Zinc in PDB 8cbj: Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex

All present enzymatic activity of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex:
2.7.11.1;

The structure of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex also contains other interesting chemical elements:

Magnesium

(Mg)

46 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex (pdb code 8cbj). 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 OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex, PDB code: 8cbj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


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 OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:244.4 occ:1.00 SG b:CYS40 2.3 161.9 1.0 SG b:CYS56 2.3 176.3 1.0 SG b:CYS37 2.3 158.9 1.0 SG b:CYS59 2.3 177.3 1.0 CB b:CYS56 3.2 176.3 1.0 CB b:CYS40 3.7 161.9 1.0 CB b:CYS59 4.0 177.3 1.0 CB b:CYS37 4.1 158.9 1.0 OG b:SER58 4.2 171.7 1.0 ND2 b:ASN42 4.2 153.2 1.0 N b:CYS59 4.4 177.3 1.0 N b:CYS40 4.4 161.9 1.0 CA b:CYS40 4.6 161.9 1.0 CA b:CYS56 4.6 176.3 1.0 CA b:CYS59 4.8 177.3 1.0 OD1 b:ASN42 4.8 153.2 1.0 CG b:ASN42 4.9 153.2 1.0 O b:CYS37 4.9 158.9 1.0 O b:CYS59 4.9 177.3 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


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 OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn101 b:304.4 occ:1.00 SG d:CYS42 2.3 153.4 1.0 SG d:CYS39 2.3 153.5 1.0 SG d:CYS21 2.3 149.9 1.0 SG d:CYS24 2.3 228.6 1.0 CB d:CYS42 3.2 153.4 1.0 CB d:CYS21 3.6 149.9 1.0 CB d:CYS24 3.7 228.6 1.0 CB d:SER26 3.8 176.9 1.0 CB d:CYS39 3.8 153.5 1.0 N d:CYS24 3.9 228.6 1.0 CB d:VAL23 4.2 184.0 1.0 N d:CYS42 4.3 153.4 1.0 CA d:CYS24 4.3 228.6 1.0 CA d:CYS42 4.3 153.4 1.0 N d:CYS39 4.5 153.5 1.0 OG d:SER26 4.5 176.9 1.0 CA d:CYS39 4.7 153.5 1.0 CG1 d:VAL23 4.8 184.0 1.0 C d:CYS24 4.8 228.6 1.0 C d:VAL23 4.8 184.0 1.0 N d:SER26 4.8 176.9 1.0 CA d:VAL23 4.9 184.0 1.0 CA d:CYS21 4.9 149.9 1.0 CA d:SER26 4.9 176.9 1.0 N d:VAL23 5.0 184.0 1.0

K.Ikeuchi, N.Ivic, R.Buschauer, J.Cheng, T.Frohlich, Y.Matsuo, O.Berninghausen, T.Inada, T.Becker, R.Beckmann. Molecular Basis For Recognition and Deubiquitination of 40S Ribosomes By OTU2. Nat Commun V. 14 2730 2023.
ISSN: ESSN 2041-1723
PubMed: 37169754
DOI: 10.1038/S41467-023-38161-W