Zinc in PDB 7xwa: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 Variant Spike Protein in Complex with Its Receptor ACE2

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 Variant Spike Protein in Complex with Its Receptor ACE2, PDB code: 7xwa was solved by T.Suzuki, K.Kimura, T.Hashiguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.39 / 3.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.51, 130.01, 101.88, 90, 92.64, 90
R / Rfree (%)	23.1 / 28.7

The binding sites of Zinc atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 Variant Spike Protein in Complex with Its Receptor ACE2 (pdb code 7xwa). 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 the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 Variant Spike Protein in Complex with Its Receptor ACE2, PDB code: 7xwa:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 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 Ba.4/5 Variant Spike Protein in Complex with Its Receptor ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:117.6 occ:0.00 NE2 A:HIS374 2.3 98.0 1.0 NE2 A:HIS378 2.3 114.0 1.0 CD2 A:HIS374 2.5 113.2 1.0 CD2 A:HIS378 2.7 117.8 1.0 OE2 A:GLU375 2.8 126.9 1.0 CE1 A:HIS378 3.4 124.1 1.0 CD A:GLU375 3.5 129.4 1.0 CE1 A:HIS374 3.6 104.9 1.0 OE1 A:GLU375 3.6 126.7 1.0 CG A:HIS374 3.9 113.4 1.0 CG A:HIS378 3.9 116.6 1.0 OE2 A:GLU402 4.1 175.0 1.0 ND1 A:HIS378 4.2 99.4 1.0 ND1 A:HIS374 4.3 101.5 1.0 CG A:GLU375 4.7 124.7 1.0 CD A:GLU402 4.7 167.1 1.0 CG A:GLU402 5.0 130.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 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 2 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Ba.4/5 Variant Spike Protein in Complex with Its Receptor ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:108.1 occ:0.00 OE2 C:GLU402 2.0 96.8 1.0 NE2 C:HIS374 2.3 108.7 1.0 NE2 C:HIS378 2.3 112.4 1.0 CD2 C:HIS374 2.5 110.0 1.0 CD2 C:HIS378 2.7 116.3 1.0 OE2 C:GLU375 2.9 103.0 1.0 CD C:GLU402 3.1 100.9 1.0 CE1 C:HIS378 3.5 117.5 1.0 CE1 C:HIS374 3.5 122.0 1.0 CD C:GLU375 3.6 106.7 1.0 OE1 C:GLU402 3.6 108.0 1.0 OE1 C:GLU375 3.7 119.3 1.0 CG C:HIS374 3.8 113.9 1.0 CG C:HIS378 3.9 108.0 1.0 ND1 C:HIS378 4.3 107.8 1.0 ND1 C:HIS374 4.3 124.5 1.0 CG C:GLU402 4.4 100.4 1.0 CG C:GLU375 4.8 102.2 1.0 O C:HIS374 5.0 98.7 1.0

I.Kimura, D.Yamasoba, T.Tamura, N.Nao, T.Suzuki, Y.Oda, S.Mitoma, J.Ito, H.Nasser, J.Zahradnik, K.Uriu, S.Fujita, Y.Kosugi, L.Wang, M.Tsuda, M.Kishimoto, H.Ito, R.Suzuki, R.Shimizu, M.M.Begum, K.Yoshimatsu, K.T.Kimura, J.Sasaki, K.Sasaki-Tabata, Y.Yamamoto, T.Nagamoto, J.Kanamune, K.Kobiyama, H.Asakura, M.Nagashima, K.Sadamasu, K.Yoshimura, K.Shirakawa, A.Takaori-Kondo, J.Kuramochi, G.Schreiber, K.J.Ishii, T.Hashiguchi, T.Ikeda, A.Saito, T.Fukuhara, S.Tanaka, K.Matsuno, K.Sato. Virological Characteristics of the Sars-Cov-2 Omicron Ba.2 Subvariants, Including Ba.4 and Ba.5. Cell V. 185 3992 2022.
ISSN: ISSN 1097-4172
PubMed: 36198317
DOI: 10.1016/J.CELL.2022.09.018