Zinc in PDB 8cvo: Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map

The structure of Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

The binding sites of Zinc atom in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map (pdb code 8cvo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map, PDB code: 8cvo:

Zinc binding site 1 out of 1 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:88.7 occ:1.00 CB S:CYS27 2.0 69.4 1.0 SG S:CYS43 2.3 70.1 1.0 SG S:CYS40 2.3 69.3 1.0 SG S:CYS24 2.4 68.3 1.0 SG S:CYS27 2.4 69.4 1.0 CB S:CYS24 3.3 68.3 1.0 CB S:CYS40 3.4 69.3 1.0 CB S:CYS43 3.4 70.1 1.0 CA S:CYS27 3.5 69.4 1.0 N S:CYS27 4.0 69.4 1.0 CB S:ARG29 4.1 63.9 1.0 N S:CYS43 4.1 70.1 1.0 C S:CYS27 4.3 69.4 1.0 N S:CYS40 4.3 69.3 1.0 O2 A:U1188 4.3 62.5 1.0 CA S:CYS43 4.4 70.1 1.0 CA S:CYS40 4.4 69.3 1.0 O2' A:U1188 4.5 62.5 1.0 N S:ARG29 4.6 63.9 1.0 N S:GLY28 4.8 66.9 1.0 CA S:CYS24 4.8 68.3 1.0 CD S:ARG29 4.8 63.9 1.0 O S:CYS27 4.9 69.4 1.0 C S:LEU39 4.9 69.9 1.0 C S:ARG26 5.0 70.7 1.0

I.B.Lomakin, S.C.Devarkar, S.Patel, A.Grada, C.G.Bunick. Sarecycline Inhibits Protein Translation in Cutibacterium Acnes 70S Ribosome Using A Two-Site Mechanism. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36864821
DOI: 10.1093/NAR/GKAD103