Zinc in PDB 7oi8: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A

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

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A 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 3A (pdb code 7oi8). 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 3A, PDB code: 7oi8:
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 3A


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 3A within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:47.1 occ:1.00 SG 0:CYS113 2.3 26.5 1.0 SG 0:CYS123 2.3 10.2 1.0 SG 0:CYS126 2.3 20.7 1.0 SG 0:CYS110 2.3 25.3 1.0 CB 0:CYS110 3.0 25.3 1.0 CB 0:CYS123 3.1 10.2 1.0 CB 0:CYS113 3.3 26.5 1.0 CB 0:CYS126 3.8 20.7 1.0 N 0:CYS113 3.9 26.5 1.0 N 0:CYS126 4.1 20.7 1.0 CA 0:CYS113 4.2 26.5 1.0 CA 0:CYS110 4.5 25.3 1.0 CA 0:CYS126 4.5 20.7 1.0 CA 0:CYS123 4.5 10.2 1.0 CB 0:TYR125 4.7 24.8 1.0 O 0:HIS115 4.8 21.6 1.0 C 0:CYS113 4.8 26.5 1.0 C 0:CYS110 4.9 25.3 1.0 N 0:GLY114 4.9 28.6 1.0 O 0:CYS110 4.9 25.3 1.0

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


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 3A within 5.0Å range: probe atom residue distance (Å) B Occ r:Zn301 b:73.1 occ:1.00 SG r:CYS73 2.3 42.6 1.0 SG I:CYS64 2.3 57.9 1.0 SG r:CYS70 2.3 47.2 1.0 SG r:CYS108 2.3 48.0 1.0 CB I:CYS64 2.7 57.9 1.0 CB r:CYS73 3.1 42.6 1.0 CA I:CYS64 3.3 57.9 1.0 OE2 r:GLU111 3.4 47.2 1.0 CB r:CYS70 3.7 47.2 1.0 CB r:CYS108 3.9 48.0 1.0 N r:CYS70 3.9 47.2 1.0 O I:CYS64 4.0 57.9 1.0 C I:CYS64 4.2 57.9 1.0 CB r:GLN69 4.2 54.0 1.0 CA r:CYS73 4.4 42.6 1.0 N I:CYS64 4.4 57.9 1.0 CA r:CYS70 4.4 47.2 1.0 N r:GLN69 4.5 54.0 1.0 CG r:GLN69 4.6 54.0 1.0 C r:GLN69 4.6 54.0 1.0 N r:CYS73 4.6 42.6 1.0 CA r:GLN69 4.7 54.0 1.0 CD r:GLU111 4.7 47.2 1.0 N r:CYS108 4.9 48.0 1.0 O I:SER63 5.0 58.6 1.0 CA r:CYS108 5.0 48.0 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