Zinc in PDB 8y16: Cryo-Em Structure of Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2

All present enzymatic activity of Cryo-Em Structure of Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2:
3.4.17.23;

The binding sites of Zinc atom in the Cryo-Em Structure of Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2 (pdb code 8y16). 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 Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2, PDB code: 8y16:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2


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 Jn.1 Spike Protein in Complex with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:30.0 occ:1.00 NE2 A:HIS378 2.1 69.6 1.0 NE2 A:HIS374 2.1 69.6 1.0 OE2 A:GLU402 2.1 69.6 1.0 OE1 A:GLU402 2.1 69.6 1.0 CD A:GLU402 2.4 69.6 1.0 CD2 A:HIS374 2.6 69.6 1.0 CE1 A:HIS378 3.0 69.6 1.0 CD2 A:HIS378 3.1 69.6 1.0 CE1 A:HIS374 3.1 69.6 1.0 CG A:HIS374 3.7 69.6 1.0 CG A:GLU402 3.8 69.6 1.0 OE2 A:GLU375 3.9 69.6 1.0 ND1 A:HIS374 3.9 69.6 1.0 ND1 A:HIS378 4.1 69.6 1.0 CG A:HIS378 4.2 69.6 1.0 CB A:GLU402 4.6 69.6 1.0 CA A:GLU402 4.6 69.6 1.0 CD A:GLU375 5.0 69.6 1.0 CB A:HIS374 5.0 69.6 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2


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 Jn.1 Spike Protein in Complex with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:30.0 occ:1.00 NE2 E:HIS378 2.1 69.6 1.0 NE2 E:HIS374 2.1 69.6 1.0 OE2 E:GLU402 2.1 69.6 1.0 OE1 E:GLU402 2.1 69.6 1.0 CD E:GLU402 2.4 69.6 1.0 CD2 E:HIS374 2.6 69.6 1.0 CE1 E:HIS378 3.0 69.6 1.0 CD2 E:HIS378 3.1 69.6 1.0 CE1 E:HIS374 3.1 69.6 1.0 CG E:HIS374 3.7 69.6 1.0 CG E:GLU402 3.8 69.6 1.0 OE2 E:GLU375 3.9 69.6 1.0 ND1 E:HIS374 3.9 69.6 1.0 ND1 E:HIS378 4.1 69.6 1.0 CG E:HIS378 4.2 69.6 1.0 CB E:GLU402 4.6 69.6 1.0 CA E:GLU402 4.6 69.6 1.0 CD E:GLU375 5.0 69.6 1.0 CB E:HIS374 5.0 69.6 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2


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 Sars-Cov-2 Omicron Jn.1 Spike Protein in Complex with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn701 b:30.0 occ:1.00 NE2 F:HIS378 2.1 69.6 1.0 NE2 F:HIS374 2.1 69.6 1.0 OE2 F:GLU402 2.1 69.6 1.0 OE1 F:GLU402 2.1 69.6 1.0 CD F:GLU402 2.4 69.6 1.0 CD2 F:HIS374 2.6 69.6 1.0 CE1 F:HIS378 3.0 69.6 1.0 CD2 F:HIS378 3.1 69.6 1.0 CE1 F:HIS374 3.1 69.6 1.0 CG F:HIS374 3.7 69.6 1.0 CG F:GLU402 3.8 69.6 1.0 OE2 F:GLU375 3.9 69.6 1.0 ND1 F:HIS374 3.9 69.6 1.0 ND1 F:HIS378 4.1 69.6 1.0 CG F:HIS378 4.2 69.6 1.0 CB F:GLU402 4.6 69.6 1.0 CA F:GLU402 4.6 69.6 1.0 CD F:GLU375 5.0 69.6 1.0 CB F:HIS374 5.0 69.6 1.0

L.J.Li, G.F.Gao. Spike Structures, Receptor Binding and Immune Escape of Sars-Cov-2 Omicron Recently-Circulating Ba.2.86.1, Jn.1, Eg.5, Eg.5.1 and Hv.1 Sub-Variants To Be Published.