Zinc in PDB 7xch: Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (Two-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 (Two-Rbd-Up State) (pdb code 7xch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (Two-Rbd-Up State), PDB code: 7xch:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (Two-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 (Two-Rbd-Up State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:753.5 occ:1.00 OE2 D:GLU402 2.0 680.7 1.0 NE2 D:HIS378 2.1 678.4 1.0 NE2 D:HIS374 2.1 687.0 1.0 CD2 D:HIS378 2.5 678.4 1.0 CD2 D:HIS374 2.9 687.0 1.0 CD D:GLU402 3.0 680.7 1.0 CE1 D:HIS374 3.2 687.0 1.0 CE1 D:HIS378 3.2 678.4 1.0 OE1 D:GLU402 3.5 680.7 1.0 CG D:HIS378 3.7 678.4 1.0 ND1 D:HIS378 3.9 678.4 1.0 CG D:HIS374 4.1 687.0 1.0 ND1 D:HIS374 4.2 687.0 1.0 CG D:GLU402 4.2 680.7 1.0 CB D:HIS378 4.9 678.4 1.0

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


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 Sars-Cov-2 Omicron Spike Protein (S-6P-Rrar) in Complex with Human ACE2 Ectodomain (Two-Rbd-Up State) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:826.9 occ:1.00 OE2 E:GLU402 2.0 708.6 1.0 NE2 E:HIS378 2.1 705.0 1.0 NE2 E:HIS374 2.1 727.3 1.0 CD2 E:HIS378 2.5 705.0 1.0 CD E:GLU402 2.5 708.6 1.0 CE1 E:HIS374 2.9 727.3 1.0 OE1 E:GLU402 3.0 708.6 1.0 CE1 E:HIS378 3.2 705.0 1.0 CD2 E:HIS374 3.3 727.3 1.0 CG E:GLU402 3.4 708.6 1.0 CG E:HIS378 3.6 705.0 1.0 ND1 E:HIS378 3.9 705.0 1.0 ND1 E:HIS374 4.1 727.3 1.0 CB E:GLU402 4.1 708.6 1.0 CG E:HIS374 4.3 727.3 1.0 CB E:HIS378 4.8 705.0 1.0 OE1 E:GLU375 4.8 719.1 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
DOI: 10.1038/S41467-022-32665-7