Zinc in PDB 8if2: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Bq.1.1 Variant Spike Protein in Complex with Its Receptor ACE2

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Bq.1.1 Variant Spike Protein in Complex with Its Receptor ACE2, PDB code: 8if2 was solved by K.Kimura, T.Suzuki, T.Hashiguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 2.78
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	120.052, 120.052, 167.416, 90, 90, 120
R / Rfree (%)	20 / 24.5

The binding sites of Zinc atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Bq.1.1 Variant Spike Protein in Complex with Its Receptor ACE2 (pdb code 8if2). 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 Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Bq.1.1 Variant Spike Protein in Complex with Its Receptor ACE2, PDB code: 8if2:

Zinc binding site 1 out of 1 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Bq.1.1 Variant Spike Protein in Complex with Its Receptor 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 the Receptor Binding Domain of Sars-Cov-2 Omicron Bq.1.1 Variant Spike Protein in Complex with Its Receptor ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:64.3 occ:1.00 OE1 A:GLU402 2.0 69.8 1.0 NE2 A:HIS374 2.3 48.9 1.0 NE2 A:HIS378 2.3 58.5 1.0 CD A:GLU402 2.6 64.0 1.0 OE2 A:GLU402 2.6 63.2 1.0 CE1 A:HIS374 3.2 67.5 1.0 CD2 A:HIS378 3.2 54.3 1.0 CE1 A:HIS378 3.3 62.6 1.0 CD2 A:HIS374 3.3 54.8 1.0 OE2 A:GLU375 4.0 60.6 1.0 CG A:GLU402 4.1 53.1 1.0 OH A:TYR515 4.1 62.5 1.0 CE1 A:TYR515 4.3 68.5 1.0 ND1 A:HIS374 4.4 67.9 1.0 CG A:HIS378 4.4 58.0 1.0 ND1 A:HIS378 4.4 61.7 1.0 CG A:HIS374 4.4 62.9 1.0 CD A:GLU375 4.5 56.2 1.0 OE1 A:GLU375 4.5 64.2 1.0 CB A:GLU402 4.7 52.9 1.0 CZ A:TYR515 4.7 64.4 1.0 CA A:GLU402 4.9 62.6 1.0

K.Kimura, T.Suzuki, T.Hashiguchi. Convergent Evolution of Sars-Cov-2 Omicron Subvariants Leading to the Emergence of Bq.1.1 Variant. Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38188-Z