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

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

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


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 3D within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:57.0 occ:1.00 SG 0:CYS113 2.3 57.6 1.0 SG 0:CYS123 2.3 35.5 1.0 SG 0:CYS126 2.3 44.6 1.0 SG 0:CYS110 2.3 53.5 1.0 CB 0:CYS123 3.0 35.5 1.0 CB 0:CYS110 3.1 53.5 1.0 CB 0:CYS113 3.4 57.6 1.0 CB 0:CYS126 3.8 44.6 1.0 N 0:CYS113 3.9 57.6 1.0 N 0:CYS126 4.0 44.6 1.0 CA 0:CYS113 4.2 57.6 1.0 CA 0:CYS123 4.5 35.5 1.0 O 0:HIS115 4.5 44.6 1.0 CA 0:CYS126 4.5 44.6 1.0 CA 0:CYS110 4.5 53.5 1.0 CB 0:TYR125 4.6 47.8 1.0 CB 0:GLU112 4.7 64.7 1.0 C 0:GLU112 4.8 64.7 1.0 N 0:GLY114 4.8 50.3 1.0 C 0:CYS123 5.0 35.5 1.0 C 0:CYS113 5.0 57.6 1.0

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


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 3D within 5.0Å range: probe atom residue distance (Å) B Occ r:Zn301 b:93.6 occ:1.00 SG r:CYS70 2.3 83.2 1.0 SG I:CYS64 2.3 95.0 1.0 SG r:CYS108 2.3 86.0 1.0 CB r:CYS73 3.0 82.8 1.0 N r:CYS70 3.6 83.2 1.0 CB I:CYS64 3.7 95.0 1.0 CB r:CYS70 3.7 83.2 1.0 SG r:CYS73 3.7 82.8 1.0 CB r:CYS108 3.9 86.0 1.0 CB r:GLN69 4.2 92.3 1.0 CA r:CYS70 4.2 83.2 1.0 CA r:CYS73 4.4 82.8 1.0 CA I:CYS64 4.4 95.0 1.0 O r:CYS70 4.5 83.2 1.0 C r:GLN69 4.6 92.3 1.0 N r:CYS73 4.6 82.8 1.0 CA r:GLN69 4.8 92.3 1.0 C r:CYS70 4.8 83.2 1.0 N r:GLN69 4.8 92.3 1.0 CE r:LYS78 4.8 77.1 1.0 OE2 r:GLU111 4.9 78.7 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