Zinc in PDB 8uuy: Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129, PDB code: 8uuy 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) 61.65 / 3.05
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 113.547, 113.547, 220.215, 90, 90, 90
R / Rfree (%) 23 / 25

Other elements in 8uuy:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129 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) Complex with Inhibitor JUN12129 (pdb code 8uuy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129, PDB code: 8uuy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8uuy

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Zinc binding site 1 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


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) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:122.5
occ:1.00
 SG A:CYS284 2.3 89.9 1.0
O A:HOH574 2.7 80.2 1.0
CB A:CYS284 3.5 89.0 1.0
O A:HOH512 3.8 86.0 1.0
NZ A:LYS274 3.8 79.7 1.0
O A:HOH588 3.9 85.4 1.0
CD A:LYS274 4.0 90.9 1.0
OE1 A:GLU263 4.0 79.8 1.0
O A:HOH570 4.4 69.0 1.0
CE1 A:TYR296 4.5 77.5 1.0
CE A:LYS274 4.6 75.7 1.0
CD1 A:ILE276 4.6 77.7 1.0
OE2 A:GLU263 4.7 83.1 1.0
CD A:GLU263 4.8 81.3 1.0
CA A:CYS284 4.9 81.3 1.0

Zinc binding site 2 out of 8 in 8uuy

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Zinc binding site 2 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


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) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:191.1
occ:1.00
 SG A:CYS192 2.3 137.6 1.0
SG A:CYS189 2.3 158.0 1.0
SG A:CYS226 2.3 142.5 1.0
SG A:CYS224 2.3 150.1 1.0
CB A:CYS192 3.1 125.5 1.0
CB A:CYS224 3.4 158.9 1.0
CB A:CYS189 3.6 157.1 1.0
N A:CYS192 3.7 144.3 1.0
CB A:CYS226 3.8 165.5 1.0
CA A:CYS192 4.0 137.8 1.0
N A:CYS226 4.1 175.5 1.0
O A:HOH578 4.3 104.0 1.0
N A:THR225 4.6 185.8 1.0
CA A:CYS226 4.6 174.4 1.0
OG1 A:THR225 4.6 164.4 1.0
CA A:CYS224 4.7 168.1 1.0
CB A:THR191 4.8 140.5 1.0
CB A:LYS228 4.8 144.0 1.0
C A:THR191 4.8 143.1 1.0
C A:CYS224 4.8 181.0 1.0
CG A:LYS228 4.9 144.0 1.0
O A:LYS228 4.9 165.0 1.0
CA A:CYS189 5.0 150.3 1.0

Zinc binding site 3 out of 8 in 8uuy

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Zinc binding site 3 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


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) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:130.2
occ:1.00
 CE1 A:HIS17 2.4 75.4 1.0
OE2 A:GLU67 2.4 79.5 1.0
NE2 A:HIS17 3.3 89.0 1.0
CG2 A:THR63 3.3 81.8 1.0
ND1 A:HIS17 3.4 99.4 1.0
O A:HOH563 3.6 71.7 1.0
CD A:GLU67 3.6 78.0 1.0
OE1 A:GLU67 4.3 79.9 1.0
CD2 A:HIS17 4.5 90.4 1.0
CG A:HIS17 4.5 93.3 1.0
CG A:GLU67 4.7 67.8 1.0
CB A:THR63 4.7 77.8 1.0

Zinc binding site 4 out of 8 in 8uuy

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Zinc binding site 4 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


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) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:68.0
occ:1.00
 CL A:CL414 2.2 79.5 1.0
ND1 A:HIS73 2.3 59.9 1.0
CL A:CL413 2.4 78.7 1.0
CG A:HIS73 3.2 67.2 1.0
CE1 A:HIS73 3.2 64.1 1.0
CB A:HIS73 3.5 65.6 1.0
CB A:ASN128 4.1 65.1 1.0
NE2 A:HIS73 4.2 67.0 1.0
CD2 A:HIS73 4.3 68.0 1.0
ND2 A:ASN128 4.7 84.4 1.0
CA A:HIS73 4.8 67.7 1.0
CG A:ASN128 4.8 76.6 1.0
O A:HIS73 4.9 68.3 1.0

