Zinc in PDB 7tn0: Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab

The structure of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 7tn0 was solved by M.Mccallum, N.Czudnochowski, J.C.Nix, T.I.Croll, Ssgcid, J.R.Dillen, G.Snell, D.Veesler, Seattle Structural Genomics Center For Infectiousdisease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.28, 183.65, 194.55, 90, 95.98, 90
R / Rfree (%)	23 / 26.8

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

Chlorine

(Cl)

21 atoms

The binding sites of Zinc atom in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab (pdb code 7tn0). 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 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 7tn0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sars-Cov-2 Omicron 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 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:94.2 occ:1.00 OE2 E:GLU402 2.0 63.8 1.0 NE2 E:HIS378 2.3 66.5 1.0 NE2 E:HIS374 2.3 47.9 1.0 CL E:CL707 2.9 78.8 1.0 O E:HOH831 3.0 48.9 1.0 CD E:GLU402 3.0 65.5 1.0 CD2 E:HIS374 3.1 58.8 1.0 CE1 E:HIS378 3.2 55.5 1.0 CD2 E:HIS378 3.3 56.3 1.0 CE1 E:HIS374 3.4 60.0 1.0 OE1 E:GLU402 3.4 54.7 1.0 OE2 E:GLU375 4.2 73.9 1.0 ND1 E:HIS378 4.3 48.0 1.0 OE1 E:GLU375 4.3 67.4 1.0 CG E:GLU402 4.3 54.5 1.0 CG E:HIS374 4.3 60.9 1.0 CG E:HIS378 4.3 46.2 1.0 ND1 E:HIS374 4.4 49.1 1.0 CD E:GLU375 4.6 69.6 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Omicron 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 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn702 b:117.1 occ:1.00 NE2 F:HIS378 2.3 86.3 1.0 NE2 F:HIS374 2.3 89.5 1.0 CL F:CL706 2.6 84.5 1.0 OE1 F:GLU402 2.7 106.4 1.0 CD2 F:HIS374 3.1 86.5 1.0 CD2 F:HIS378 3.1 89.7 1.0 CE1 F:HIS378 3.3 78.5 1.0 CD F:GLU402 3.4 95.5 1.0 CE1 F:HIS374 3.4 95.5 1.0 OE2 F:GLU402 3.4 104.6 1.0 OE2 F:GLU375 3.9 91.6 1.0 OE1 F:GLU375 4.2 88.3 1.0 CG F:HIS378 4.3 78.2 1.0 ND1 F:HIS378 4.3 79.6 1.0 CG F:HIS374 4.3 82.3 1.0 ND1 F:HIS374 4.4 82.4 1.0 CD F:GLU375 4.4 94.5 1.0 CG F:GLU402 4.8 83.2 1.0

M.Mccallum, N.Czudnochowski, L.E.Rosen, S.K.Zepeda, J.E.Bowen, A.C.Walls, K.Hauser, A.Joshi, C.Stewart, J.R.Dillen, A.E.Powell, T.I.Croll, J.Nix, H.W.Virgin, D.Corti, G.Snell, D.Veesler. Structural Basis of Sars-Cov-2 Omicron Immune Evasion and Receptor Engagement. Science V. 375 864 2022.
ISSN: ESSN 1095-9203
PubMed: 35076256
DOI: 10.1126/SCIENCE.ABN8652