Zinc in PDB 7y9z: Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (One-Rbd-Up State)

The binding sites of Zinc atom in the Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (One-Rbd-Up State) (pdb code 7y9z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (One-Rbd-Up State), PDB code: 7y9z:

Zinc binding site 1 out of 1 in the Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (One-Rbd-Up State)


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 Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (One-Rbd-Up State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:162.8 occ:1.00 NE2 D:HIS378 2.1 158.0 1.0 NE2 D:HIS374 2.2 164.7 1.0 CD2 D:HIS374 2.8 164.7 1.0 CA D:GLY405 2.8 163.1 1.0 CE1 D:HIS374 3.0 164.7 1.0 CD2 D:HIS378 3.0 158.0 1.0 CE1 D:HIS378 3.0 158.0 1.0 C D:GLY405 3.1 163.1 1.0 CA D:GLU402 3.1 157.7 1.0 N D:GLU406 3.1 164.5 1.0 OE1 D:GLU402 3.3 157.7 1.0 N D:GLY405 3.4 163.1 1.0 N D:ALA403 3.4 158.8 1.0 C D:GLU402 3.6 157.7 1.0 CG D:HIS374 3.6 164.7 1.0 ND1 D:HIS374 3.7 164.7 1.0 CB D:GLU402 3.8 157.7 1.0 O D:HIS401 3.9 155.5 1.0 O D:GLY405 3.9 163.1 1.0 CB D:GLU406 4.0 164.5 1.0 CA D:GLU406 4.0 164.5 1.0 ND1 D:HIS378 4.1 158.0 1.0 CG D:HIS378 4.1 158.0 1.0 N D:GLU402 4.2 157.7 1.0 CD D:GLU402 4.4 157.7 1.0 O D:HIS374 4.5 164.7 1.0 C D:HIS401 4.5 155.5 1.0 O D:GLU402 4.6 157.7 1.0 CA D:ALA403 4.7 158.8 1.0 C D:VAL404 4.7 159.6 1.0 CG D:GLU402 4.7 157.7 1.0 C D:ALA403 4.8 158.8 1.0 CB D:HIS374 4.8 164.7 1.0 O D:ALA403 4.9 158.8 1.0 OE1 D:GLU406 4.9 164.5 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