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Chlorine in PDB 7qck: Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone

Enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone

All present enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone:
3.4.19.12;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone, PDB code: 7qck was solved by W.Ewert, S.Gunther, P.Reinke, S.Falke, J.Lieske, F.Miglioli, M.Carcelli, V.Srinivasan, C.Betzel, H.Han, K.Lorenzen, C.Guenther, S.Niebling, M.Garcia-Alai, W.Hinrichs, D.Rogolino, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.16 / 1.92
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.368, 83.368, 134.237, 90, 90, 120
R / Rfree (%) 20.2 / 22.4

Other elements in 7qck:

The structure of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone (pdb code 7qck). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone, PDB code: 7qck:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7qck

Go back to Chlorine Binding Sites List in 7qck
Chlorine binding site 1 out of 3 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:40.2
occ:1.00
 H A:PHE127 2.4 42.9 1.0
HA A:GLN133 3.0 40.8 1.0
HA A:LYS126 3.1 44.1 1.0
O A:HOH596 3.1 43.8 1.0
HG2 A:GLN133 3.1 42.0 1.0
HD1 A:PHE127 3.2 42.1 1.0
O A:HOH516 3.2 40.5 1.0
O A:HOH673 3.2 52.2 1.0
N A:PHE127 3.2 35.8 1.0
HB2 A:PHE127 3.3 38.6 1.0
HD1 A:TYR136 3.3 47.1 1.0
CA A:LYS126 3.9 36.8 1.0
HG3 A:LYS126 3.9 69.1 1.0
CA A:GLN133 3.9 34.0 1.0
CD1 A:PHE127 3.9 35.1 1.0
CG A:GLN133 4.0 35.0 1.0
CB A:PHE127 4.0 32.2 1.0
C A:LYS126 4.0 32.6 1.0
HB3 A:GLN133 4.1 41.7 1.0
CA A:PHE127 4.1 33.4 1.0
HB3 A:TYR136 4.1 39.1 1.0
CD1 A:TYR136 4.2 39.3 1.0
CB A:GLN133 4.2 34.7 1.0
HB3 A:LYS126 4.2 52.0 1.0
O A:PHE127 4.3 35.8 1.0
HG3 A:GLN133 4.4 42.0 1.0
CG A:PHE127 4.4 29.4 1.0
CB A:LYS126 4.5 43.3 1.0
O A:LEU125 4.5 40.8 1.0
CG A:LYS126 4.6 57.6 1.0
C A:PHE127 4.7 40.4 1.0
O A:GLN133 4.7 36.1 1.0
N A:GLN133 4.7 31.5 1.0
HE1 A:TYR136 4.7 49.9 1.0
HB3 A:PHE127 4.8 38.6 1.0
C A:GLN133 4.8 34.0 1.0
CB A:TYR136 4.9 32.6 1.0
HH21 A:ARG140 5.0 77.6 1.0
CE1 A:TYR136 5.0 41.6 1.0
CE1 A:PHE127 5.0 34.5 1.0
HE21 A:GLN133 5.0 54.1 1.0
HA A:PHE127 5.0 40.1 1.0
O A:HOH625 5.0 45.6 1.0
HG2 A:LYS126 5.0 69.1 1.0
O A:LEU132 5.0 33.0 1.0

Chlorine binding site 2 out of 3 in 7qck

Go back to Chlorine Binding Sites List in 7qck
Chlorine binding site 2 out of 3 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:70.2
occ:1.00
 OD1 A:ASP108 2.9 41.5 1.0
HB3 A:HIS89 3.0 46.7 1.0
ND1 A:HIS89 3.1 44.8 1.0
HE1 A:TRP93 3.4 47.5 1.0
HA A:HIS89 3.6 47.8 1.0
CB A:HIS89 3.7 38.9 1.0
CG A:HIS89 3.8 47.1 1.0
CG A:ASP108 3.9 46.8 1.0
NE1 A:TRP93 4.1 39.6 1.0
HG11 A:VAL159 4.1 53.6 1.0
CA A:HIS89 4.1 39.8 1.0
HD1 A:TRP93 4.1 43.0 1.0
OD2 A:ASP108 4.1 47.5 1.0
O A:HIS89 4.2 41.4 1.0
HB2 A:LYS92 4.2 50.3 1.0
CE1 A:HIS89 4.2 51.8 1.0
HD2 A:LYS92 4.2 79.5 1.0
HE1 A:HIS89 4.4 62.2 1.0
CD1 A:TRP93 4.5 35.9 1.0
C A:HIS89 4.5 40.9 1.0
HB2 A:HIS89 4.5 46.7 1.0
CG1 A:VAL159 4.9 44.6 1.0

Chlorine binding site 3 out of 3 in 7qck

Go back to Chlorine Binding Sites List in 7qck
Chlorine binding site 3 out of 3 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,5- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:75.0
occ:1.00
 H A:LYS45 2.4 66.1 1.0
HB2 A:LYS45 3.0 67.6 1.0
N A:LYS45 3.2 55.1 1.0
HA A:ILE44 3.3 63.3 1.0
HG23 A:ILE44 3.3 67.0 1.0
CB A:LYS45 3.8 56.3 1.0
HG12 A:ILE44 3.9 68.0 1.0
CA A:LYS45 4.0 54.6 1.0
CA A:ILE44 4.0 52.7 1.0
HD2 A:LYS45 4.1 73.3 1.0
C A:ILE44 4.1 55.9 1.0
NE2 A:HIS47 4.1 63.9 1.0
CG2 A:ILE44 4.2 55.8 1.0
HG3 A:LYS45 4.2 74.4 1.0
O A:LYS45 4.2 52.4 1.0
HD3 A:LYS45 4.3 73.3 1.0
CG A:LYS45 4.4 62.0 1.0
CD A:LYS45 4.5 61.1 1.0
CB A:ILE44 4.5 52.0 1.0
HB3 A:LYS45 4.5 67.6 1.0
C A:LYS45 4.6 47.1 1.0
HG22 A:ILE44 4.6 67.0 1.0
CG1 A:ILE44 4.7 56.7 1.0
HD2 A:HIS47 4.7 75.4 1.0
HG21 A:ILE44 4.8 67.0 1.0
CD2 A:HIS47 4.9 62.9 1.0
HA A:LYS45 4.9 65.5 1.0
O A:LYS43 5.0 59.5 1.0

Reference:

W.Ewert, S.Gunther, F.Miglioli, S.Falke, P.Y.A.Reinke, S.Niebling, C.Gunther, H.Han, V.Srinivasan, H.Brognaro, J.Lieske, K.Lorenzen, M.M.Garcia-Alai, C.Betzel, M.Carcelli, W.Hinrichs, D.Rogolino, A.Meents. Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of Sars-Cov-2 Papain-Like Protease. Front Chem V. 10 32431 2022.
ISSN: ESSN 2296-2646
PubMed: 35480391
DOI: 10.3389/FCHEM.2022.832431
Page generated: Sun Jul 13 06:17:16 2025

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