Chlorine in PDB 7qcj: Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone

Enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone

All present enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone:
3.4.19.12;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone, PDB code: 7qcj 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) 49.24 / 1.84
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.487, 83.487, 134.472, 90, 90, 120
R / Rfree (%) 17.6 / 19.8

Other elements in 7qcj:

The structure of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- 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-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone (pdb code 7qcj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone, PDB code: 7qcj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7qcj

Go back to Chlorine Binding Sites List in 7qcj
Chlorine binding site 1 out of 5 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- 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-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:71.1
occ:1.00
 HB3 A:HIS89 2.9 47.5 1.0
OD2 A:ASP108 3.1 41.7 1.0
ND1 A:HIS89 3.2 42.8 1.0
HE1 A:TRP93 3.4 43.9 1.0
HA A:HIS89 3.5 43.4 1.0
CB A:HIS89 3.6 39.6 1.0
CG A:HIS89 3.9 38.8 1.0
HD2 A:LYS92 3.9 89.6 1.0
HB2 A:LYS92 4.0 54.7 1.0
CA A:HIS89 4.0 36.2 1.0
O A:HIS89 4.1 38.2 1.0
NE1 A:TRP93 4.1 36.5 1.0
HD1 A:TRP93 4.1 41.5 1.0
CG A:ASP108 4.1 45.5 1.0
HG11 A:VAL159 4.3 57.4 1.0
CE1 A:HIS89 4.3 55.2 1.0
OD1 A:ASP108 4.4 48.8 1.0
C A:HIS89 4.4 34.7 1.0
CD1 A:TRP93 4.4 34.6 1.0
HB2 A:HIS89 4.5 47.5 1.0
HE1 A:HIS89 4.6 66.3 1.0
HB3 A:LYS92 4.7 54.7 1.0
CB A:LYS92 4.8 45.6 1.0
CD A:LYS92 4.8 74.7 1.0
HD3 A:LYS92 5.0 89.6 1.0
HZ2 A:LYS92 5.0 101.6 1.0

Chlorine binding site 2 out of 5 in 7qcj

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Chlorine binding site 2 out of 5 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- 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-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:35.7
occ:1.00
 H A:PHE127 2.4 40.2 1.0
HA A:GLN133 3.0 37.2 1.0
HA A:LYS126 3.1 40.7 1.0
HG2 A:GLN133 3.1 38.6 1.0
O A:HOH551 3.1 37.8 1.0
O A:HOH719 3.1 52.0 1.0
HD2 A:PHE127 3.1 33.3 1.0
HB2 A:PHE127 3.2 35.4 1.0
O A:HOH559 3.2 42.9 1.0
HD1 A:TYR136 3.3 40.4 1.0
N A:PHE127 3.3 33.5 1.0
HD3 A:LYS126 3.6 114.6 1.0
HZ3 A:LYS126 3.7 104.6 1.0
CA A:LYS126 3.9 34.0 1.0
CA A:GLN133 3.9 31.0 1.0
CD2 A:PHE127 3.9 27.8 1.0
CG A:GLN133 3.9 32.2 1.0
CB A:PHE127 4.0 29.5 1.0
HB3 A:LYS126 4.0 50.0 1.0
C A:LYS126 4.1 30.9 1.0
HB3 A:TYR136 4.1 34.8 1.0
HB3 A:GLN133 4.1 39.1 1.0
CA A:PHE127 4.2 30.9 1.0
CD1 A:TYR136 4.2 33.6 1.0
CB A:GLN133 4.2 32.6 1.0
HG3 A:GLN133 4.3 38.6 1.0
O A:PHE127 4.3 31.6 1.0
CG A:PHE127 4.4 28.0 1.0
CB A:LYS126 4.5 41.6 1.0
CD A:LYS126 4.5 95.5 1.0
O A:LEU125 4.6 36.7 1.0
NZ A:LYS126 4.6 87.2 1.0
O A:GLN133 4.6 33.1 1.0
C A:PHE127 4.7 35.6 1.0
HE1 A:TYR136 4.7 44.0 1.0
N A:GLN133 4.8 27.1 1.0
HB3 A:PHE127 4.8 35.4 1.0
O A:HOH534 4.8 63.0 1.0
C A:GLN133 4.8 30.7 1.0
HE2 A:LYS126 4.8 108.7 1.0
CE A:LYS126 4.9 90.6 1.0
O A:HOH697 4.9 45.9 1.0
CB A:TYR136 4.9 29.0 1.0
HZ2 A:LYS126 4.9 104.6 1.0
CE1 A:TYR136 4.9 36.7 1.0
HE21 A:GLN133 4.9 48.8 1.0
CE2 A:PHE127 5.0 30.5 1.0
HA A:PHE127 5.0 37.1 1.0

