Chlorine in PDB 7xo8: Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound

All present enzymatic activity of Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound:
3.4.17.23;

The structure of Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Chlorine atom in the Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound (pdb code 7xo8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound, PDB code: 7xo8:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl901 b:52.3 occ:1.00 NH1 D:ARG169 2.9 67.2 1.0 NZ D:LYS481 3.1 50.6 1.0 NE D:ARG169 3.5 67.2 1.0 CZ D:ARG169 3.6 67.2 1.0 CB D:ASP499 3.7 59.0 1.0 NE1 D:TRP477 3.8 51.4 1.0 CH2 D:TRP478 4.0 54.4 1.0 CZ2 D:TRP477 4.0 51.4 1.0 CE2 D:TRP477 4.3 51.4 1.0 CG D:ASP499 4.4 59.0 1.0 CZ2 D:TRP165 4.4 67.8 1.0 CE D:LYS481 4.4 50.6 1.0 CZ2 D:TRP478 4.5 54.4 1.0 CZ3 D:TRP478 4.6 54.4 1.0 OD2 D:ASP499 4.7 59.0 1.0 CA D:ASP499 4.8 59.0 1.0 CD D:ARG169 4.8 67.2 1.0 O D:ASP499 4.8 59.0 1.0 C D:ASP499 4.9 59.0 1.0 NH2 D:ARG169 4.9 67.2 1.0 CD1 D:TRP477 5.0 51.4 1.0 NE1 D:TRP165 5.0 67.8 1.0

Chlorine binding site 2 out of 3 in the Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl901 b:52.3 occ:1.00 NH1 F:ARG169 2.9 67.2 1.0 NZ F:LYS481 3.1 50.6 1.0 NE F:ARG169 3.5 67.2 1.0 CZ F:ARG169 3.6 67.2 1.0 CB F:ASP499 3.7 59.0 1.0 NE1 F:TRP477 3.8 51.4 1.0 CH2 F:TRP478 4.0 54.4 1.0 CZ2 F:TRP477 4.0 51.4 1.0 CE2 F:TRP477 4.3 51.4 1.0 CG F:ASP499 4.4 59.0 1.0 CZ2 F:TRP165 4.4 67.8 1.0 CE F:LYS481 4.4 50.6 1.0 CZ2 F:TRP478 4.5 54.4 1.0 CZ3 F:TRP478 4.6 54.4 1.0 OD2 F:ASP499 4.7 59.0 1.0 CA F:ASP499 4.8 59.0 1.0 CD F:ARG169 4.8 67.2 1.0 O F:ASP499 4.8 59.0 1.0 C F:ASP499 4.9 59.0 1.0 NH2 F:ARG169 4.9 67.2 1.0 CD1 F:TRP477 5.0 51.4 1.0 NE1 F:TRP165 5.0 67.8 1.0

Chlorine binding site 3 out of 3 in the Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sars-Cov-2 Omicron Ba.2 Variant Spike Trimer with Three Human ACE2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl901 b:52.3 occ:1.00 NH1 E:ARG169 2.9 67.2 1.0 NZ E:LYS481 3.1 50.6 1.0 NE E:ARG169 3.5 67.2 1.0 CZ E:ARG169 3.6 67.2 1.0 CB E:ASP499 3.7 59.0 1.0 NE1 E:TRP477 3.8 51.4 1.0 CH2 E:TRP478 4.0 54.4 1.0 CZ2 E:TRP477 4.0 51.4 1.0 CE2 E:TRP477 4.3 51.4 1.0 CG E:ASP499 4.4 59.0 1.0 CZ2 E:TRP165 4.4 67.8 1.0 CE E:LYS481 4.4 50.6 1.0 CZ2 E:TRP478 4.5 54.4 1.0 CZ3 E:TRP478 4.6 54.4 1.0 OD2 E:ASP499 4.7 59.0 1.0 CA E:ASP499 4.8 59.0 1.0 CD E:ARG169 4.8 67.2 1.0 O E:ASP499 4.8 59.0 1.0 C E:ASP499 4.9 59.0 1.0 NH2 E:ARG169 4.9 67.2 1.0 CD1 E:TRP477 5.0 51.4 1.0 NE1 E:TRP165 5.0 67.8 1.0

Y.Xu, C.Wu, X.Cao, C.Gu, H.Liu, M.Jiang, X.Wang, Q.Yuan, K.Wu, J.Liu, D.Wang, X.He, X.Wang, S.J.Deng, H.E.Xu, W.Yin. Structural and Biochemical Mechanism For Increased Infectivity and Immune Evasion of Omicron Ba.2 Variant Compared to Ba.1 and Their Possible Mouse Origins. Cell Res. V. 32 609 2022.
ISSN: ISSN 1001-0602
PubMed: 35641567
DOI: 10.1038/S41422-022-00672-4