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Zinc in PDB 8cx9: Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism

Enzymatic activity of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism

All present enzymatic activity of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism:
3.4.19.12;

Protein crystallography data

The structure of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism, PDB code: 8cx9 was solved by A.U.Singer, C.L.Slater, A.Patel, R.Russel, B.L.Mark, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.79 / 3.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.58, 174.86, 121.56, 90, 95.74, 90
R / Rfree (%) 22.5 / 27

Other elements in 8cx9:

The structure of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Bromine (Br) 6 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism (pdb code 8cx9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism, PDB code: 8cx9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8cx9

Go back to Zinc Binding Sites List in 8cx9
Zinc binding site 1 out of 4 in the Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:66.6
occ:1.00
 SG B:CYS192 2.3 86.7 1.0
SG B:CYS189 2.3 74.6 1.0
SG B:CYS224 2.3 87.0 1.0
SG B:CYS226 2.3 80.3 1.0
CB B:CYS189 3.0 76.5 1.0
CB B:CYS224 3.0 76.1 1.0
CB B:CYS226 3.4 86.7 1.0
N B:CYS226 3.9 89.0 1.0
CB B:CYS192 3.9 84.5 1.0
N B:THR225 4.3 71.6 1.0
CA B:CYS226 4.3 86.5 1.0
CA B:CYS224 4.4 65.7 1.0
N B:CYS192 4.5 82.5 1.0
CA B:CYS189 4.5 75.5 1.0
C B:CYS224 4.6 64.7 1.0
CB B:LYS228 4.8 46.8 1.0
CA B:CYS192 4.8 83.1 1.0
C B:THR225 4.9 77.9 1.0
OG1 B:THR225 4.9 78.4 1.0

Zinc binding site 2 out of 4 in 8cx9

Go back to Zinc Binding Sites List in 8cx9
Zinc binding site 2 out of 4 in the Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:57.3
occ:1.00
 SG A:CYS189 2.3 52.2 1.0
SG A:CYS224 2.3 40.0 1.0
SG A:CYS226 2.3 43.4 1.0
SG A:CYS192 2.3 72.3 1.0
CB A:CYS224 3.1 49.1 1.0
CB A:CYS189 3.4 67.2 1.0
CB A:CYS226 3.5 48.4 1.0
CB A:CYS192 3.5 82.4 1.0
N A:CYS226 3.9 57.7 1.0
N A:CYS192 4.2 74.1 1.0
CA A:CYS226 4.4 55.5 1.0
N A:THR225 4.4 46.6 1.0
CA A:CYS224 4.5 48.5 1.0
CA A:CYS192 4.5 74.6 1.0
C A:CYS224 4.7 51.4 1.0
CA A:CYS189 4.7 54.8 1.0
C A:THR191 4.9 60.6 1.0
C A:THR225 5.0 54.4 1.0
CB A:THR191 5.0 55.7 1.0

Zinc binding site 3 out of 4 in 8cx9

Go back to Zinc Binding Sites List in 8cx9
Zinc binding site 3 out of 4 in the Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:49.1
occ:1.00
 SG C:CYS192 2.3 68.1 1.0
SG C:CYS224 2.3 69.0 1.0
SG C:CYS189 2.3 74.4 1.0
SG C:CYS226 2.3 111.5 1.0
CB C:CYS189 3.3 73.5 1.0
CB C:CYS192 3.5 63.2 1.0
CB C:CYS224 3.7 79.8 1.0
CB C:CYS226 3.7 74.0 1.0
N C:CYS192 4.1 64.2 1.0
N C:CYS226 4.1 57.3 1.0
CB C:LYS228 4.3 38.7 1.0
CA C:CYS192 4.4 68.7 1.0
CA C:CYS226 4.5 60.2 1.0
N C:THR225 4.6 50.7 1.0
CA C:CYS189 4.7 45.0 1.0
OG1 C:THR225 4.8 68.0 1.0
N C:LYS228 4.9 68.0 1.0
CA C:CYS224 4.9 65.6 1.0
CB C:THR191 5.0 68.0 1.0

Zinc binding site 4 out of 4 in 8cx9

Go back to Zinc Binding Sites List in 8cx9
Zinc binding site 4 out of 4 in the Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Sars-COV2 Plpro (C111S) in Complex with A Dimeric Ubv That Inhibits Activity By An Unusual Allosteric Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:185.9
occ:1.00
 SG D:CYS189 2.3 127.7 1.0
SG D:CYS226 2.3 135.9 1.0
SG D:CYS224 2.3 121.5 1.0
SG D:CYS192 2.3 152.7 1.0
CB D:CYS224 3.4 108.2 1.0
CB D:CYS192 3.6 164.5 1.0
CB D:CYS189 3.6 138.2 1.0
CB D:LYS228 3.8 91.5 1.0
CB D:CYS226 4.1 133.3 1.0
N D:LYS228 4.3 98.9 1.0
N D:CYS226 4.6 131.8 1.0
CA D:LYS228 4.6 94.2 1.0
N D:CYS192 4.8 156.1 1.0
CA D:CYS192 4.8 161.1 1.0
CA D:CYS224 4.8 100.8 1.0
CA D:CYS226 4.8 127.5 1.0
CA D:CYS189 4.8 133.8 1.0
N D:GLY227 4.8 115.8 1.0
C D:CYS189 4.8 130.4 1.0
OG1 D:THR191 4.9 148.3 1.0

Reference:

V.J.E.Van Vliet, N.Huynh, J.Pala, A.Patel, A.Singer, C.Slater, J.Chung, M.Van Huizen, J.Teyra, S.Miersch, G.K.Luu, W.Ye, N.Sharma, S.S.Ganaie, R.Russell, C.Chen, M.Maynard, G.K.Amarasinghe, B.L.Mark, M.Kikkert, S.S.Sidhu. Ubiquitin Variants Potently Inhibit Sars-Cov-2 Plpro and Viral Replication Via A Novel Site Distal to the Protease Active Site. Plos Pathog. V. 18 11065 2022.
ISSN: ESSN 1553-7374
PubMed: 36548304
DOI: 10.1371/JOURNAL.PPAT.1011065
Page generated: Wed Oct 30 18:58:28 2024

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