Zinc in PDB 7ood: Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells

The structure of Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	25 atoms
Potassium	(K)	1 atom

The binding sites of Zinc atom in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells (pdb code 7ood). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells, PDB code: 7ood:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ y:Zn102 b:84.8 occ:1.00 SG y:CYS30 2.3 69.2 1.0 SG y:CYS33 2.3 72.1 1.0 SG y:CYS45 2.4 66.8 1.0 SG y:CYS43 2.5 64.5 1.0 CB y:CYS30 3.4 69.2 1.0 CB y:CYS33 3.4 72.1 1.0 CB y:CYS45 3.6 66.8 1.0 CB y:CYS43 3.7 64.5 1.0 CA y:CYS33 4.3 72.1 1.0 C y:CYS33 4.3 72.1 1.0 N y:CYS45 4.4 66.8 1.0 N y:CYS33 4.6 72.1 1.0 O y:GLN31 4.6 71.4 1.0 CA y:CYS45 4.6 66.8 1.0 CB y:LYS35 4.7 63.4 1.0 N y:GLY34 4.7 68.4 1.0 O y:CYS33 4.7 72.1 1.0 CA y:CYS30 4.7 69.2 1.0 O y:CYS30 4.9 69.2 1.0 C y:CYS30 4.9 69.2 1.0 C y:GLY34 5.0 68.4 1.0

Zinc binding site 2 out of 3 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 2:Zn101 b:96.6 occ:1.00 ND1 2:HIS32 1.8 74.0 1.0 SG 2:CYS11 2.1 85.6 1.0 CB 2:CYS11 2.1 85.6 1.0 SG 2:CYS14 2.1 81.0 1.0 CE1 2:HIS32 2.3 74.0 1.0 SG 2:CYS27 2.9 76.8 1.0 CG 2:HIS32 3.1 74.0 1.0 CA 2:CYS11 3.2 85.6 1.0 CB 2:CYS27 3.2 76.8 1.0 N 2:CYS11 3.2 85.6 1.0 NE2 2:HIS32 3.6 74.0 1.0 OG1 2:THR29 3.6 74.7 1.0 CB 2:HIS32 3.8 74.0 1.0 CB 2:CYS14 3.8 81.0 1.0 CD2 2:HIS32 3.9 74.0 1.0 C 2:ILE10 4.2 77.6 1.0 C 2:CYS11 4.3 85.6 1.0 N 2:CYS14 4.5 81.0 1.0 CA 2:CYS14 4.6 81.0 1.0 CA 2:CYS27 4.6 76.8 1.0 CB 2:ILE10 4.8 77.6 1.0 O 2:CYS11 4.9 85.6 1.0 N 2:LYS12 4.9 98.2 1.0 CA 2:ILE10 4.9 77.6 1.0 N 2:ILE10 5.0 77.6 1.0 O 2:ILE10 5.0 77.6 1.0

Zinc binding site 3 out of 3 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ z:Zn101 b:84.4 occ:1.00 SG z:CYS38 2.3 65.6 1.0 SG z:CYS14 2.3 71.2 1.0 SG z:CYS41 2.3 69.6 1.0 SG z:CYS11 2.3 68.5 1.0 CB z:CYS11 3.1 68.5 1.0 CB z:CYS38 3.5 65.6 1.0 CB z:CYS14 3.5 71.2 1.0 CB z:CYS41 3.7 69.6 1.0 N z:CYS14 3.9 71.2 1.0 N z:CYS41 4.2 69.6 1.0 CA z:CYS14 4.3 71.2 1.0 CA z:CYS11 4.6 68.5 1.0 CA z:CYS41 4.6 69.6 1.0 CB z:ASP13 4.7 71.1 1.0 CB z:ARG40 4.7 68.2 1.0 CG2 z:VAL45 4.8 63.2 1.0 CA z:CYS38 4.9 65.6 1.0 N z:ASP13 4.9 71.1 1.0 C z:ASP13 4.9 71.1 1.0 C z:CYS14 4.9 71.2 1.0 N z:ARG15 4.9 70.4 1.0 CB z:VAL45 5.0 63.2 1.0

L.Xue, S.Lenz, M.Zimmermann-Kogadeeva, D.Tegunov, P.Cramer, P.Bork, J.Rappsilber, J.Mahamid. Visualizing Translation Dynamics at Atomic Detail Inside A Bacterial Cell. Nature V. 610 205 2022.
ISSN: ESSN 1476-4687
PubMed: 36171285
DOI: 10.1038/S41586-022-05255-2