Sodium in PDB 6z5t: Sars-Cov-2 Macrodomain in Complex with Adp-Ribose

All present enzymatic activity of Sars-Cov-2 Macrodomain in Complex with Adp-Ribose:
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-Ribose, PDB code: 6z5t 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)	55.98 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.782, 76.334, 82.326, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.9

The binding sites of Sodium atom in the Sars-Cov-2 Macrodomain in Complex with Adp-Ribose (pdb code 6z5t). 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 Macrodomain in Complex with Adp-Ribose, PDB code: 6z5t:
Jump to Sodium binding site number: 1; 2;

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


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-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:33.8 occ:1.00 O A:HOH525 2.7 25.6 1.0 O A:HOH559 2.8 34.9 1.0 O A:HOH526 2.9 38.1 1.0 O A:HOH580 2.9 29.9 1.0 N A:ASN224 3.1 20.9 1.0 OH A:TYR365 3.7 32.8 1.0 CG A:LYS223 3.8 19.4 1.0 CB A:ASN224 3.8 17.1 1.0 CA A:LYS223 3.9 19.2 1.0 CZ A:TYR365 3.9 23.9 1.0 C A:LYS223 4.0 25.4 1.0 CA A:ASN224 4.0 17.4 1.0 O A:GLY212 4.0 26.7 1.0 O A:HOH639 4.1 34.0 1.0 CE1 A:TYR365 4.2 23.7 1.0 CB A:LYS223 4.3 20.2 1.0 O A:ASN224 4.4 24.0 1.0 O A:HOH513 4.4 36.1 1.0 CE2 A:TYR365 4.5 26.1 1.0 C A:ASN224 4.6 24.5 1.0 O A:HOH545 4.6 37.6 1.0 O A:ILE222 4.9 20.8 1.0 CD1 A:TYR365 5.0 23.9 1.0

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


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-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:35.0 occ:1.00 O B:HOH572 2.7 27.8 1.0 O B:HOH639 2.7 38.2 1.0 N B:ASN224 3.0 22.9 1.0 O B:HOH592 3.0 41.7 1.0 O B:HOH547 3.4 36.6 1.0 CB B:ASN224 3.7 18.8 1.0 OH B:TYR365 3.7 34.0 1.0 CG B:LYS223 3.7 18.0 1.0 CA B:LYS223 3.8 18.9 1.0 CA B:ASN224 3.8 20.9 1.0 CZ B:TYR365 3.8 28.8 1.0 C B:LYS223 3.9 19.7 1.0 CE1 B:TYR365 4.2 30.9 1.0 O B:GLY212 4.2 24.4 1.0 O B:ASN224 4.2 30.3 1.0 O B:HOH583 4.2 39.1 1.0 CB B:LYS223 4.3 23.7 1.0 CE2 B:TYR365 4.4 30.4 1.0 C B:ASN224 4.4 20.6 1.0 O B:HOH671 4.5 37.3 1.0 CD1 B:TYR365 4.9 23.6 1.0 O B:ILE222 4.9 20.9 1.0 CG B:ASN224 5.0 24.5 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