Zinc in PDB 7k5i: Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome

All present enzymatic activity of Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome:
4.2.99.18;

The structure of Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome (pdb code 7k5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome, PDB code: 7k5i:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn201 b:30.0 occ:1.00 SG d:CYS24 1.8 64.2 1.0 SG d:CYS42 1.8 66.0 1.0 SG d:CYS21 2.4 65.9 1.0 CB d:CYS42 3.2 66.0 1.0 CB d:CYS24 3.3 64.2 1.0 CB d:CYS39 3.3 65.6 1.0 CB d:CYS21 3.5 65.9 1.0 SG d:CYS39 4.1 65.6 1.0 N d:CYS24 4.1 64.2 1.0 N d:CYS39 4.3 65.6 1.0 CA d:CYS24 4.3 64.2 1.0 CA d:CYS39 4.4 65.6 1.0 CA d:CYS42 4.5 66.0 1.0 CB d:VAL23 4.6 63.6 1.0 N d:CYS42 4.7 66.0 1.0 O2' 2:G1495 4.8 85.4 1.0 N3 2:G1495 4.9 85.4 1.0 C d:VAL23 4.9 63.6 1.0 CA d:CYS21 5.0 65.9 1.0 C d:CYS24 5.0 64.2 1.0

Zinc binding site 2 out of 3 in the Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn500 b:0.9 occ:1.00 SG f:CYS144 1.9 0.7 1.0 SG f:CYS141 2.3 0.5 1.0 SG f:CYS126 2.3 0.5 1.0 SG f:CYS121 2.4 0.9 1.0 CB f:CYS126 3.5 0.5 1.0 CB f:CYS141 3.5 0.5 1.0 CB f:CYS144 3.6 0.7 1.0 CB f:CYS121 3.7 0.9 1.0 CB f:LYS143 3.9 0.7 1.0 CG1 f:VAL130 4.0 0.9 1.0 N f:CYS144 4.0 0.7 1.0 CA f:CYS144 4.4 0.7 1.0 CB f:SER123 4.6 0.3 1.0 C f:LYS143 4.7 0.7 1.0 CG f:LYS143 4.8 0.7 1.0 CA f:CYS126 4.8 0.5 1.0 CA f:LYS143 4.9 0.7 1.0 CA f:CYS141 4.9 0.5 1.0 OG f:SER123 5.0 0.3 1.0 C f:CYS126 5.0 0.5 1.0

Zinc binding site 3 out of 3 in the Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 NSP1 in Complex with Human 40S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:65.8 occ:1.00 SG a:CYS23 1.2 52.8 1.0 SG a:CYS26 2.3 53.5 1.0 SG a:CYS74 2.4 48.2 1.0 SG a:CYS77 2.4 50.7 1.0 CB a:CYS23 2.6 52.8 1.0 CB a:CYS77 3.4 50.7 1.0 N a:CYS26 3.5 53.5 1.0 CB a:CYS74 3.6 48.2 1.0 N a:CYS74 3.7 48.2 1.0 CB a:CYS26 3.7 53.5 1.0 CA a:CYS23 3.9 52.8 1.0 N a:ASN25 4.1 56.1 1.0 CA a:CYS26 4.2 53.5 1.0 CA a:CYS74 4.2 48.2 1.0 C a:ASN25 4.3 56.1 1.0 CA a:ASN25 4.4 56.1 1.0 C a:CYS23 4.4 52.8 1.0 CB a:ASN25 4.5 56.1 1.0 N a:THR24 4.5 55.9 1.0 C a:TYR73 4.6 51.6 1.0 CA a:TYR73 4.7 51.6 1.0 CA a:CYS77 4.7 50.7 1.0 N a:ALA27 4.7 49.3 1.0 OD1 a:ASN25 4.8 56.1 1.0 CG a:ASN25 4.8 56.1 1.0 N a:CYS77 4.9 50.7 1.0 O a:CYS23 4.9 52.8 1.0 C a:CYS26 5.0 53.5 1.0

M.Shi, L.Wang, P.Fontana, S.Vora, Y.Zhang, T.M.Fu, J.Lieberman, H.Wu. Sars-Cov-2 NSP1 Suppresses Host But Not Viral Translation Through A Bipartite Mechanism. Biorxiv 2020.
PubMed: 32995777
DOI: 10.1101/2020.09.18.302901