Zinc in PDB 7oi9: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3B

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

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3B 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 3B (pdb code 7oi9). 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 3B, PDB code: 7oi9:
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 3B


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 3B within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:53.7 occ:1.00 SG 0:CYS113 2.3 40.6 1.0 SG 0:CYS110 2.3 33.0 1.0 SG 0:CYS123 2.3 20.9 1.0 SG 0:CYS126 2.3 29.4 1.0 CB 0:CYS123 2.9 20.9 1.0 CB 0:CYS110 3.0 33.0 1.0 CB 0:CYS113 3.1 40.6 1.0 N 0:CYS113 3.6 40.6 1.0 CB 0:CYS126 3.9 29.4 1.0 CA 0:CYS113 3.9 40.6 1.0 OE2 0:GLU112 4.1 45.8 1.0 CD 0:GLU112 4.2 45.8 1.0 CG 0:GLU112 4.3 45.8 1.0 CA 0:CYS123 4.4 20.9 1.0 CA 0:CYS110 4.5 33.0 1.0 N 0:CYS126 4.6 29.4 1.0 O 0:HIS115 4.7 34.9 1.0 C 0:GLU112 4.7 45.8 1.0 OE1 0:GLU112 4.8 45.8 1.0 CA 0:CYS126 4.8 29.4 1.0 C 0:CYS113 4.8 40.6 1.0 N 0:GLY114 4.9 37.5 1.0 N 0:CYS123 5.0 20.9 1.0

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


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 3B within 5.0Å range: probe atom residue distance (Å) B Occ r:Zn301 b:54.4 occ:1.00 SG I:CYS64 2.3 54.6 1.0 SG r:CYS70 2.3 49.8 1.0 SG r:CYS108 2.3 44.9 1.0 CB I:CYS64 3.2 54.6 1.0 CB r:CYS73 3.3 49.7 1.0 CB r:CYS70 3.4 49.8 1.0 N r:CYS70 3.4 49.8 1.0 CA r:CYS70 4.0 49.8 1.0 CB r:CYS108 4.0 44.9 1.0 CA I:CYS64 4.1 54.6 1.0 CB r:GLN69 4.1 53.2 1.0 SG r:CYS73 4.2 49.7 1.0 C r:GLN69 4.4 53.2 1.0 O r:CYS70 4.5 49.8 1.0 N r:CYS73 4.5 49.7 1.0 CE r:LYS78 4.5 42.8 1.0 CA r:CYS73 4.5 49.7 1.0 C r:CYS70 4.6 49.8 1.0 CA r:GLN69 4.7 53.2 1.0 N r:GLN69 4.8 53.2 1.0 N r:CYS108 4.9 44.9 1.0 O I:CYS64 5.0 54.6 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