Zinc in PDB 7oi7: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2:
3.1.1.29;

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2 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 2 (pdb code 7oi7). 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 2, PDB code: 7oi7:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:83.3 occ:1.00 SG r:CYS70 2.3 73.6 1.0 SG r:CYS108 2.3 73.5 1.0 SG I:CYS64 2.3 83.9 1.0 CG r:GLN69 3.3 75.6 1.0 NE2 r:GLN69 3.3 75.6 1.0 CB r:CYS73 3.4 76.9 1.0 CB r:CYS70 3.6 73.6 1.0 CB I:CYS64 3.7 83.9 1.0 N r:CYS70 3.7 73.6 1.0 CD r:GLN69 3.8 75.6 1.0 CB r:CYS108 4.0 73.5 1.0 SG r:CYS73 4.2 76.9 1.0 CA r:CYS70 4.2 73.6 1.0 CA r:CYS73 4.5 76.9 1.0 CA I:CYS64 4.5 83.9 1.0 CE r:LYS78 4.6 68.5 1.0 N r:CYS73 4.6 76.9 1.0 CB r:GLN69 4.6 75.6 1.0 C r:GLN69 4.7 75.6 1.0 O r:CYS70 4.7 73.6 1.0 N r:GLN69 4.8 75.6 1.0 CA r:GLN69 4.9 75.6 1.0 C r:CYS70 4.9 73.6 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:53.7 occ:1.00 SG 0:CYS113 2.3 32.4 1.0 SG 0:CYS123 2.3 21.1 1.0 SG 0:CYS110 2.3 28.6 1.0 SG 0:CYS126 2.3 26.5 1.0 CB 0:CYS123 2.8 21.1 1.0 CB 0:CYS110 3.0 28.6 1.0 CB 0:CYS113 3.3 32.4 1.0 CB 0:CYS126 3.8 26.5 1.0 OE2 0:GLU112 3.8 45.2 1.0 N 0:CYS126 4.1 26.5 1.0 N 0:CYS113 4.3 32.4 1.0 O 0:HIS115 4.3 25.6 1.0 CA 0:CYS123 4.3 21.1 1.0 CA 0:CYS113 4.3 32.4 1.0 CA 0:CYS110 4.4 28.6 1.0 CD 0:GLU112 4.5 45.2 1.0 CA 0:CYS126 4.6 26.5 1.0 CB 0:TYR125 4.8 28.4 1.0 C 0:CYS123 4.9 21.1 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