Zinc 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:

Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Sars-Cov-2 Papain-Like Protease Bound to N-(2,4- Dihydroxybenzylidene)-Thiosemicarbazone, PDB code: 7qcj:

Zinc binding site 1 out of 1 in 7qcj

Go back to Zinc Binding Sites List in 7qcj
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn407

b:74.2
occ:1.00
 SG A:CYS192 2.3 125.9 1.0
SG A:CYS189 2.3 81.2 1.0
SG A:CYS224 2.4 88.3 1.0
SG A:CYS226 2.4 92.7 1.0
HB3 A:CYS224 3.2 90.1 1.0
HB2 A:CYS192 3.2 108.3 1.0
CB A:CYS189 3.3 83.8 1.0
HB3 A:CYS189 3.3 100.6 1.0
CB A:CYS224 3.3 75.1 1.0
HB A:THR191 3.4 127.3 1.0
CB A:CYS192 3.4 90.3 1.0
HB2 A:CYS189 3.4 100.6 1.0
H A:CYS226 3.4 124.0 1.0
H A:CYS192 3.5 113.6 1.0
HB2 A:CYS224 3.6 90.1 1.0
HB3 A:LYS228 3.7 111.8 1.0
HB3 A:CYS226 3.8 118.4 1.0
CB A:CYS226 3.8 98.7 1.0
N A:CYS192 3.9 94.7 1.0
HB2 A:LYS228 4.0 111.8 1.0
HB3 A:CYS192 4.1 108.3 1.0
N A:CYS226 4.2 103.3 1.0
H A:THR191 4.2 116.8 1.0
H A:THR225 4.2 132.0 1.0
CA A:CYS192 4.3 109.1 1.0
CB A:LYS228 4.3 93.1 1.0
CB A:THR191 4.3 106.1 1.0
HG22 A:THR225 4.3 133.6 1.0
HB2 A:CYS226 4.5 118.4 1.0
H A:LYS228 4.5 111.9 1.0
HG22 A:THR191 4.6 121.5 1.0
CA A:CYS226 4.6 112.2 1.0
N A:THR225 4.6 110.0 1.0
C A:THR191 4.6 96.7 1.0
CA A:CYS224 4.7 68.8 1.0
HA A:CYS192 4.7 130.9 1.0
CA A:CYS189 4.7 82.7 1.0
CA A:THR191 4.8 98.4 1.0
N A:THR191 4.8 97.3 1.0
C A:CYS224 4.9 104.8 1.0
CG2 A:THR191 5.0 101.3 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: Wed Oct 30 09:38:50 2024

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