Sodium in PDB 8udy: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25, PDB code: 8udy was solved by F.Forouhar, H.Liu, A.Zack, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.69 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.306, 81.593, 51.806, 90, 114.87, 90
R / Rfree (%)	17.6 / 21.6

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25 (pdb code 8udy). 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 3CL Protease with Inhibitor 25, PDB code: 8udy:

Sodium binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25


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 3CL Protease with Inhibitor 25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:66.4 occ:0.50 O A:HOH571 2.1 61.3 1.0 O A:VAL125 3.6 41.1 1.0 CA A:TYR126 3.9 36.4 1.0 O A:LYS5 4.0 48.2 1.0 CB A:ALA7 4.0 38.4 1.0 N A:ALA7 4.2 35.5 1.0 C A:VAL125 4.3 41.4 1.0 N A:TYR126 4.5 33.7 1.0 CB A:TYR126 4.6 42.8 1.0 C A:TYR126 4.7 40.5 1.0 N A:GLN127 4.7 36.4 1.0 C A:LYS5 4.7 41.0 1.0 CA A:ALA7 4.7 39.3 1.0 C A:MET6 4.9 35.2 1.0 CG1 A:VAL125 4.9 50.9 1.0 CA A:MET6 4.9 36.0 1.0

H.Liu, A.Zask, F.Forouhar, S.Iketani, A.Williams, D.R.Vaz, D.Habashi, K.Choi, S.J.Resnick, S.J.Hong, D.H.Lovett, T.Bai, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Small Molecule Non-Covalent Coronavirus 3CL Protease Inhibitors From Dna-Encoded Chemical Library Screening. Nat Commun V. 16 152 2025.
ISSN: ESSN 2041-1723
PubMed: 39747827
DOI: 10.1038/S41467-024-55421-5