Sodium in PDB 7qf0: Crystal Structure of the Sars-Cov-2 Rbd in Complex with the Human Antibody CV2.2325

The structure of Crystal Structure of the Sars-Cov-2 Rbd in Complex with the Human Antibody CV2.2325, PDB code: 7qf0 was solved by I.Fernandez, R.Pederzoli, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.80 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	84.565, 148.875, 145.093, 90, 90, 90
R / Rfree (%)	18.5 / 22.1

The structure of Crystal Structure of the Sars-Cov-2 Rbd in Complex with the Human Antibody CV2.2325 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Rbd in Complex with the Human Antibody CV2.2325 (pdb code 7qf0). 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 Rbd in Complex with the Human Antibody CV2.2325, PDB code: 7qf0:

Sodium binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2 Rbd in Complex with the Human Antibody CV2.2325


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 Rbd in Complex with the Human Antibody CV2.2325 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:56.5 occ:1.00 OG A:SER514 2.6 57.8 1.0 OD2 A:ASP398 2.9 42.6 1.0 O A:VAL512 2.9 45.8 1.0 CB A:SER514 3.1 51.3 1.0 O A:TYR396 3.2 46.4 1.0 N A:SER514 3.2 48.1 1.0 CG A:ASP398 3.3 43.4 1.0 C A:VAL512 3.6 44.0 1.0 C A:TYR396 3.7 49.4 1.0 CB A:TYR396 3.7 50.8 1.0 CA A:SER514 3.8 49.8 1.0 CG1 A:VAL512 3.8 37.2 1.0 OD1 A:ASP398 3.8 42.1 1.0 N A:ASP398 3.9 43.8 1.0 NH2 A:ARG355 3.9 39.5 1.0 C A:LEU513 3.9 48.5 1.0 CB A:ASP398 4.0 41.7 1.0 OH A:TYR423 4.0 44.3 1.0 CB A:VAL512 4.1 38.8 1.0 CA A:LEU513 4.2 44.8 1.0 N A:LEU513 4.2 45.4 1.0 CA A:TYR396 4.3 49.2 1.0 N A:ALA397 4.3 48.3 1.0 CE1 A:PHE464 4.4 43.6 1.0 CA A:VAL512 4.5 41.4 1.0 CA A:ALA397 4.6 46.7 1.0 CA A:ASP398 4.6 42.1 1.0 C A:ALA397 4.6 45.2 1.0 O A:LEU513 4.8 50.8 1.0 CZ A:ARG355 4.8 41.5 1.0 NE A:ARG355 4.9 44.0 1.0 CZ A:PHE464 5.0 43.4 1.0 C A:SER514 5.0 55.5 1.0 CG A:TYR396 5.0 52.5 1.0

I.Fernandez, F.A.Rey. Potent Antibodies Against Sars-Cov-2 Isolated From A Patient To Be Published.