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Sodium in PDB 7jyc: Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir, PDB code: 7jyc was solved by B.Andi, D.Kumaran, D.F.Kreitler, A.S.Soares, W.Shi, J.Jakoncic, M.R.Fuchs, J.Keereetaweep, J.Shanklin, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.188, 52.507, 45.693, 90.00, 102.71, 90.00
R / Rfree (%) 17.5 / 21.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir (pdb code 7jyc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir, PDB code: 7jyc:

Sodium binding site 1 out of 1 in 7jyc

Go back to Sodium Binding Sites List in 7jyc
Sodium binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Narlaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:52.7
occ:0.50
 N A:ALA285 3.3 28.2 1.0
OG A:SER284 3.4 39.0 1.0
N A:LEU286 3.9 33.7 1.0
CA A:SER284 4.0 33.0 1.0
CA A:ALA285 4.1 32.1 1.0
C A:SER284 4.1 31.2 1.0
CB A:SER284 4.2 32.4 1.0
CB A:ALA285 4.2 32.6 1.0
CG A:LEU286 4.3 46.1 1.0
C A:ALA285 4.4 31.5 1.0
CB A:LEU286 4.5 40.4 1.0
CD1 A:LEU286 4.8 45.6 1.0
CA A:LEU286 4.8 36.0 1.0

Reference:

B.Andi, D.Kumaran, D.F.Kreitler, A.S.Soares, W.Shi, J.Jakoncic, M.R.Fuchs, J.Keereetaweep, J.Shanklin, S.Mcsweeney. Hepatitis C Virus NSP3/NSP4A Inhibitors As Promising Lead Compounds For the Design of New Covalent Inhibitors For Sars-Cov-2 3CLPRO/Mpro Protease To Be Published.
Page generated: Mon Aug 18 10:18:04 2025

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