Zinc in PDB 8ppk: Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit

All present enzymatic activity of Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit:
4.2.99.18;

The structure of Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit also contains other interesting chemical elements:

Magnesium

(Mg)

111 atoms

The binding sites of Zinc atom in the Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit (pdb code 8ppk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit, PDB code: 8ppk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:155.0 occ:1.00 SG a:CYS26 2.2 87.4 1.0 SG a:CYS74 2.3 75.4 1.0 SG a:CYS77 2.3 101.7 1.0 SG a:CYS23 2.3 97.5 1.0 CB a:CYS77 2.9 73.6 1.0 CB a:CYS23 3.2 75.1 1.0 CB a:CYS26 3.4 69.9 1.0 CB a:CYS74 3.5 61.0 1.0 N a:CYS26 3.8 78.6 1.0 N a:CYS74 3.9 56.1 1.0 CA a:CYS77 4.1 65.9 1.0 N a:CYS77 4.1 66.9 1.0 CA a:CYS26 4.1 73.5 1.0 CA a:CYS74 4.3 49.5 1.0 CB a:ASN25 4.5 73.5 1.0 C a:ASN25 4.6 76.0 1.0 CA a:CYS23 4.7 69.3 1.0 CB a:ARG28 4.8 64.5 1.0 C a:CYS26 4.8 76.4 1.0 C a:CYS74 4.9 67.3 1.0 CA a:ASN25 4.9 70.5 1.0 N a:ASN25 4.9 75.0 1.0 OD1 a:ASN25 5.0 92.1 1.0

Zinc binding site 2 out of 3 in the Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn201 b:150.7 occ:1.00 SG d:CYS39 2.2 112.0 1.0 SG d:CYS24 2.3 104.6 1.0 SG d:CYS42 2.3 117.8 1.0 SG d:CYS21 2.3 109.3 1.0 CB d:CYS42 3.0 98.0 1.0 CB d:CYS21 3.2 91.5 1.0 CB d:CYS24 3.4 96.9 1.0 CB d:CYS39 3.5 99.5 1.0 N d:CYS24 3.7 99.5 1.0 N d:CYS39 4.0 98.4 1.0 CA d:CYS24 4.1 96.3 1.0 CA d:CYS42 4.2 93.2 1.0 N d:CYS42 4.2 85.9 1.0 CA d:CYS39 4.3 98.7 1.0 CB d:VAL23 4.3 81.3 1.0 CA d:CYS21 4.7 84.2 1.0 C d:VAL23 4.7 89.8 1.0 O2' 2:G1495 4.8 101.2 1.0 O d:CYS39 4.8 106.0 1.0 C d:CYS24 4.8 95.9 1.0 C d:CYS39 4.8 103.6 1.0 CA d:VAL23 4.9 82.3 1.0 N d:VAL23 4.9 91.5 1.0 N3 2:G1495 4.9 96.3 1.0 CG d:MET38 5.0 96.3 1.0 CG1 d:VAL23 5.0 85.5 1.0 N2 2:G1495 5.0 89.4 1.0

Zinc binding site 3 out of 3 in the Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bat-Hp-Cov NSP1 and EIF1 Bound to the Human 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn500 b:328.4 occ:1.00 SG f:CYS126 2.2 287.2 1.0 SG f:CYS144 2.3 263.6 1.0 SG f:CYS141 2.3 269.6 1.0 SG f:CYS121 2.3 288.4 1.0 CB f:CYS121 3.1 284.3 1.0 CB f:CYS141 3.2 267.1 1.0 CB f:CYS126 3.4 285.1 1.0 CB f:CYS144 3.6 261.8 1.0 OG f:SER123 3.6 281.8 1.0 CB f:SER123 4.0 281.9 1.0 O f:CYS126 4.2 286.5 1.0 N f:CYS144 4.2 262.2 1.0 CA f:CYS144 4.4 262.0 1.0 CA f:CYS121 4.6 283.2 1.0 CA f:CYS141 4.6 266.8 1.0 CB f:LEU146 4.6 261.0 1.0 CA f:CYS126 4.6 285.2 1.0 C f:CYS126 4.9 285.5 1.0 C f:LYS143 4.9 249.6 1.0 CD2 f:LEU146 4.9 260.7 1.0 C f:CYS141 5.0 266.3 1.0 N f:SER123 5.0 281.8 1.0

K.Schubert, E.D.Karousis, I.Ban, C.P.Lapointe, M.Leibundgut, E.Baumlin, E.Kummerant, A.Scaiola, T.Schonhut, J.Ziegelmuller, J.D.Puglisi, O.Muhlemann, N.Ban. Universal Features of NSP1-Mediated Translational Shutdown By Coronaviruses. Mol.Cell V. 83 3546 2023.
ISSN: ISSN 1097-2765
PubMed: 37802027
DOI: 10.1016/J.MOLCEL.2023.09.002