Sodium in PDB 9grq: Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline

All present enzymatic activity of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline:
2.1.1.57;

The structure of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline, PDB code: 9grq was solved by V.Kremling, J.Sprenger, D.Oberthuer, A.Kiene, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.10 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.63, 166.63, 51.52, 90, 90, 120
R / Rfree (%)	18.5 / 19.1

The structure of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline (pdb code 9grq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline, PDB code: 9grq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7211 b:36.7 occ:1.00 O A:HOH7337 2.6 25.6 1.0 O A:ASP6923 2.8 26.0 1.0 O A:ALA6858 2.8 31.3 1.0 C A:ASP6923 3.7 28.7 1.0 N A:ALA6858 3.7 29.6 1.0 C A:ALA6858 3.8 30.7 1.0 CE A:MET6863 3.9 28.8 1.0 N A:SER6964 4.0 22.8 1.0 CA A:ALA6858 4.2 31.3 1.0 CA A:GLY6963 4.2 23.9 1.0 CB A:LEU6924 4.3 26.8 1.0 CB A:ASP6923 4.3 27.2 1.0 CB A:ALA6858 4.3 31.1 1.0 CB A:SER6964 4.4 24.4 1.0 CB A:LEU6857 4.4 27.1 1.0 OG A:SER6964 4.4 26.0 1.0 C A:GLY6963 4.5 25.2 1.0 CA A:ASP6923 4.5 28.4 1.0 N A:LEU6924 4.5 26.0 1.0 C A:LEU6857 4.5 31.7 1.0 CA A:LEU6924 4.6 25.5 1.0 CA A:LEU6857 4.6 30.0 1.0 O A:GLY6962 4.6 27.2 1.0 CD2 A:LEU6857 4.7 29.4 1.0 CD1 A:LEU6924 4.7 32.6 1.0 CA A:SER6964 4.8 25.8 1.0 CG A:LEU6924 5.0 32.8 1.0

Sodium binding site 2 out of 2 in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Theophylline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7227 b:42.8 occ:1.00 O A:HOH7407 2.6 31.6 1.0 OH A:TYR6930 2.6 33.5 1.0 OG1 A:THR6970 2.7 23.7 1.0 CE1 A:TYR6930 3.2 27.6 1.0 CZ A:TYR6930 3.3 33.0 1.0 CB A:LYS6935 3.4 41.0 1.0 CB A:THR6970 3.6 24.1 1.0 O1 A:EDO7224 3.8 50.5 1.0 OG1 A:THR6934 3.8 39.6 1.0 CB A:HIS6972 3.9 29.4 1.0 CD A:LYS6935 4.0 51.2 1.0 CG A:LYS6935 4.0 48.5 1.0 CA A:LYS6935 4.0 39.7 1.0 CG2 A:THR6970 4.1 22.8 1.0 N A:HIS6972 4.1 24.8 1.0 N A:SER6973 4.2 23.7 1.0 N A:LYS6935 4.2 43.0 1.0 C1 A:EDO7224 4.3 49.9 1.0 CA A:HIS6972 4.4 26.8 1.0 ND1 A:HIS6972 4.5 30.3 1.0 CD1 A:TYR6930 4.5 27.0 1.0 CB A:SER6973 4.5 22.8 1.0 C A:HIS6972 4.6 26.6 1.0 O A:HOH7313 4.6 46.9 1.0 CG A:HIS6972 4.7 32.0 1.0 CE2 A:TYR6930 4.7 31.8 1.0 C A:THR6934 4.9 43.4 1.0 N A:GLU6971 4.9 22.4 1.0 CA A:THR6970 5.0 24.6 1.0 CA A:SER6973 5.0 26.9 1.0

V.Kremling, J.Sprenger, D.Oberthuer, H.N.Chapman, P.Middendorf, S.Falke, A.Kiene, B.Klopprogge, T.E.S.Scheer, A.Creon. Crystal Structures of Sars-Cov-2 Methyltransferase NSP10-16 with CAP0-Site Binders To Be Published.