Chlorine in PDB 7qcm: Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone

Enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone

All present enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone:
3.4.19.12;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone, PDB code: 7qcm 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) 49.04 / 1.77
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.065, 83.065, 134.064, 90, 90, 120
R / Rfree (%) 18.1 / 20.7

Other elements in 7qcm:

The structure of Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)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-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone (pdb code 7qcm). 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-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone, PDB code: 7qcm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7qcm

Go back to Chlorine Binding Sites List in 7qcm
Chlorine binding site 1 out of 3 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)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-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:36.4
occ:1.00
 H A:PHE127 2.3 36.3 1.0
HB2 A:PHE127 3.0 33.1 1.0
HA A:GLN133 3.0 33.9 1.0
HD2 A:PHE127 3.0 33.1 1.0
HA A:LYS126 3.1 41.0 1.0
HG2 A:GLN133 3.1 38.0 1.0
O A:HOH556 3.1 36.7 1.0
N A:PHE127 3.1 30.2 1.0
O A:HOH537 3.1 40.2 1.0
HD2 A:TYR136 3.2 40.0 1.0
CB A:PHE127 3.8 27.5 1.0
CD2 A:PHE127 3.8 27.6 1.0
CA A:LYS126 3.9 34.1 1.0
CA A:GLN133 3.9 28.1 1.0
CG A:GLN133 4.0 31.6 1.0
C A:LYS126 4.0 28.6 1.0
CA A:PHE127 4.0 28.2 1.0
HB3 A:TYR136 4.1 32.9 1.0
CD2 A:TYR136 4.1 33.3 1.0
HB3 A:LYS126 4.2 49.9 1.0
HB3 A:GLN133 4.2 37.0 1.0
CG A:PHE127 4.2 28.7 1.0
CB A:GLN133 4.3 30.7 1.0
HG2 A:LYS126 4.3 72.0 1.0
HG3 A:GLN133 4.3 38.0 1.0
O A:PHE127 4.3 30.6 1.0
CB A:LYS126 4.5 41.5 1.0
O A:LEU125 4.6 36.1 1.0
HB3 A:PHE127 4.6 33.1 1.0
C A:PHE127 4.6 32.1 1.0
O A:GLN133 4.7 30.0 1.0
HE2 A:TYR136 4.7 43.6 1.0
N A:GLN133 4.7 28.5 1.0
O A:HOH599 4.8 59.8 1.0
C A:GLN133 4.8 33.5 1.0
HA A:PHE127 4.8 33.9 1.0
CG A:LYS126 4.9 60.0 1.0
CE2 A:PHE127 4.9 27.6 1.0
CB A:TYR136 4.9 27.3 1.0
O A:HOH725 4.9 46.0 1.0
CE2 A:TYR136 4.9 36.2 1.0
HD3 A:LYS126 4.9 86.5 1.0
O A:LEU132 5.0 30.2 1.0
HE2 A:PHE127 5.0 33.2 1.0
CG A:TYR136 5.0 29.8 1.0

Chlorine binding site 2 out of 3 in 7qcm

Go back to Chlorine Binding Sites List in 7qcm
Chlorine binding site 2 out of 3 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)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-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:77.0
occ:1.00
 H A:LYS297 2.4 71.2 1.0
HA A:TYR296 3.1 72.0 1.0
O A:LYS297 3.3 61.0 1.0
N A:LYS297 3.3 59.3 1.0
CA A:TYR296 3.9 59.9 0.2
CA A:TYR296 3.9 59.9 0.8
HB3 A:LYS297 4.1 77.6 1.0
C A:TYR296 4.1 63.1 1.0
C A:LYS297 4.2 59.6 1.0
CA A:LYS297 4.2 57.0 1.0
CD2 A:TYR296 4.3 57.3 0.8
CG A:TYR296 4.4 53.3 0.8
O A:GLU295 4.4 52.6 1.0
HD2 A:TYR296 4.5 68.8 0.8
CD2 A:TYR296 4.5 56.0 0.2
CG A:TYR296 4.5 53.8 0.2
HD2 A:TYR296 4.6 67.3 0.2
CB A:LYS297 4.6 64.6 1.0
HG A:SER293 4.6 56.0 1.0
CE2 A:TYR296 4.6 53.5 0.8
CD1 A:TYR296 4.7 48.9 0.8
CB A:TYR296 4.7 54.4 0.2
CB A:TYR296 4.8 54.2 0.8
HB2 A:LYS297 4.8 77.6 1.0
N A:TYR296 5.0 58.3 1.0
CZ A:TYR296 5.0 56.0 0.8
CE2 A:TYR296 5.0 55.3 0.2
CD1 A:TYR296 5.0 53.8 0.2
HE2 A:TYR296 5.0 64.2 0.8
HB2 A:TYR296 5.0 65.3 0.2
CE1 A:TYR296 5.0 50.2 0.8

Chlorine binding site 3 out of 3 in 7qcm

Go back to Chlorine Binding Sites List in 7qcm
Chlorine binding site 3 out of 3 in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(3-Methoxy-4- Hydroxy-Acetophenone)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-(3-Methoxy-4- Hydroxy-Acetophenone)Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:61.2
occ:1.00
 ND1 A:HIS89 2.8 43.4 1.0
OD2 A:ASP108 2.9 38.3 1.0
HB3 A:HIS89 3.1 44.2 1.0
O A:HOH720 3.1 57.7 1.0
HE1 A:TRP93 3.5 42.6 1.0
HA A:HIS89 3.6 43.8 1.0
CG A:HIS89 3.7 42.5 1.0
CB A:HIS89 3.7 36.7 1.0
CE1 A:HIS89 3.8 57.5 1.0
CG A:ASP108 3.9 39.9 1.0
HE1 A:HIS89 3.9 69.1 1.0
HG11 A:VAL159 4.1 44.6 1.0
CA A:HIS89 4.1 36.4 1.0
OD1 A:ASP108 4.2 46.4 1.0
O A:HIS89 4.2 35.3 1.0
NE1 A:TRP93 4.2 35.4 1.0
HD1 A:TRP93 4.3 40.9 1.0
HD2 A:LYS92 4.3 74.0 1.0
HB2 A:LYS92 4.3 47.8 1.0
C A:HIS89 4.5 33.9 1.0
CD1 A:TRP93 4.6 34.0 1.0
HB2 A:HIS89 4.6 44.2 1.0
CG1 A:VAL159 4.9 37.1 1.0
CD2 A:HIS89 4.9 41.8 1.0
HG12 A:VAL159 4.9 44.6 1.0
NE2 A:HIS89 4.9 45.9 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 03:11:36 2024

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