Zinc in PDB 7oia: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3C

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3C:
3.1.1.29;

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3C also contains other interesting chemical elements:

Magnesium

(Mg)

49 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3C (pdb code 7oia). 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 Late Human 39S Mitoribosome Assembly Intermediates, State 3C, PDB code: 7oia:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3C


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 Late Human 39S Mitoribosome Assembly Intermediates, State 3C within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:29.0 occ:1.00 SG 0:CYS123 2.3 13.1 1.0 SG 0:CYS113 2.3 20.6 1.0 SG 0:CYS110 2.3 21.3 1.0 SG 0:CYS126 2.3 17.6 1.0 CB 0:CYS110 3.0 21.3 1.0 CB 0:CYS123 3.0 13.1 1.0 CB 0:CYS113 3.3 20.6 1.0 CB 0:CYS126 3.8 17.6 1.0 N 0:CYS126 4.0 17.6 1.0 N 0:CYS113 4.1 20.6 1.0 CA 0:CYS113 4.3 20.6 1.0 CA 0:CYS110 4.5 21.3 1.0 CA 0:CYS123 4.5 13.1 1.0 CA 0:CYS126 4.5 17.6 1.0 CB 0:TYR125 4.6 18.4 1.0 OE1 0:GLU112 4.7 23.9 1.0 O 0:HIS115 4.8 17.0 1.0 C 0:CYS110 4.9 21.3 1.0 C 0:CYS113 4.9 20.6 1.0 N 0:GLY114 5.0 17.8 1.0 N 0:TYR125 5.0 18.4 1.0 C 0:TYR125 5.0 18.4 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3C


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 Late Human 39S Mitoribosome Assembly Intermediates, State 3C within 5.0Å range: probe atom residue distance (Å) B Occ r:Zn301 b:34.1 occ:1.00 SG I:CYS64 2.3 32.0 1.0 SG r:CYS70 2.3 30.1 1.0 SG r:CYS108 2.3 28.2 1.0 CB r:CYS73 3.2 29.9 1.0 CB I:CYS64 3.4 32.0 1.0 CB r:CYS108 3.7 28.2 1.0 CB r:CYS70 3.8 30.1 1.0 N r:CYS70 4.0 30.1 1.0 SG r:CYS73 4.1 29.9 1.0 CA I:CYS64 4.4 32.0 1.0 CA r:CYS73 4.4 29.9 1.0 CA r:CYS70 4.4 30.1 1.0 N r:CYS73 4.4 29.9 1.0 CE r:LYS78 4.5 25.0 1.0 CB r:GLN69 4.6 32.7 1.0 O r:CYS70 4.9 30.1 1.0 C r:GLN69 5.0 32.7 1.0 CA r:CYS108 5.0 28.2 1.0

J.Cheng, O.Berninghausen, R.Beckmann. A Distinct Assembly Pathway of the Human 39S Late Pre-Mitoribosome. Nat Commun V. 12 4544 2021.
ISSN: ESSN 2041-1723
PubMed: 34315873
DOI: 10.1038/S41467-021-24818-X