Zinc in PDB 8t4s: Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit

All present enzymatic activity of Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit:
4.2.99.18;

The structure of Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium

(Mg)

97 atoms

The binding sites of Zinc atom in the Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit (pdb code 8t4s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit, PDB code: 8t4s:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:114.3 occ:1.00 SG a:CYS26 2.3 71.9 1.0 SG a:CYS77 2.3 80.0 1.0 SG a:CYS74 2.3 70.1 1.0 SG a:CYS23 2.3 79.3 1.0 CB a:CYS77 3.0 70.3 1.0 CB a:CYS23 3.2 74.5 1.0 CB a:CYS74 3.4 66.7 1.0 CB a:CYS26 3.5 70.8 1.0 N a:CYS26 3.8 68.3 1.0 N a:CYS74 3.9 69.1 1.0 N a:CYS77 4.1 70.8 1.0 CA a:CYS77 4.1 68.0 1.0 CA a:CYS74 4.2 64.7 1.0 O a:CYS74 4.2 76.2 1.0 CA a:CYS26 4.2 69.7 1.0 CB a:ASN25 4.5 69.2 1.0 CB a:ARG28 4.6 68.9 1.0 C a:CYS74 4.6 69.1 1.0 CA a:CYS23 4.7 73.5 1.0 C a:CYS26 4.9 73.3 1.0 C a:ASN25 4.9 70.0 1.0

Zinc binding site 2 out of 3 in the Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn201 b:66.0 occ:1.00 SG d:CYS24 2.3 41.1 1.0 SG d:CYS39 2.3 46.0 1.0 SG d:CYS42 2.3 38.5 1.0 SG d:CYS21 2.3 36.9 1.0 CB d:CYS42 3.1 34.8 1.0 CB d:CYS21 3.3 28.2 1.0 CB d:CYS39 3.4 29.6 1.0 CB d:CYS24 3.5 30.8 1.0 N d:CYS39 3.9 30.0 1.0 N d:CYS24 3.9 31.3 1.0 CA d:CYS39 4.2 26.8 1.0 N d:CYS42 4.3 27.5 1.0 CA d:CYS42 4.3 24.9 1.0 CA d:CYS24 4.3 26.9 1.0 CB d:VAL23 4.5 21.3 1.0 CA d:CYS21 4.7 22.1 1.0 O2' 2:G1495 4.7 37.3 1.0 C d:CYS39 4.8 30.8 1.0 O d:CYS39 4.8 40.5 1.0 C d:VAL23 4.9 29.5 1.0 C d:CYS24 5.0 34.5 1.0

Zinc binding site 3 out of 3 in the Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mers-Cov NSP1 Protein Bound to the Human 40S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn500 b:127.5 occ:1.00 SG f:CYS141 2.3 81.4 1.0 SG f:CYS121 2.3 105.5 1.0 SG f:CYS126 2.3 113.1 1.0 SG f:CYS144 2.3 95.5 1.0 CB f:CYS126 3.1 112.5 1.0 CB f:CYS121 3.3 100.1 1.0 OG f:SER123 3.4 108.2 1.0 CB f:CYS141 3.5 76.4 1.0 CB f:CYS144 3.6 88.2 1.0 N f:CYS144 3.8 85.5 1.0 CB f:SER123 4.0 108.2 1.0 CA f:CYS144 4.3 86.2 1.0 CB f:LYS143 4.5 78.4 1.0 CA f:CYS126 4.5 111.2 1.0 CA f:CYS121 4.7 98.8 1.0 CG2 f:VAL130 4.7 100.5 1.0 CA f:CYS141 4.8 75.3 1.0 C f:LYS143 4.9 78.9 1.0 CB f:LEU146 4.9 77.2 1.0 C f:CYS144 5.0 88.3 1.0

S.C.Devarkar, M.Vetick, S.Balaji, I.B.Lomakin, L.Yang, D.Jin, W.V.Gilbert, S.Chen, Y.Xiong. Structural Basis For Translation Inhibition By Mers-Cov NSP1 Reveals A Conserved Mechanism For Betacoronaviruses Cell Rep 2023.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2023.113156