Sodium in PDB 6z72: Sars-Cov-2 Macrodomain in Complex with Adp-Hpm

All present enzymatic activity of Sars-Cov-2 Macrodomain in Complex with Adp-Hpm:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Sars-Cov-2 Macrodomain in Complex with Adp-Hpm, PDB code: 6z72 was solved by V.Zorzini, J.Rack, I.Ahel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.50 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.811, 83.126, 84.276, 90.00, 94.41, 90.00
R / Rfree (%)	21.8 / 26.3

The binding sites of Sodium atom in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpm (pdb code 6z72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpm, PDB code: 6z72:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpm


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 Macrodomain in Complex with Adp-Hpm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:46.3 occ:1.00 O A:HOH552 2.4 39.1 1.0 N A:SER211 3.0 53.1 1.0 OE2 A:GLU230 3.1 49.0 1.0 CG2 A:VAL234 3.4 50.0 1.0 O A:SER211 3.5 54.7 1.0 O A:SER209 3.6 52.2 1.0 CA A:PHE210 3.7 51.4 1.0 NZ A:LYS223 3.7 53.2 1.0 C A:PHE210 3.7 55.5 1.0 CA A:SER211 3.9 54.3 1.0 CD A:GLU230 3.9 48.7 1.0 OE1 A:GLU230 4.0 49.0 1.0 CB A:SER211 4.0 53.3 1.0 C A:SER211 4.1 53.7 1.0 CE1 A:TYR213 4.4 49.8 1.0 C A:SER209 4.5 55.0 1.0 N A:PHE210 4.5 59.6 1.0 CB A:PHE210 4.6 50.9 1.0 CD1 A:PHE210 4.9 54.3 1.0 O A:PHE210 4.9 56.7 1.0 CB A:VAL234 4.9 55.2 1.0 CD A:LYS233 4.9 56.0 1.0 CB A:LYS233 5.0 50.2 1.0

Sodium binding site 2 out of 4 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpm


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 Macrodomain in Complex with Adp-Hpm within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:51.4 occ:1.00 OG B:SER211 3.2 60.0 1.0 OE2 B:GLU230 3.3 53.7 1.0 N B:SER211 3.3 51.7 1.0 NZ B:LYS223 3.7 55.4 1.0 O B:SER209 3.7 56.8 1.0 OE1 B:GLU230 3.7 49.7 1.0 CG2 B:VAL234 3.8 53.2 1.0 O B:SER211 3.8 51.5 1.0 CD B:GLU230 3.9 52.1 1.0 CA B:PHE210 4.1 51.3 1.0 C B:PHE210 4.1 51.8 1.0 CA B:SER211 4.1 59.0 1.0 CB B:SER211 4.2 58.7 1.0 C B:SER211 4.4 63.9 1.0 CD B:LYS233 4.4 54.8 1.0 CB B:LYS233 4.5 50.3 1.0 C B:SER209 4.7 58.6 1.0 N B:PHE210 4.9 51.5 1.0 CE1 B:TYR213 5.0 50.4 1.0

Sodium binding site 3 out of 4 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpm within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:51.6 occ:1.00 O C:HOH525 2.2 29.7 1.0 OG C:SER211 3.3 54.9 1.0 CD C:LYS233 3.7 45.3 1.0 NZ C:LYS223 3.9 34.8 1.0 CB C:LYS233 4.0 36.2 1.0 OE1 C:GLU230 4.2 29.9 1.0 CG2 C:VAL234 4.3 32.5 1.0 N C:SER211 4.4 40.9 1.0 O C:SER209 4.4 39.6 1.0 CG C:LYS233 4.5 37.4 1.0 O C:SER211 4.5 34.8 1.0 CB C:SER211 4.5 45.0 1.0 OE2 C:GLU230 4.6 30.4 1.0 CD C:GLU230 4.8 23.9 1.0 NZ C:LYS233 4.8 43.8 1.0 CA C:SER211 4.9 41.4 1.0 CE C:LYS233 4.9 46.4 1.0

Sodium binding site 4 out of 4 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpm within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:33.3 occ:1.00 O D:HOH577 2.6 42.0 1.0 OE2 D:GLU230 2.8 38.5 1.0 N D:SER211 3.1 30.6 1.0 OE1 D:GLU230 3.4 32.2 1.0 O D:SER211 3.4 27.9 1.0 NZ D:LYS223 3.5 33.3 1.0 CD D:GLU230 3.5 37.8 1.0 CG2 D:VAL234 3.7 32.1 1.0 CA D:PHE210 3.8 33.2 1.0 CA D:SER211 3.9 31.1 1.0 C D:PHE210 3.9 33.3 1.0 CB D:SER211 4.0 31.1 1.0 O D:SER209 4.0 45.9 1.0 C D:SER211 4.1 30.7 1.0 CE1 D:TYR213 4.2 26.2 1.0 CB D:PHE210 4.7 29.3 1.0 CD1 D:PHE210 4.8 38.1 1.0 N D:PHE210 4.8 40.4 1.0 C D:SER209 4.8 46.3 1.0 CE D:LYS223 4.8 30.7 1.0 CD1 D:TYR213 5.0 22.0 1.0 OH D:TYR213 5.0 19.9 1.0 CG D:GLU230 5.0 33.9 1.0

J.G.M.Rack, V.Zorzini, Z.Zhu, M.Schuller, D.Ahel, I.Ahel. Viral Macrodomains: A Structural and Evolutionary Assessment of the Pharmacological Potential. Open Biology V. 10 00237 2020.
ISSN: ESSN 2046-2441
PubMed: 33202171
DOI: 10.1098/RSOB.200237