Sodium in PDB 7ntt: Crystal Structure of the Sars-Cov-2 Main Protease

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease, PDB code: 7ntt was solved by E.Dupre, V.Villeret, X.Hanoulle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.95 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.76, 53.98, 114.35, 90, 101.18, 90
R / Rfree (%)	20.7 / 25.5

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Main Protease (pdb code 7ntt). 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 the Sars-Cov-2 Main Protease, PDB code: 7ntt:

Sodium binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2 Main Protease


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 the Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.2 occ:1.00 H A:LYS137 2.3 30.8 1.0 O A:ALA129 2.6 24.0 1.0 HB2 A:CYS128 2.9 26.7 1.0 HA A:ILE136 2.9 26.5 1.0 H A:ALA129 3.0 21.9 1.0 OE2 A:GLU290 3.0 34.5 1.0 HH21 B:ARG4 3.0 39.7 1.0 N A:LYS137 3.1 30.7 1.0 HD3 A:ARG131 3.2 21.4 1.0 HH22 B:ARG4 3.2 39.7 1.0 HD2 A:ARG131 3.4 21.4 1.0 HB A:ILE136 3.4 28.4 1.0 NH2 B:ARG4 3.5 39.5 1.0 OE1 A:GLU290 3.5 25.4 1.0 HD2 A:LYS137 3.6 46.8 1.0 HB2 A:LYS137 3.6 36.6 1.0 CA A:ILE136 3.6 26.6 1.0 CD A:GLU290 3.6 32.3 1.0 N A:ALA129 3.7 21.7 1.0 HG2 A:ARG131 3.7 21.3 1.0 CD A:ARG131 3.7 21.4 1.0 C A:ALA129 3.7 22.0 1.0 HG3 A:LYS137 3.7 41.1 1.0 CB A:CYS128 3.8 26.2 1.0 C A:ILE136 3.9 28.5 1.0 HB3 A:ALA129 3.9 22.4 1.0 CB A:ILE136 4.0 28.7 1.0 CA A:LYS137 4.1 33.5 1.0 HH11 A:ARG131 4.1 19.2 1.0 O A:LYS137 4.1 36.5 1.0 CB A:LYS137 4.1 36.0 1.0 CA A:ALA129 4.2 22.0 1.0 CG A:LYS137 4.2 41.2 1.0 CG A:ARG131 4.2 21.3 1.0 HB3 A:CYS128 4.3 26.7 1.0 CD A:LYS137 4.3 47.0 1.0 HG21 A:ILE136 4.4 28.7 1.0 C A:LYS137 4.4 33.1 1.0 H A:ARG131 4.4 22.9 1.0 HA A:CYS128 4.5 24.2 1.0 HG A:CYS128 4.5 30.7 0.0 CB A:ALA129 4.5 22.6 1.0 C A:CYS128 4.6 22.1 1.0 CA A:CYS128 4.6 24.4 1.0 O A:THR135 4.7 21.2 1.0 CG2 A:ILE136 4.7 28.7 1.0 SG A:CYS128 4.7 30.6 1.0 HG3 A:ARG131 4.7 21.3 1.0 CZ B:ARG4 4.8 40.5 1.0 N A:MET130 4.9 23.8 1.0 N A:ARG131 4.9 22.8 1.0 N A:ILE136 4.9 22.4 1.0 NH1 A:ARG131 4.9 18.0 1.0 HA A:MET130 4.9 24.9 1.0 HA A:LYS137 4.9 33.3 1.0 HG22 A:ILE136 4.9 28.7 1.0 HD3 A:LYS137 5.0 46.8 1.0

E.Dupre, V.Villeret, X.Hanoulle. Crystal Structure of the Sars-Cov-2 Main Protease To Be Published.