Zinc in PDB 7ya0: Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar)

The binding sites of Zinc atom in the Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar) (pdb code 7ya0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar), PDB code: 7ya0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn704 b:93.7 occ:1.00 OE2 D:GLU402 2.0 644.0 1.0 NE2 D:HIS378 2.1 984.8 1.0 NE2 D:HIS374 2.1 80.3 1.0 CD2 D:HIS374 2.3 83.7 1.0 CD D:GLU402 2.8 638.8 1.0 CD2 D:HIS378 2.9 982.6 1.0 OE1 D:GLU402 3.1 643.5 1.0 CE1 D:HIS374 3.2 79.0 1.0 CE1 D:HIS378 3.2 975.4 1.0 CG D:HIS374 3.4 81.1 1.0 ND1 D:HIS374 3.8 79.6 1.0 CG D:HIS378 4.1 977.4 1.0 CG D:GLU402 4.2 635.8 1.0 ND1 D:HIS378 4.2 976.9 1.0 CB D:HIS374 4.6 83.0 1.0 O D:HIS374 5.0 79.3 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn704 b:246.0 occ:1.00 OE2 E:GLU402 2.0 995.0 1.0 NE2 E:HIS378 2.1 472.8 1.0 NE2 E:HIS374 2.1 557.7 1.0 CD E:GLU402 2.7 992.9 1.0 OE1 E:GLU402 2.7 994.5 1.0 CD2 E:HIS378 2.7 464.9 1.0 CD2 E:HIS374 2.8 551.2 1.0 CE1 E:HIS374 3.3 553.1 1.0 CE1 E:HIS378 3.3 467.6 1.0 CG E:HIS378 4.0 457.7 1.0 CG E:HIS374 4.0 545.5 1.0 CG E:GLU402 4.1 988.2 1.0 ND1 E:HIS378 4.2 461.4 1.0 ND1 E:HIS374 4.2 545.6 1.0 OE2 E:GLU375 4.7 512.2 1.0 CB E:GLU402 4.9 986.4 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of HACE2-Bound Sars-Cov-2 Omicron Spike Protein with L371S, P373S and F375S Mutations (S-6P-Rrar) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn704 b:251.9 occ:1.00 OE2 F:GLU402 2.0 525.8 1.0 NE2 F:HIS378 2.1 560.2 1.0 NE2 F:HIS374 2.1 508.5 1.0 CD2 F:HIS374 2.5 504.8 1.0 OE1 F:GLU402 2.6 525.7 1.0 CD F:GLU402 2.6 523.9 1.0 CD2 F:HIS378 2.8 556.5 1.0 CE1 F:HIS378 3.2 553.5 1.0 CE1 F:HIS374 3.4 501.7 1.0 CG F:HIS374 3.8 501.1 1.0 CG F:HIS378 3.9 552.3 1.0 ND1 F:HIS378 4.1 551.9 1.0 CG F:GLU402 4.1 518.9 1.0 ND1 F:HIS374 4.2 499.9 1.0 OE2 F:GLU375 5.0 340.1 1.0

Z.Zhao, J.Zhou, M.Tian, M.Huang, S.Liu, Y.Xie, P.Han, C.Bai, P.Han, A.Zheng, L.Fu, Y.Gao, Q.Peng, Y.Li, Y.Chai, Z.Zhang, X.Zhao, H.Song, J.Qi, Q.Wang, P.Wang, G.F.Gao. Omicron Sars-Cov-2 Mutations Stabilize Spike Up-Rbd Conformation and Lead to A Non-Rbm-Binding Monoclonal Antibody Escape. Nat Commun V. 13 4958 2022.
ISSN: ESSN 2041-1723
PubMed: 36002453
DOI: 10.1038/S41467-022-32665-7