Zinc in PDB 8p6p: Mycoplasma Pneumoniae Small Ribosomal Subunit in Chloramphenicol- Treated Cells

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

Magnesium

(Mg)

103 atoms

The binding sites of Zinc atom in the Mycoplasma Pneumoniae Small Ribosomal Subunit in Chloramphenicol- Treated Cells (pdb code 8p6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mycoplasma Pneumoniae Small Ribosomal Subunit in Chloramphenicol- Treated Cells, PDB code: 8p6p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn101 b:86.1 occ:1.00 SG M:CYS27 2.3 68.4 1.0 SG M:CYS43 2.3 63.0 1.0 SG M:CYS40 2.4 62.3 1.0 SG M:CYS24 2.6 65.9 1.0 CB M:CYS43 3.2 63.0 1.0 CB M:CYS40 3.2 62.3 1.0 CB M:CYS27 3.3 68.4 1.0 CB M:CYS24 3.5 65.9 1.0 N M:CYS40 3.8 62.3 1.0 N M:CYS27 3.9 68.4 1.0 CA M:CYS40 4.0 62.3 1.0 N M:CYS43 4.1 63.0 1.0 CA M:CYS27 4.1 68.4 1.0 CA M:CYS43 4.2 63.0 1.0 C M:CYS40 4.5 62.3 1.0 O M:CYS40 4.6 62.3 1.0 C M:CYS27 4.7 68.4 1.0 CG1 M:VAL39 4.7 61.7 1.0 CB M:ARG29 4.7 64.5 1.0 O2' 5:U1177 4.8 65.8 1.0 C M:VAL39 4.9 61.7 1.0 CB M:ARG26 4.9 68.1 1.0

Zinc binding site 2 out of 2 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn201 b:112.7 occ:1.00 ND1 Q:HIS82 2.0 80.8 1.0 SG Q:CYS79 2.3 83.8 1.0 SG Q:CYS41 2.3 89.4 1.0 SG Q:CYS44 2.4 92.7 1.0 CE1 Q:HIS82 2.9 80.8 1.0 CG Q:HIS82 3.1 80.8 1.0 CB Q:CYS79 3.2 83.8 1.0 CB Q:CYS41 3.3 89.4 1.0 CB Q:HIS82 3.6 80.8 1.0 CB Q:CYS44 3.7 92.7 1.0 N Q:CYS79 3.8 83.8 1.0 N Q:CYS44 4.0 92.7 1.0 NE2 Q:HIS82 4.1 80.8 1.0 CA Q:CYS79 4.1 83.8 1.0 CD2 Q:HIS82 4.2 80.8 1.0 CA Q:CYS44 4.2 92.7 1.0 N Q:HIS82 4.5 80.8 1.0 CA Q:HIS82 4.7 80.8 1.0 CA Q:CYS41 4.7 89.4 1.0 C Q:CYS79 4.8 83.8 1.0 C Q:PHE43 4.9 89.9 1.0 C Q:ASN78 5.0 81.7 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