Zinc in PDB 8spi: Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2

All present enzymatic activity of Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2:
3.4.17.23;

The structure of Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2, PDB code: 8spi was solved by W.Zhang, K.Shi, H.Aihara, F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.85 / 3.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.365, 116.205, 108.767, 90, 96.6, 90
R / Rfree (%)	19 / 24.4

The structure of Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2 (pdb code 8spi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2, PDB code: 8spi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed 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 Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:111.8 occ:1.00 NE2 A:HIS374 2.0 83.3 1.0 NE2 A:HIS378 2.0 94.4 1.0 O A:HOH801 2.3 58.9 1.0 CD2 A:HIS374 2.8 85.1 1.0 CD2 A:HIS378 2.8 72.7 1.0 OE2 A:GLU402 2.9 82.9 1.0 CE1 A:HIS378 3.0 89.5 1.0 CE1 A:HIS374 3.2 70.2 1.0 OE2 A:GLU375 3.7 70.5 1.0 CD A:GLU402 3.7 83.3 1.0 OE1 A:GLU402 3.8 80.9 1.0 CG A:HIS378 3.9 63.0 1.0 CG A:HIS374 4.0 74.2 1.0 ND1 A:HIS378 4.0 64.7 1.0 ND1 A:HIS374 4.2 69.6 1.0 OE1 A:GLU375 4.2 67.0 1.0 CD A:GLU375 4.2 71.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed 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 Crystal Structure of Chimeric Omicron Rbd (Strain Xbb.1.5) Complexed with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:92.1 occ:1.00 OE2 B:GLU402 2.0 57.0 1.0 NE2 B:HIS378 2.1 48.9 1.0 NE2 B:HIS374 2.1 54.8 1.0 O B:HOH801 2.3 32.4 1.0 CD2 B:HIS374 2.9 51.8 1.0 CD2 B:HIS378 2.9 49.8 1.0 CD B:GLU402 2.9 48.7 1.0 CE1 B:HIS378 3.1 45.0 1.0 OE1 B:GLU402 3.1 53.6 1.0 CE1 B:HIS374 3.2 50.3 1.0 OE2 B:GLU375 3.7 48.7 1.0 CG B:HIS378 4.0 37.5 1.0 ND1 B:HIS378 4.1 35.0 1.0 CG B:HIS374 4.1 43.3 1.0 ND1 B:HIS374 4.2 43.3 1.0 CG B:GLU402 4.3 43.8 1.0 OE1 B:GLU375 4.3 39.1 1.0 CD B:GLU375 4.3 37.1 1.0 CA B:GLU402 5.0 41.4 1.0

W.Zhang, K.Shi, Q.Geng, H.Aihara, F.Li. Structural Evolution of Sars-Cov-2 Omicron in Human Receptor Recognition To Be Published.