Zinc in PDB 8uug: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303, PDB code: 8uug was solved by A.Ansari, B.Tan, F.X.Ruiz, E.Arnold, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.05 / 2.74
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.2, 114.2, 218.557, 90, 90, 90
R / Rfree (%) 20 / 23.3

Other elements in 8uug:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 (pdb code 8uug). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303, PDB code: 8uug:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8uug

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Zinc binding site 1 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


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 JUN12303 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:42.6
occ:1.00
 CL A:CL411 2.2 48.4 1.0
CL A:CL412 2.2 46.9 1.0
ND1 A:HIS73 2.3 37.9 1.0
CG A:HIS73 3.1 40.6 1.0
CB A:HIS73 3.3 39.0 1.0
CE1 A:HIS73 3.3 41.9 1.0
CB A:ASN128 4.1 45.7 1.0
CD2 A:HIS73 4.3 45.7 1.0
NE2 A:HIS73 4.4 44.8 1.0
O A:HOH522 4.7 56.9 1.0
CA A:HIS73 4.7 42.2 1.0
CG A:PRO129 4.7 34.6 1.0
CD A:PRO129 4.7 42.5 1.0
O A:HIS73 4.8 45.0 1.0
N A:PRO129 4.9 43.0 1.0
ND2 A:ASN128 4.9 46.4 1.0
CG A:ASN128 4.9 48.4 1.0
O A:HOH608 5.0 50.5 1.0
C A:ASN128 5.0 42.6 1.0

Zinc binding site 2 out of 5 in 8uug

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Zinc binding site 2 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


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 JUN12303 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:114.3
occ:1.00
 SG A:CYS189 2.3 102.5 1.0
SG A:CYS192 2.3 79.4 1.0
SG A:CYS226 2.3 114.1 1.0
SG A:CYS224 2.3 104.5 1.0
CB A:CYS192 3.2 97.2 1.0
CB A:CYS226 3.3 114.6 1.0
CB A:CYS224 3.3 104.3 1.0
CB A:CYS189 3.3 99.1 1.0
N A:CYS192 3.8 101.8 1.0
N A:CYS226 3.8 119.6 1.0
CA A:CYS192 4.1 99.2 1.0
CA A:CYS226 4.1 116.7 1.0
O A:HOH656 4.4 91.1 1.0
O A:HOH612 4.5 93.1 1.0
N A:THR225 4.5 125.5 1.0
CA A:CYS224 4.6 116.0 1.0
CB A:THR191 4.7 97.2 1.0
CA A:CYS189 4.8 97.8 1.0
C A:CYS224 4.8 119.6 1.0
C A:THR191 4.9 99.7 1.0
C A:CYS226 4.9 121.0 1.0
C A:THR225 4.9 117.5 1.0

Zinc binding site 3 out of 5 in 8uug

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Zinc binding site 3 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


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 JUN12303 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:167.4
occ:1.00
 ND1 A:HIS272 2.3 91.6 1.0
SG A:CYS111 2.3 71.5 1.0
O A:HOH607 2.6 91.3 1.0
NE1 A:TRP106 2.7 79.8 1.0
CE1 A:HIS272 3.0 90.6 1.0
CE2 A:TRP106 3.3 100.2 1.0
CB A:CYS111 3.3 64.0 1.0
CZ2 A:TRP106 3.4 114.5 1.0
CG A:HIS272 3.5 80.4 1.0
CD1 A:TRP106 3.8 98.3 1.0
O A:GLY271 3.8 70.5 1.0
CA A:HIS272 4.0 71.8 1.0
CB A:HIS272 4.1 66.0 1.0
NE2 A:HIS272 4.2 73.3 1.0
CA A:ASN109 4.3 63.3 1.0
N A:CYS111 4.4 40.6 1.0
OD1 A:ASN109 4.4 71.6 1.0
CA A:CYS111 4.5 51.0 1.0
CD2 A:HIS272 4.5 67.9 1.0
O A:HOH626 4.5 56.3 1.0
CD2 A:TRP106 4.6 95.6 1.0
C A:ASN109 4.7 62.4 1.0
N A:TYR273 4.7 69.4 1.0
C A:GLY271 4.7 70.6 1.0
CH2 A:TRP106 4.8 108.4 1.0
CB A:ASN109 4.8 64.4 1.0
CG A:TRP106 4.9 96.7 1.0
N A:HIS272 4.9 64.4 1.0
C A:HIS272 4.9 68.3 1.0
O A:ASN109 5.0 61.2 1.0

Zinc binding site 4 out of 5 in 8uug

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Zinc binding site 4 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


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 JUN12303 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:145.1
occ:1.00
 ZN A:ZN408 2.3 75.7 1.0
ND1 A:HIS89 2.3 71.9 1.0
NZ A:LYS92 2.8 84.4 1.0
CE A:LYS92 3.0 78.2 1.0
CE1 A:HIS89 3.1 71.6 1.0
CG A:HIS89 3.2 67.5 1.0
O A:HOH672 3.3 50.4 1.0
O A:HOH539 3.3 77.6 1.0
CB A:HIS89 3.6 59.9 1.0
CA A:HIS89 3.7 53.4 1.0
NE2 A:HIS89 4.0 66.8 1.0
CD2 A:HIS89 4.1 63.3 1.0
OD2 A:ASP108 4.2 52.5 1.0
CD A:LYS92 4.5 69.8 1.0
O A:ASN88 4.5 54.3 1.0
O A:HIS89 4.6 52.4 1.0
N A:HIS89 4.6 60.0 1.0
C A:HIS89 4.6 54.4 1.0
C A:ASN88 4.9 57.6 1.0

Zinc binding site 5 out of 5 in 8uug

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Zinc binding site 5 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


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 JUN12303 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:75.7
occ:1.00
 OD2 A:ASP108 1.9 52.5 1.0
ZN A:ZN407 2.3 145.1 1.0
ND1 A:HIS89 2.3 71.9 1.0
CG A:ASP108 3.0 52.5 1.0
O A:HOH672 3.1 50.4 1.0
CE1 A:HIS89 3.2 71.6 1.0
CG A:HIS89 3.4 67.5 1.0
OD1 A:ASP108 3.5 83.3 1.0
CB A:HIS89 3.7 59.9 1.0
CG1 A:VAL159 4.0 47.0 1.0
NE1 A:TRP93 4.2 49.3 1.0
CB A:ASP108 4.3 49.4 1.0
NE2 A:HIS89 4.4 66.8 1.0
O A:HOH675 4.4 70.6 1.0
CA A:HIS89 4.4 53.4 1.0
CD2 A:HIS89 4.5 63.3 1.0
NZ A:LYS92 4.9 84.4 1.0
CE A:LYS92 4.9 78.2 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 12:29:28 2024

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