O A:ASN88 4.8 66.7 1.0
N A:HIS89 4.9 54.6 1.0

Zinc binding site 2 out of 6 in 8uuv

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Zinc binding site 2 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197


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) with Inhibitor JUN12197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:55.8
occ:1.00
 ND1 A:HIS73 2.3 42.8 1.0
CL A:CL410 2.3 66.2 1.0
CL A:CL409 2.3 66.8 1.0
CG A:HIS73 3.1 46.9 1.0
CB A:HIS73 3.2 47.3 1.0
CE1 A:HIS73 3.4 53.7 1.0
CB A:ASN128 4.1 48.9 1.0
CD2 A:HIS73 4.3 57.2 1.0
NE2 A:HIS73 4.4 72.5 1.0
CA A:HIS73 4.6 51.2 1.0
O A:HIS73 4.6 56.4 1.0
CG A:PRO129 4.7 51.0 1.0
CD A:PRO129 4.7 50.2 1.0
N A:PRO129 4.9 60.6 1.0

Zinc binding site 3 out of 6 in 8uuv

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Zinc binding site 3 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:82.9
occ:1.00
 OD2 A:ASP108 2.0 67.1 1.0
ND1 A:HIS89 2.3 74.0 1.0
ZN A:ZN402 2.3 155.5 1.0
O A:HOH551 2.4 49.2 1.0
CE1 A:HIS89 3.1 78.6 1.0
CG A:ASP108 3.2 61.7 1.0
O A:HOH508 3.2 80.0 1.0
CG A:HIS89 3.3 68.2 1.0
CB A:HIS89 3.7 74.3 1.0
OD1 A:ASP108 3.7 71.5 1.0
CG1 A:VAL159 4.2 63.3 1.0
NE2 A:HIS89 4.2 58.3 1.0
NE1 A:TRP93 4.3 57.6 1.0
CD2 A:HIS89 4.3 62.1 1.0
CA A:HIS89 4.4 61.8 1.0
CB A:ASP108 4.4 35.6 1.0
NZ A:LYS92 4.9 99.8 1.0
CE A:LYS92 4.9 97.6 1.0

Zinc binding site 4 out of 6 in 8uuv

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Zinc binding site 4 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:214.5
occ:1.00
 SG A:CYS111 2.1 85.5 1.0
ND1 A:HIS272 2.4 104.1 1.0
CB A:CYS111 2.8 84.5 1.0
CE1 A:HIS272 3.3 97.6 1.0
CG A:HIS272 3.4 108.3 1.0
NE1 A:TRP106 3.5 96.8 1.0
CB A:HIS272 3.8 89.6 1.0
CA A:HIS272 3.8 78.3 1.0
N A:CYS111 4.0 53.6 1.0
CA A:CYS111 4.0 48.9 1.0
O A:GLY271 4.3 80.1 1.0
NE2 A:HIS272 4.3 100.8 1.0
CA A:ASN109 4.4 76.7 1.0
CD1 A:TRP106 4.4 114.9 1.0
N A:TYR273 4.4 74.3 1.0
CD2 A:HIS272 4.4 113.9 1.0
C A:ASN109 4.5 64.9 1.0
CE2 A:TRP106 4.5 119.0 1.0
O A:ASN109 4.7 55.4 1.0
C A:HIS272 4.7 76.6 1.0
OD1 A:ASN109 4.8 83.0 1.0
CZ2 A:TRP106 4.8 122.1 1.0
CB A:ASN109 4.9 73.9 1.0
N A:HIS272 4.9 71.0 1.0
C A:GLY271 5.0 80.1 1.0

Zinc binding site 5 out of 6 in 8uuv

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Zinc binding site 5 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:156.9
occ:1.00
 SG A:CYS192 2.3 96.1 1.0
SG A:CYS189 2.3 132.3 1.0
SG A:CYS224 2.3 114.5 1.0
CB A:CYS226 2.5 103.3 1.0
CB A:CYS189 3.0 127.5 1.0
CB A:CYS192 3.1 117.4 1.0
N A:CYS226 3.3 142.0 1.0
CA A:CYS226 3.5 124.9 1.0
CB A:CYS224 3.5 123.6 1.0
N A:CYS192 3.8 131.6 1.0
CA A:CYS192 4.1 123.0 1.0
O A:HOH502 4.3 84.5 1.0
OG1 A:THR225 4.3 143.9 1.0
N A:THR225 4.4 142.8 1.0
CA A:CYS189 4.4 126.0 1.0
C A:THR225 4.5 134.7 1.0
C A:CYS226 4.6 108.4 1.0
C A:CYS224 4.7 135.6 1.0
CA A:CYS224 4.7 126.4 1.0
O A:CYS226 4.8 115.4 1.0
CB A:THR191 4.8 119.7 1.0
C A:CYS189 4.9 125.3 1.0
C A:THR191 4.9 129.2 1.0
CA A:THR225 4.9 139.5 1.0

Zinc binding site 6 out of 6 in 8uuv

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Zinc binding site 6 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:202.8
occ:1.00
 CE1 A:HIS17 1.9 106.2 1.0
OE2 A:GLU67 2.2 101.3 1.0
NE2 A:HIS17 2.3 97.4 1.0
ND1 A:HIS17 3.0 101.8 1.0
CD A:GLU67 3.2 79.8 1.0
CD2 A:HIS17 3.4 95.5 1.0
OE1 A:GLU67 3.5 74.2 1.0
O A:HOH511 3.6 75.6 1.0
CG A:HIS17 3.8 98.2 1.0
CG2 A:THR63 3.9 77.5 1.0
CB A:ASN15 4.1 75.6 1.0
CG A:GLU67 4.6 62.3 1.0
O A:ASN15 4.9 78.6 1.0
CG A:ASN15 5.0 100.7 1.0

Reference:

B.Tan, X.Zhang, A.Ansari, P.Jadhav, H.Tan, K.Li, A.Chopra, A.Ford, X.Chi, F.X.Ruiz, E.Arnold, X.Deng, J.Wang. Design of A Sars-Cov-2 Papain-Like Protease Inhibitor with Antiviral Efficacy in A Mouse Model Science V. 383 1434 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADM9724
Page generated: Thu Oct 31 12:30:22 2024

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