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Bromine 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
Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 6 binding sites of Bromine 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 Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 8cx9

Go back to Bromine Binding Sites List in 8cx9
Bromine binding site 1 out of 6 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 Bromine with other atoms in the Br 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:Br402

b:77.5
occ:1.00
 CG B:GLN229 3.4 56.7 1.0
C B:LYS228 3.5 76.3 1.0
N B:GLN229 3.6 64.4 1.0
CA B:LYS228 3.6 78.4 1.0
O B:GLY227 3.6 73.8 1.0
O B:LYS228 4.0 74.0 1.0
CB B:GLN229 4.1 63.3 1.0
CA B:GLN229 4.2 63.2 1.0
C B:GLY227 4.5 72.6 1.0
N B:LYS228 4.5 77.1 1.0
CD B:GLN229 4.5 59.5 1.0
CB B:LYS228 4.7 46.8 1.0

Bromine binding site 2 out of 6 in 8cx9

Go back to Bromine Binding Sites List in 8cx9
Bromine binding site 2 out of 6 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 Bromine with other atoms in the Br 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:Br402

b:88.0
occ:1.00
 CG2 A:THR257 3.0 49.5 1.0
OH A:TYR305 3.6 49.5 1.0
CB A:THR257 3.6 46.3 1.0
OH A:TYR251 3.8 52.5 1.0
O A:GLU252 4.2 52.6 1.0
CD2 A:LEU253 4.2 48.5 1.0
OG1 A:THR257 4.4 49.2 1.0
CZ A:TYR251 4.4 42.9 1.0
CE2 A:TYR251 4.5 43.2 1.0
CA A:LEU253 4.6 41.6 1.0
CZ A:TYR305 4.7 52.0 1.0
N A:LYS254 4.7 50.2 1.0
O A:THR257 4.7 39.1 1.0
C A:THR257 4.8 44.0 1.0
CA A:THR257 4.8 45.8 1.0
CE1 A:TYR305 4.9 47.8 1.0
CD1 A:PHE258 5.0 44.4 1.0

Bromine binding site 3 out of 6 in 8cx9

Go back to Bromine Binding Sites List in 8cx9
Bromine binding site 3 out of 6 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 Bromine with other atoms in the Br 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
A:Br403

b:86.2
occ:1.00
 N A:PHE127 3.3 43.0 1.0
CA A:LYS126 3.3 41.9 1.0
O A:LEU125 3.8 44.1 1.0
C A:LYS126 3.8 42.2 1.0
CB A:LYS126 3.9 44.1 1.0
CD2 A:TYR136 4.1 51.9 1.0
CE1 A:TYR137 4.2 72.9 1.0
N A:LYS126 4.3 47.1 1.0
OH A:TYR137 4.4 78.5 1.0
CA A:PHE127 4.4 37.2 1.0
C A:LEU125 4.5 44.9 1.0
CD2 A:PHE127 4.5 31.3 1.0
CB A:PHE127 4.5 34.2 1.0
CG A:GLN133 4.6 62.3 1.0
CZ A:TYR137 4.6 66.9 1.0
O A:PHE127 4.6 42.2 1.0
CA A:GLN133 4.7 43.5 1.0
CE2 A:TYR136 4.8 50.8 1.0
CB A:TYR136 4.9 46.6 1.0
CG A:PHE127 4.9 34.8 1.0
CG A:TYR136 4.9 45.0 1.0
O A:GLN133 5.0 50.9 1.0

Bromine binding site 4 out of 6 in 8cx9

Go back to Bromine Binding Sites List in 8cx9
Bromine binding site 4 out of 6 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 Bromine with other atoms in the Br 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:Br402

b:104.4
occ:1.00
 CG D:HIS17 3.7 66.3 1.0
OD2 D:ASP61 3.8 63.7 1.0
CD2 D:HIS17 3.9 56.1 1.0
CG2 D:THR63 3.9 60.3 1.0
CB D:THR63 3.9 67.0 1.0
OD1 D:ASP61 3.9 68.3 1.0
ND1 D:HIS17 4.1 70.0 1.0
CB D:HIS17 4.1 75.3 1.0
NE2 D:HIS17 4.2 56.0 1.0
CD2 D:LEU64 4.2 56.0 1.0
CG D:ASP61 4.2 62.9 1.0
CE1 D:HIS17 4.3 66.5 1.0
CG D:LEU64 4.5 50.3 1.0
OG1 D:THR63 4.6 72.4 1.0

Bromine binding site 5 out of 6 in 8cx9

Go back to Bromine Binding Sites List in 8cx9
Bromine binding site 5 out of 6 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 Bromine with other atoms in the Br binding site number 5 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
E:Br101

b:62.2
occ:1.00
 N E:LEU49 3.2 44.3 1.0
O C:GLY227 3.5 66.4 1.0
CA E:MET48 3.7 56.1 1.0
C C:LYS228 3.9 59.4 1.0
CB E:MET48 3.9 35.8 1.0
C E:MET48 3.9 59.0 1.0
CB E:LEU49 4.0 44.9 1.0
O C:LYS228 4.0 59.8 1.0
N C:GLN229 4.0 56.4 1.0
NE2 C:GLN229 4.1 47.0 1.0
CA E:LEU49 4.2 43.2 1.0
CG C:GLN229 4.2 47.1 1.0
CA C:LYS228 4.2 65.3 1.0
CB C:GLN229 4.2 55.8 1.0
CD C:GLN229 4.4 47.5 1.0
CA C:GLN229 4.4 48.3 1.0
O E:LEU49 4.4 38.3 1.0
C C:GLY227 4.5 66.8 1.0
N C:LYS228 4.8 68.0 1.0
C E:LEU49 4.8 37.2 1.0
O E:GLY47 4.9 63.6 1.0

Bromine binding site 6 out of 6 in 8cx9

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Bromine binding site 6 out of 6 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 Bromine with other atoms in the Br binding site number 6 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
F:Br101

b:82.3
occ:1.00
 N F:LEU49 3.1 48.4 1.0
CA F:MET48 3.5 50.3 1.0
N A:GLN229 3.6 44.4 1.0
CA A:LYS228 3.7 55.0 1.0
O A:GLY227 3.7 60.1 1.0
C A:LYS228 3.7 49.5 1.0
C F:MET48 3.8 52.5 1.0
O F:GLY47 3.9 44.5 1.0
CB A:GLN229 4.0 44.7 1.0
CB F:LEU49 4.1 55.5 1.0
CB F:MET48 4.2 35.3 1.0
CA F:LEU49 4.2 48.2 1.0
CG A:GLN229 4.2 47.4 1.0
CA A:GLN229 4.3 43.4 1.0
CG F:MET48 4.4 35.3 1.0
O A:LYS228 4.5 47.1 1.0
N F:MET48 4.5 43.6 1.0
NE2 A:GLN229 4.6 50.4 1.0
C A:GLY227 4.6 55.1 1.0
CB A:LYS228 4.6 53.2 1.0
N A:LYS228 4.6 53.5 1.0
C F:GLY47 4.7 41.9 1.0
O F:LEU49 4.7 60.2 1.0
NH1 B:ARG138 4.8 27.1 1.0
CD A:LYS228 4.9 44.9 1.0
C F:LEU49 5.0 53.3 1.0
CD A:GLN229 5.0 49.0 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: Thu Jul 11 04:59:52 2024

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