Zinc in PDB 8zdb: Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3

All present enzymatic activity of Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3:
2.7.11.1; 4.2.99.18;

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3 (pdb code 8zdb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3, PDB code: 8zdb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3 within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:17.4 occ:1.00 SG a:CYS23 2.3 10.3 1.0 SG a:CYS74 2.3 8.8 1.0 SG a:CYS26 2.4 14.9 1.0 CB a:CYS23 3.2 10.3 1.0 CB a:CYS74 3.3 8.8 1.0 N a:CYS26 3.4 14.9 1.0 CB a:CYS26 3.5 14.9 1.0 N a:CYS74 3.6 8.8 1.0 CB a:CYS77 3.7 11.6 1.0 SG a:CYS77 3.7 11.6 1.0 CA a:CYS74 4.0 8.8 1.0 CA a:CYS26 4.0 14.9 1.0 CB a:ASN25 4.1 12.9 1.0 C a:ASN25 4.3 12.9 1.0 N a:ASN25 4.5 12.9 1.0 N a:ALA27 4.5 10.0 1.0 CG a:ARG28 4.5 4.4 1.0 CA a:ASN25 4.5 12.9 1.0 O a:CYS74 4.5 8.8 1.0 CA a:CYS23 4.5 10.3 1.0 C a:TYR73 4.7 4.6 1.0 CB a:ARG28 4.7 4.4 1.0 C a:CYS74 4.7 8.8 1.0 C a:CYS26 4.8 14.9 1.0 C a:CYS23 4.8 10.3 1.0 N a:ARG28 4.8 4.4 1.0 CA a:CYS77 4.9 11.6 1.0 N a:CYS77 4.9 11.6 1.0 O a:CYS23 5.0 10.3 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Human Ubiquitylated 40S Ribosome with RIOK3 within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn201 b:32.0 occ:1.00 CB d:CYS39 2.5 25.1 1.0 SG d:CYS39 2.6 25.1 1.0 SG d:CYS42 2.8 23.6 1.0 CB d:CYS24 3.4 31.6 1.0 C1' 2:G1495 3.5 36.2 1.0 O2' 2:G1495 3.6 36.2 1.0 SG d:CYS24 3.9 31.6 1.0 SG d:CYS21 4.0 31.2 1.0 CB d:CYS42 4.1 23.6 1.0 CA d:CYS39 4.1 25.1 1.0 C8 2:G1495 4.1 36.2 1.0 CB d:ASN26 4.1 31.8 1.0 C2' 2:G1495 4.2 36.2 1.0 N9 2:G1495 4.2 36.2 1.0 CB d:CYS21 4.3 31.2 1.0 O4' 2:G1495 4.3 36.2 1.0 ND2 d:ASN26 4.6 31.8 1.0 N d:CYS39 4.7 25.1 1.0 N d:CYS42 4.8 23.6 1.0 CA d:CYS24 4.8 31.6 1.0 CG d:ASN26 4.9 31.8 1.0 C d:CYS39 4.9 25.1 1.0

J.Cheng, Z.Huang, M.Wang, Y.Li, R.Beckmann, J.Cheng. N/A N/A.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2025.01.013