Zinc in PDB 8p8b: Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells

All present enzymatic activity of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells:
5.2.1.8;

The structure of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells also contains other interesting chemical elements:

Potassium	(K)	1 atom
Magnesium	(Mg)	229 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells (pdb code 8p8b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells, PDB code: 8p8b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mycoplasma Pneumoniae Large Ribosomal Subunit 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 Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 2:Zn101 b:105.7 occ:1.00 SG 2:CYS27 2.4 78.1 1.0 SG 2:CYS14 2.6 68.0 1.0 CD2 2:HIS32 2.8 50.4 1.0 CB 2:CYS27 3.2 70.1 1.0 SG 2:CYS11 3.2 78.0 1.0 CG 2:HIS32 3.4 50.9 1.0 CB 2:HIS32 3.5 49.1 1.0 CB 2:CYS11 3.7 61.6 1.0 NE2 2:HIS32 4.0 51.4 1.0 CB 2:CYS14 4.1 61.9 1.0 N 2:CYS11 4.2 66.5 1.0 N 2:CYS14 4.2 62.7 1.0 CB 2:THR29 4.4 53.1 1.0 CA 2:CYS14 4.4 59.5 1.0 CA 2:CYS11 4.6 59.4 1.0 O 2:THR29 4.7 48.3 1.0 ND1 2:HIS32 4.7 56.2 1.0 CA 2:CYS27 4.7 62.2 1.0 N 2:THR29 4.8 56.6 1.0 CE1 2:HIS32 4.9 54.0 1.0 CB 2:ILE10 4.9 51.2 1.0 C 2:ASP13 5.0 66.7 1.0

Zinc binding site 2 out of 4 in the Mycoplasma Pneumoniae Large Ribosomal Subunit 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 Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ x:Zn201 b:5.1 occ:1.00 SG x:CYS39 2.4 3.5 1.0 SG x:CYS42 2.5 4.8 1.0 SG x:CYS19 2.5 1.4 1.0 SG x:CYS16 2.5 5.6 1.0 CB x:CYS42 3.1 5.2 1.0 O x:ALA17 3.2 13.7 1.0 N x:CYS42 3.5 4.2 1.0 CB x:CYS16 3.6 0.4 1.0 CB x:CYS39 3.7 4.7 1.0 O x:CYS19 3.7 8.4 1.0 CA x:CYS42 3.9 6.2 1.0 CB x:CYS19 4.1 6.9 1.0 N x:CYS39 4.2 8.8 1.0 C x:LYS41 4.2 1.1 1.0 N x:CYS19 4.2 1.7 1.0 CB x:LYS41 4.4 5.0 1.0 C x:ALA17 4.4 7.9 1.0 CA x:CYS39 4.5 6.9 1.0 CA x:CYS19 4.5 2.3 1.0 C x:CYS19 4.6 3.5 1.0 CA x:LYS41 4.7 2.6 1.0 N x:ALA17 4.7 5.8 1.0 N x:LYS41 4.7 9.1 1.0 C x:CYS16 4.9 2.8 1.0 C x:CYS39 4.9 5.7 1.0 CA x:CYS16 4.9 1.2 1.0 O x:LYS41 5.0 1.9 1.0

Zinc binding site 3 out of 4 in the Mycoplasma Pneumoniae Large Ribosomal Subunit 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 Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ y:Zn103 b:116.8 occ:1.00 SG y:CYS43 2.4 71.7 1.0 SG y:CYS33 2.4 78.3 1.0 SG y:CYS30 2.5 70.7 1.0 SG y:CYS45 2.8 65.9 1.0 CB y:CYS30 3.4 54.7 1.0 CB y:CYS43 3.5 63.5 1.0 CB y:CYS33 3.6 68.0 1.0 CB y:CYS45 3.8 60.5 1.0 N y:CYS33 4.2 65.1 1.0 N y:CYS45 4.2 57.6 1.0 CA y:CYS33 4.5 69.2 1.0 CG y:LYS35 4.6 63.0 1.0 CA y:CYS45 4.6 57.0 1.0 N y:SER44 4.7 62.6 1.0 CA y:CYS30 4.9 55.1 1.0 CA y:CYS43 4.9 54.9 1.0 O y:MET47 4.9 65.7 1.0 CB y:MET47 4.9 54.9 1.0 NZ y:LYS35 5.0 64.8 1.0 C y:LYS32 5.0 65.4 1.0

Zinc binding site 4 out of 4 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ z:Zn101 b:91.0 occ:1.00 SG z:CYS38 2.4 41.0 1.0 SG z:CYS14 2.4 64.5 1.0 SG z:CYS11 2.5 67.3 1.0 SG z:CYS41 2.6 65.2 1.0 CB z:CYS11 3.4 50.9 1.0 CB z:CYS38 3.7 31.8 1.0 N z:CYS14 3.7 66.2 1.0 CB z:CYS14 3.7 63.7 1.0 CB z:CYS41 4.0 54.7 1.0 N z:CYS41 4.1 49.0 1.0 CB z:ASP13 4.2 64.6 1.0 CB z:ARG40 4.2 47.0 1.0 CA z:CYS14 4.3 66.3 1.0 CG1 z:VAL45 4.5 34.7 1.0 N z:ASP13 4.7 61.9 1.0 C z:ASP13 4.7 65.4 1.0 CA z:CYS41 4.7 50.8 1.0 CA z:ASP13 4.7 64.0 1.0 CA z:CYS11 4.8 48.5 1.0 C z:ARG40 5.0 47.7 1.0

L.Xue, C.M.T.Spahn, M.Schacherl, J.Mahamid. Structural Insights Into Context-Dependent Inhibitory Mechanisms of Chloramphenicol in Cells Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01441-0