Zinc in PDB 8wdr: Crystal Structure of Bq.1.1 Rbd Complexed with Human ACE2

All present enzymatic activity of Crystal Structure of Bq.1.1 Rbd Complexed with Human ACE2:
3.4.17.23;

The structure of Crystal Structure of Bq.1.1 Rbd Complexed with Human ACE2, PDB code: 8wdr was solved by W.Li, Y.Xie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 3.47
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.583, 135.407, 154.48, 90, 90, 90
R / Rfree (%)	21.2 / 26.9

The binding sites of Zinc atom in the Crystal Structure of Bq.1.1 Rbd Complexed with Human ACE2 (pdb code 8wdr). 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 Bq.1.1 Rbd Complexed with Human ACE2, PDB code: 8wdr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bq.1.1 Rbd 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 Bq.1.1 Rbd Complexed with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:74.8 occ:1.00 OE2 A:GLU402 2.0 73.1 1.0 NE2 A:HIS378 2.1 64.1 1.0 NE2 A:HIS374 2.1 81.3 1.0 OE1 A:GLU402 2.4 85.1 1.0 CD A:GLU402 2.5 79.8 1.0 CD2 A:HIS374 2.9 71.4 1.0 CD2 A:HIS378 2.9 59.9 1.0 CE1 A:HIS378 3.2 62.9 1.0 CE1 A:HIS374 3.2 76.1 1.0 OE2 A:GLU375 3.3 86.1 1.0 CD A:GLU375 4.0 78.0 1.0 OE1 A:GLU375 4.0 84.3 1.0 CG A:GLU402 4.0 78.9 1.0 CG A:HIS378 4.1 52.1 1.0 CG A:HIS374 4.1 68.5 1.0 ND1 A:HIS378 4.2 62.5 1.0 ND1 A:HIS374 4.2 71.9 1.0 CA A:GLU402 5.0 69.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bq.1.1 Rbd 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 Bq.1.1 Rbd Complexed with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:58.4 occ:1.00 OE2 C:GLU402 2.0 53.2 1.0 NE2 C:HIS374 2.1 57.5 1.0 NE2 C:HIS378 2.1 52.1 1.0 CD C:GLU402 2.8 55.4 1.0 CE1 C:HIS374 2.9 47.6 1.0 OE1 C:GLU402 2.9 51.8 1.0 CD2 C:HIS378 3.0 50.1 1.0 CD2 C:HIS374 3.2 57.7 1.0 CE1 C:HIS378 3.2 57.7 1.0 OE2 C:GLU375 3.5 71.9 1.0 ND1 C:HIS374 4.0 49.0 1.0 CG C:GLU402 4.1 72.3 1.0 CG C:HIS378 4.2 47.1 1.0 CG C:HIS374 4.2 53.1 1.0 ND1 C:HIS378 4.2 52.7 1.0 CD C:GLU375 4.5 72.2 1.0 OE1 C:GLU375 5.0 80.9 1.0

W.Li, Z.Xu, T.Niu, Y.Xie, Z.Zhao, D.Li, Q.He, W.Sun, K.Shi, W.Guo, Z.Chang, K.Liu, Z.Fan, J.Qi, G.F.Gao. Key Mechanistic Features of the Trade-Off Between Antibody Escape and Host Cell Binding in the Sars-Cov-2 Omicron Variant Spike Proteins. Embo J. V. 43 1484 2024.
ISSN: ESSN 1460-2075
PubMed: 38467833
DOI: 10.1038/S44318-024-00062-Z