Sodium in PDB 7tgr: Structure of Sars-Cov-2 Main Protease in Complex with GC376

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease in Complex with GC376:
3.4.22.69;

The structure of Structure of Sars-Cov-2 Main Protease in Complex with GC376, PDB code: 7tgr was solved by M.A.Esler, K.Shi, H.Aihara, R.S.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.85 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.565, 52.939, 45.904, 90, 102.55, 90
R / Rfree (%)	18.2 / 22.5

The structure of Structure of Sars-Cov-2 Main Protease in Complex with GC376 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Potassium	(K)	1 atom

The binding sites of Sodium atom in the Structure of Sars-Cov-2 Main Protease in Complex with GC376 (pdb code 7tgr). 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 Structure of Sars-Cov-2 Main Protease in Complex with GC376, PDB code: 7tgr:

Sodium binding site 1 out of 1 in the Structure of Sars-Cov-2 Main Protease in Complex with GC376


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Sars-Cov-2 Main Protease in Complex with GC376 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:38.2 occ:1.00 OD2 A:ASP176 2.2 31.9 1.0 OD1 A:ASN180 3.0 36.4 1.0 OE1 A:GLU178 3.1 46.0 1.0 CG A:ASP176 3.1 31.2 1.0 OD1 A:ASP176 3.5 30.4 1.0 CG A:ASN180 3.8 31.7 1.0 CD A:ARG105 3.9 35.0 1.0 O A:HOH652 3.9 40.1 1.0 CB A:ASN180 4.0 27.6 1.0 CB A:GLU178 4.0 28.8 1.0 CD A:GLU178 4.1 45.1 1.0 NH1 A:ARG105 4.1 29.1 1.0 CG A:GLU178 4.4 32.9 1.0 CB A:ASP176 4.4 26.5 1.0 CB A:ARG105 4.7 33.2 1.0 NE A:ARG105 4.7 34.4 1.0 CG A:ARG105 4.7 30.2 1.0 CZ A:ARG105 4.8 34.3 1.0

S.A.Moghadasi, M.A.Esler, Y.Otsuka, J.T.Becker, S.N.Moraes, C.B.Anderson, S.Chamakuri, C.Belica, C.Wick, D.A.Harki, D.W.Young, L.Scampavia, T.P.Spicer, K.Shi, H.Aihara, W.L.Brown, R.S.Harris. Gain-of-Signal Assays For Probing Inhibition of Sars-Cov-2 M Pro /3CL Pro in Living Cells. Mbio V. 13 78422 2022.
ISSN: ESSN 2150-7511
PubMed: 35471084
DOI: 10.1128/MBIO.00784-22