Zinc in PDB 7oie: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B:
3.1.1.29;

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B (pdb code 7oie). 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 5B, PDB code: 7oie:
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 5B


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 5B within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:21.3 occ:1.00 SG 0:CYS123 2.3 0.6 1.0 SG 0:CYS126 2.3 4.5 1.0 SG 0:CYS113 2.3 18.8 1.0 SG 0:CYS110 2.3 17.4 1.0 CB 0:CYS123 3.2 0.6 1.0 CB 0:CYS110 3.2 17.4 1.0 CB 0:CYS113 3.7 18.8 1.0 CB 0:CYS126 3.8 4.5 1.0 N 0:CYS113 4.0 18.8 1.0 CB 0:GLU112 4.0 19.8 1.0 N 0:CYS126 4.3 4.5 1.0 CA 0:CYS113 4.4 18.8 1.0 C 0:GLU112 4.6 19.8 1.0 O 0:CYS110 4.6 17.4 1.0 CA 0:CYS110 4.7 17.4 1.0 CA 0:CYS126 4.7 4.5 1.0 CA 0:CYS123 4.7 0.6 1.0 CA 0:GLU112 4.8 19.8 1.0 O 0:HIS115 4.8 14.9 1.0 OE1 0:GLU112 4.9 19.8 1.0 C 0:CYS110 5.0 17.4 1.0 CG 0:GLU112 5.0 19.8 1.0 CB 0:TYR125 5.0 16.6 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B


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 5B within 5.0Å range: probe atom residue distance (Å) B Occ r:Zn301 b:59.9 occ:1.00 SG I:CYS64 2.3 31.9 1.0 SG r:CYS70 2.3 18.5 1.0 SG r:CYS108 2.3 17.0 1.0 SG r:CYS73 2.4 17.6 1.0 CB I:CYS64 2.8 31.9 1.0 N r:CYS70 3.5 18.5 1.0 CB r:CYS70 3.6 18.5 1.0 CB r:CYS73 3.6 17.6 1.0 CA I:CYS64 3.8 31.9 1.0 OE1 r:GLU111 4.0 11.9 1.0 CB r:CYS108 4.1 17.0 1.0 CA r:CYS70 4.1 18.5 1.0 CB r:GLN69 4.4 24.1 1.0 O I:CYS64 4.4 31.9 1.0 CE r:LYS78 4.5 15.8 1.0 O r:CYS70 4.5 18.5 1.0 C r:GLN69 4.5 24.1 1.0 N r:GLN69 4.6 24.1 1.0 N r:CYS73 4.6 17.6 1.0 C I:CYS64 4.6 31.9 1.0 CA r:CYS73 4.7 17.6 1.0 CA r:GLN69 4.7 24.1 1.0 C r:CYS70 4.8 18.5 1.0 N I:CYS64 4.8 31.9 1.0 CD r:GLU111 4.9 11.9 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