Sodium in PDB 8g62: Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004

All present enzymatic activity of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004:
3.4.19.12; 3.4.22.69;

The structure of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004, PDB code: 8g62 was solved by J.Osipiuk, C.Tesar, M.Endres, R.Jedrzejczak, D.Luci, S.Kales, A.Simeonov, G.Rai, N.Drayman, S.Tay, S.Oakes, M.Rosner, B.Chen, N.Dulin, J.Solway, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), Center For Structural Biology Of Infectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.06 / 2.17
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	170.02, 170.02, 97.588, 90, 90, 90
R / Rfree (%)	18 / 21.4

The structure of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Zinc	(Zn)	3 atoms

The binding sites of Sodium atom in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 (pdb code 8g62). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004, PDB code: 8g62:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:62.8 occ:1.00 O A:LEU120 2.3 45.8 1.0 O A:HOH637 2.4 59.9 1.0 O A:ILE123 2.4 50.3 1.0 OH A:TYR136 3.1 56.0 1.0 C A:LEU120 3.4 47.0 1.0 C A:ILE123 3.7 51.0 1.0 CZ A:TYR136 3.9 51.9 1.0 CE2 A:TYR136 4.0 52.5 1.0 CA A:GLN121 4.1 45.2 1.0 N A:GLN121 4.2 45.0 1.0 C A:GLN121 4.2 47.7 1.0 N A:ILE123 4.2 49.1 1.0 N A:LEU125 4.3 52.2 1.0 O A:LEU125 4.3 57.4 1.0 CA A:LEU120 4.5 46.6 1.0 N A:GLN122 4.5 49.6 1.0 N A:GLU124 4.5 55.4 1.0 CA A:GLU124 4.6 56.6 1.0 CA A:ILE123 4.6 49.6 1.0 O A:GLN121 4.6 49.1 1.0 C A:GLU124 4.9 53.8 1.0 CB A:LEU125 4.9 55.3 1.0 CG1 A:ILE123 4.9 48.0 1.0 CB A:LEU120 5.0 45.6 1.0

Sodium binding site 2 out of 2 in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:69.3 occ:1.00 O B:LEU120 2.5 49.3 1.0 O B:HOH610 2.5 69.7 1.0 O B:ILE123 2.5 53.3 1.0 OH B:TYR136 3.2 59.9 1.0 C B:LEU120 3.6 48.5 1.0 C B:ILE123 3.7 53.7 1.0 CE2 B:TYR136 3.8 57.4 1.0 CZ B:TYR136 3.9 56.3 1.0 O B:LEU125 3.9 57.9 1.0 N B:LEU125 4.1 53.5 1.0 CA B:GLN121 4.5 46.8 1.0 N B:GLN121 4.5 47.2 1.0 CB B:LEU125 4.5 57.3 1.0 CA B:GLU124 4.5 59.6 1.0 N B:ILE123 4.5 48.6 1.0 N B:GLU124 4.5 56.3 1.0 CA B:LEU120 4.5 46.6 1.0 O B:HOH642 4.6 60.1 1.0 C B:GLN121 4.6 48.7 1.0 C B:GLU124 4.7 56.0 1.0 CA B:LEU125 4.7 58.1 1.0 CA B:ILE123 4.8 50.5 1.0 C B:LEU125 4.8 60.0 1.0 CB B:LEU120 4.9 47.5 1.0 N B:GLN122 4.9 49.1 1.0 CG1 B:ILE123 4.9 50.0 1.0

J.Osipiuk, C.Tesar, M.Endres, R.Jedrzejczak, D.Luci, S.Kales, A.Simeonov, G.Rai, N.Drayman, S.Tay, S.Oakes, M.Rosner, B.Chen, N.Dulin, J.Solway, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), Center For Structural Biology Of Infectiousdiseases (Csbid). Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 To Be Published.