Sodium in PDB 8ue0: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47, PDB code: 8ue0 was solved by F.Forouhar, H.Liu, A.Zack, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, K.Choi, 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)	32.71 / 2.16
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.309, 82.011, 52.202, 90, 115.61, 90
R / Rfree (%)	16.1 / 21.3

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Fluorine	(F)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47 (pdb code 8ue0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47, PDB code: 8ue0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47


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 47 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:58.5 occ:0.50 O A:HOH526 2.7 56.9 1.0 O A:LYS5 3.6 41.4 1.0 O A:VAL125 3.9 39.1 1.0 CA A:TYR126 4.1 30.9 1.0 C A:LYS5 4.4 38.1 1.0 N A:ALA7 4.4 37.2 1.0 CB A:ALA7 4.5 32.9 1.0 N A:GLN127 4.6 28.1 1.0 CB A:TYR126 4.6 44.4 1.0 C A:VAL125 4.8 30.3 1.0 C A:TYR126 4.8 28.2 1.0 CB A:LYS5 4.8 58.4 1.0 CA A:MET6 4.9 41.4 1.0 N A:TYR126 4.9 33.2 1.0 N A:MET6 4.9 38.4 1.0 C A:MET6 5.0 39.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:79.8 occ:1.00 OD2 A:ASP263 2.4 87.5 1.0 OD1 A:ASN221 2.4 90.8 1.0 O A:ASN221 2.6 73.1 1.0 O A:PHE223 2.7 96.3 1.0 O A:ASP263 2.8 71.3 1.0 OG A:SER267 3.3 81.5 1.0 C A:ASN221 3.3 80.5 1.0 CG A:ASN221 3.3 88.0 1.0 CG A:ASP263 3.5 91.0 1.0 C A:ASP263 3.7 72.4 1.0 N A:ASN221 3.7 68.5 1.0 C A:PHE223 3.8 92.2 1.0 N A:PHE223 3.8 88.3 1.0 CB A:ALA266 3.8 82.1 1.0 CA A:ASN221 3.9 73.9 1.0 N A:SER267 4.1 66.2 1.0 CA A:ASP263 4.1 77.7 1.0 CB A:ASN221 4.2 82.5 1.0 ND2 A:ASN221 4.2 88.8 1.0 N A:ARG222 4.2 85.0 1.0 C A:ARG222 4.2 93.9 1.0 CA A:PHE223 4.2 85.2 1.0 OD1 A:ASP263 4.3 95.6 1.0 CB A:ASP263 4.4 87.3 1.0 CB A:SER267 4.5 69.4 1.0 CA A:ARG222 4.6 90.1 1.0 CB A:PHE223 4.6 85.3 1.0 C A:ALA266 4.6 73.3 1.0 CA A:ALA266 4.7 69.3 1.0 CA A:SER267 4.7 60.6 1.0 N A:MET264 4.7 64.6 1.0 O A:ARG222 4.8 100.1 1.0 N A:THR224 4.9 94.6 1.0 C A:LEU220 4.9 65.1 1.0 N A:ALA266 5.0 72.0 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