Zinc in PDB 8df5: Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab

All present enzymatic activity of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab:
3.4.17.23;

The structure of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 8df5 was solved by M.Mccallum, Seattle Structural Genomics Center For Infectious Disease(Ssgcid), G.Snell, D.Veesler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.27 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.531, 126.773, 145.663, 91.78, 103.66, 96.02
R / Rfree (%)	17.7 / 21.7

The structure of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab also contains other interesting chemical elements:

Chlorine

(Cl)

22 atoms

The binding sites of Zinc atom in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab (pdb code 8df5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 8df5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1101 b:88.5 occ:1.00 OE1 E:GLU402 2.0 79.2 1.0 NE2 E:HIS374 2.3 75.6 1.0 NE2 E:HIS378 2.3 77.5 1.0 CL E:CL1116 2.8 88.1 1.0 CD E:GLU402 2.8 79.1 1.0 CD2 E:HIS374 3.0 78.9 1.0 OE2 E:GLU402 3.0 84.8 1.0 CD2 E:HIS378 3.2 70.8 1.0 CE1 E:HIS378 3.3 75.3 1.0 CE1 E:HIS374 3.4 80.0 1.0 OE2 E:GLU375 3.6 76.8 1.0 O E:HOH1229 3.8 70.3 1.0 CG E:GLU402 4.2 75.0 1.0 CG E:HIS374 4.2 82.3 1.0 CD E:GLU375 4.4 74.1 1.0 OE1 E:GLU375 4.4 75.9 1.0 ND1 E:HIS378 4.4 72.7 1.0 ND1 E:HIS374 4.4 83.3 1.0 CG E:HIS378 4.4 69.5 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1201 b:87.0 occ:1.00 OE2 F:GLU402 1.9 75.2 1.0 NE2 F:HIS378 2.3 70.3 1.0 NE2 F:HIS374 2.3 71.5 1.0 CD F:GLU402 2.9 69.3 1.0 CL F:CL1215 2.9 92.0 1.0 CD2 F:HIS378 3.0 69.4 1.0 CD2 F:HIS374 3.1 72.4 1.0 OE1 F:GLU402 3.2 64.4 1.0 O F:HOH1387 3.3 61.9 1.0 CE1 F:HIS378 3.4 65.2 1.0 CE1 F:HIS374 3.4 70.8 1.0 O F:HOH1338 3.5 65.8 1.0 OE2 F:GLU375 3.6 74.3 1.0 CG F:HIS378 4.2 65.1 1.0 OE1 F:GLU375 4.2 73.6 1.0 CG F:GLU402 4.3 59.7 1.0 CD F:GLU375 4.3 71.8 1.0 CG F:HIS374 4.3 70.2 1.0 ND1 F:HIS378 4.3 65.0 1.0 ND1 F:HIS374 4.4 69.5 1.0

T.N.Starr, A.J.Greaney, W.W.Hannon, A.N.Loes, K.Hauser, J.R.Dillen, E.Ferri, A.G.Farrell, B.Dadonaite, M.Mccallum, K.A.Matreyek, D.Corti, D.Veesler, G.Snell, J.D.Bloom. Shifting Mutational Constraints in the Sars-Cov-2 Receptor-Binding Domain During Viral Evolution. Science V. 377 420 2022.
ISSN: ESSN 1095-9203
PubMed: 35762884
DOI: 10.1126/SCIENCE.ABO7896