Zinc binding site 5 out of 8 in 8uuy

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Zinc binding site 5 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


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) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:97.9
occ:1.00
 O A:HOH510 2.1 52.9 1.0
O A:HOH530 2.2 61.8 1.0
NE2 A:HIS175 2.3 77.1 1.0
CE1 A:HIS175 3.1 77.0 1.0
CD2 A:HIS175 3.2 85.6 1.0
O A:HOH592 3.7 53.0 1.0
ND1 A:HIS175 4.1 76.0 1.0
O A:HIS73 4.2 68.3 1.0
CG A:HIS175 4.2 74.4 1.0

Zinc binding site 6 out of 8 in 8uuy

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Zinc binding site 6 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


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) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:181.6
occ:1.00
 ZN A:ZN411 2.2 193.7 1.0
ND1 A:HIS89 2.5 104.1 1.0
O A:HOH531 2.8 104.6 1.0
CG A:HIS89 3.4 97.9 1.0
CE1 A:HIS89 3.5 94.7 1.0
CB A:HIS89 3.7 99.0 1.0
CA A:HIS89 4.3 89.0 1.0
OD2 A:ASP108 4.4 60.6 1.0
O A:HOH552 4.5 123.0 1.0
CD2 A:HIS89 4.6 101.5 1.0
NE2 A:HIS89 4.6 92.5 1.0
CD A:LYS92 4.7 102.3 1.0
NZ A:LYS92 4.8 104.3 1.0

Zinc binding site 7 out of 8 in 8uuy

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Zinc binding site 7 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn411

b:193.7
occ:1.00
 ZN A:ZN410 2.2 181.6 1.0
OD2 A:ASP108 2.3 60.6 1.0
O A:HOH552 2.8 123.0 1.0
CG A:ASP108 3.2 77.7 1.0
OD1 A:ASP108 3.4 111.4 1.0
ND1 A:HIS89 3.5 104.1 1.0
CB A:HIS89 3.6 99.0 1.0
CG A:HIS89 3.8 97.9 1.0
CB A:ASP108 4.6 62.9 1.0
CE1 A:HIS89 4.6 94.7 1.0
CA A:HIS89 4.6 89.0 1.0
NE1 A:TRP93 4.8 75.8 1.0
CG1 A:VAL159 4.9 78.3 1.0
CD2 A:HIS89 5.0 101.5 1.0
O A:HOH531 5.0 104.6 1.0

Zinc binding site 8 out of 8 in 8uuy

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Zinc binding site 8 out of 8 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Inhibitor JUN12129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn412

b:97.5
occ:1.00
 SG A:CYS111 2.3 78.2 1.0
O A:HOH505 2.3 93.4 1.0
ND1 A:HIS272 2.3 105.9 1.0
O A:HOH565 2.5 85.8 1.0
CE1 A:HIS272 2.8 103.7 1.0
O A:HOH558 3.0 87.6 1.0
CB A:CYS111 3.1 80.8 1.0
O A:HOH583 3.4 119.2 1.0
CG A:HIS272 3.6 100.6 1.0
O A:HOH581 3.9 88.2 1.0
NE2 A:HIS272 4.0 97.2 1.0
O A:GLY271 4.0 96.6 1.0
N A:CYS111 4.1 76.4 1.0
CA A:HIS272 4.2 88.0 1.0
CA A:CYS111 4.2 62.3 1.0
CB A:HIS272 4.2 94.9 1.0
OD1 A:ASN109 4.4 86.3 1.0
CD2 A:HIS272 4.4 95.7 1.0
CA A:ASN109 4.5 81.3 1.0
C A:ASN109 4.7 79.8 1.0
N A:TYR273 4.8 90.2 1.0
C A:GLY271 5.0 85.9 1.0
N A:ASN110 5.0 76.8 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 12:32:16 2024

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