Zinc in PDB 6zoj: Sars-Cov-2-NSP1-40S Complex, Composite Map

All present enzymatic activity of Sars-Cov-2-NSP1-40S Complex, Composite Map:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13; 4.2.99.18;

The structure of Sars-Cov-2-NSP1-40S Complex, Composite Map also contains other interesting chemical elements:

Magnesium

(Mg)

166 atoms

The binding sites of Zinc atom in the Sars-Cov-2-NSP1-40S Complex, Composite Map (pdb code 6zoj). 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-NSP1-40S Complex, Composite Map, PDB code: 6zoj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Sars-Cov-2-NSP1-40S Complex, Composite Map


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-NSP1-40S Complex, Composite Map within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:69.2 occ:1.00 SG a:CYS26 2.3 27.9 1.0 SG a:CYS74 2.3 26.4 1.0 SG a:CYS77 2.3 28.1 1.0 SG a:CYS23 2.3 27.0 1.0 CB a:CYS77 3.2 28.1 1.0 CB a:CYS23 3.3 27.0 1.0 CB a:CYS26 3.5 27.9 1.0 CB a:CYS74 3.8 26.4 1.0 N a:CYS26 3.8 27.9 1.0 N a:CYS74 4.1 26.4 1.0 CA a:CYS26 4.2 27.9 1.0 CB a:ASN25 4.3 28.0 1.0 N a:CYS77 4.3 28.1 1.0 CA a:CYS77 4.3 28.1 1.0 CA a:CYS74 4.5 26.4 1.0 CB a:ARG28 4.7 24.3 1.0 C a:ASN25 4.7 28.0 1.0 CA a:CYS23 4.8 27.0 1.0 C a:CYS26 4.8 27.9 1.0 CA a:ASN25 4.9 28.0 1.0 N a:ASN25 4.9 28.0 1.0 N a:ALA27 5.0 26.0 1.0

Zinc binding site 2 out of 3 in the Sars-Cov-2-NSP1-40S Complex, Composite Map


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-NSP1-40S Complex, Composite Map within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn201 b:38.8 occ:1.00 SG d:CYS39 2.2 19.7 1.0 SG d:CYS24 2.3 22.4 1.0 SG d:CYS42 2.3 18.4 1.0 SG d:CYS21 2.3 22.3 1.0 CB d:CYS42 3.2 18.4 1.0 CB d:CYS21 3.3 22.3 1.0 CB d:CYS24 3.6 22.4 1.0 CB d:CYS39 3.7 19.7 1.0 N d:CYS24 3.8 22.4 1.0 N d:CYS39 4.0 19.7 1.0 CA d:CYS24 4.2 22.4 1.0 CA d:CYS39 4.4 19.7 1.0 CB d:VAL23 4.4 20.7 1.0 N d:CYS42 4.4 18.4 1.0 CA d:CYS42 4.4 18.4 1.0 C d:VAL23 4.7 20.7 1.0 CA d:CYS21 4.8 22.3 1.0 O d:CYS39 4.9 19.7 1.0 N d:VAL23 4.9 20.7 1.0 CA d:VAL23 4.9 20.7 1.0 C d:CYS24 4.9 22.4 1.0 C d:CYS39 4.9 19.7 1.0

Zinc binding site 3 out of 3 in the Sars-Cov-2-NSP1-40S Complex, Composite Map


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-NSP1-40S Complex, Composite Map within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn500 b:0.3 occ:1.00 SG f:CYS144 2.3 69.3 1.0 SG f:CYS141 2.3 66.4 1.0 SG f:CYS121 2.4 74.1 1.0 SG f:CYS126 2.4 77.4 1.0 CB f:CYS126 3.2 77.4 1.0 CB f:CYS141 3.2 66.4 1.0 CB f:CYS121 3.2 74.1 1.0 CB f:CYS144 3.5 69.3 1.0 OG f:SER123 3.6 78.1 1.0 CB f:SER123 3.9 78.1 1.0 N f:CYS144 4.1 69.3 1.0 CA f:CYS144 4.4 69.3 1.0 CA f:CYS126 4.6 77.4 1.0 CA f:CYS141 4.7 66.4 1.0 CB f:LEU146 4.7 67.8 1.0 CA f:CYS121 4.7 74.1 1.0 O f:CYS126 4.8 77.4 1.0 C f:LYS143 4.9 67.1 1.0 CB f:LYS143 4.9 67.1 1.0 N f:SER123 5.0 78.1 1.0 N f:CYS126 5.0 77.4 1.0

K.Schubert, E.D.Karousis, A.Jomaa, A.Scaiola, B.Echeverria, L.A.Gurzeler, M.Leibundgut, V.Thiel, O.Muhlemann, N.Ban. Sars-Cov-2 NSP1 Binds the Ribosomal Mrna Channel to Inhibit Translation. Nat.Struct.Mol.Biol. V. 27 959 2020.
ISSN: ESSN 1545-9985
PubMed: 32908316
DOI: 10.1038/S41594-020-0511-8