Chlorine binding site 3 out of 5 in 7qcj

Go back to Chlorine Binding Sites List in 7qcj
Chlorine binding site 3 out of 5 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- 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-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:86.7
occ:1.00
 ND1 A:HIS255 3.0 59.0 1.0
HB3 A:HIS255 3.0 61.9 1.0
O A:HOH737 3.2 75.2 1.0
CG A:HIS255 3.8 63.2 1.0
CB A:HIS255 3.8 51.5 1.0
CE1 A:HIS255 4.0 68.9 1.0
HE1 A:HIS255 4.1 82.7 1.0
HB2 A:HIS255 4.3 61.9 1.0
O A:HIS255 4.7 51.8 1.0
CA A:HIS255 5.0 52.1 1.0
HZ2 A:LYS254 5.0 107.5 1.0

Chlorine binding site 4 out of 5 in 7qcj

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Chlorine binding site 4 out of 5 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:63.5
occ:1.00
 HD2 A:LYS105 2.8 61.3 1.0
O A:HOH739 3.0 65.0 1.0
HB2 A:LYS105 3.0 42.5 1.0
O A:HOH708 3.1 50.3 1.0
HG3 A:PRO96 3.2 43.3 1.0
HB3 A:PRO96 3.2 45.9 1.0
HD3 A:PRO96 3.3 42.0 1.0
HB3 A:LYS94 3.4 47.6 1.0
HB2 A:LYS94 3.5 47.6 1.0
HB2 A:ALA288 3.6 42.4 1.0
CD A:LYS105 3.8 51.1 1.0
CG A:PRO96 3.8 36.1 1.0
CB A:LYS94 3.9 39.7 1.0
CB A:LYS105 3.9 35.4 1.0
CB A:PRO96 3.9 38.2 1.0
HB1 A:ALA288 4.0 42.4 1.0
CD A:PRO96 4.0 35.0 1.0
HG3 A:LYS94 4.0 52.8 1.0
HB3 A:LYS105 4.2 42.5 1.0
HG3 A:LYS105 4.2 54.5 1.0
HE3 A:LYS105 4.2 79.6 1.0
CG A:LYS105 4.2 45.4 1.0
CB A:ALA288 4.2 35.4 1.0
HD3 A:LYS105 4.3 61.3 1.0
CG A:LYS94 4.5 44.0 1.0
CE A:LYS105 4.5 66.3 1.0
HB2 A:PRO96 4.6 45.9 1.0
HD2 A:PRO96 4.7 42.0 1.0
HG2 A:PRO96 4.7 43.3 1.0
HB3 A:ALA288 4.7 42.4 1.0
N A:PRO96 4.8 33.6 1.0
HE2 A:LYS105 4.9 79.6 1.0
CA A:PRO96 4.9 33.7 1.0
H A:LYS105 5.0 38.9 1.0
HA A:PRO96 5.0 40.5 1.0
HA A:LYS105 5.0 44.5 1.0

Chlorine binding site 5 out of 5 in 7qcj

Go back to Chlorine Binding Sites List in 7qcj
Chlorine binding site 5 out of 5 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:54.9
occ:1.00
 H A:LYS306 2.2 47.5 1.0
HA A:TYR305 2.9 47.4 1.0
HA A:PHE258 2.9 47.2 1.0
N A:LYS306 3.1 39.6 1.0
HB2 A:LYS306 3.3 66.0 1.0
HB3 A:TYR305 3.3 44.6 1.0
HD1 A:TYR305 3.5 49.9 1.0
CA A:PHE258 3.6 39.4 1.0
OG1 A:THR259 3.6 39.2 1.0
CA A:TYR305 3.6 39.5 1.0
C A:PHE258 3.7 37.3 1.0
H A:THR259 3.7 41.5 1.0
N A:THR259 3.8 34.5 1.0
C A:TYR305 3.8 41.3 1.0
HG3 A:LYS306 3.9 86.1 1.0
CB A:TYR305 3.9 37.2 1.0
N A:PHE258 3.9 41.5 1.0
CB A:LYS306 3.9 55.0 1.0
CA A:LYS306 4.1 35.8 1.0
HG1 A:THR259 4.1 47.0 1.0
HG2 A:LYS306 4.2 86.1 1.0
CG A:LYS306 4.2 71.7 1.0
H A:PHE258 4.2 49.8 1.0
CD1 A:TYR305 4.3 41.6 1.0
O A:PHE258 4.3 38.0 1.0
C A:THR257 4.3 45.0 1.0
O A:THR257 4.3 45.3 1.0
O A:LYS306 4.5 39.7 1.0
CG A:TYR305 4.6 39.6 1.0
HA A:THR259 4.6 39.2 1.0
CA A:THR259 4.6 32.6 1.0
O A:HOH599 4.6 47.9 1.0
CB A:THR259 4.6 34.5 1.0
O A:PHE304 4.7 33.3 1.0
HB2 A:TYR305 4.7 44.6 1.0
C A:LYS306 4.8 41.7 1.0
HB3 A:LYS306 4.8 66.0 1.0
HA A:LYS306 4.8 43.0 1.0
N A:TYR305 4.9 34.1 1.0
CB A:PHE258 4.9 42.5 1.0
HB A:THR259 5.0 41.4 1.0
HB2 A:PHE258 5.0 51.0 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: Tue Jul 30 03:11:30 2024

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