Zinc in PDB 9d89: E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)

The structure of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) also contains other interesting chemical elements:

Magnesium	(Mg)	204 atoms
Potassium	(K)	93 atoms

The binding sites of Zinc atom in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) (pdb code 9d89). 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 E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement), PDB code: 9d89:

Zinc binding site 1 out of 1 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:88.9 occ:1.00 ND1 C:HIS33 2.2 96.9 1.0 SG C:CYS14 2.3 84.4 1.0 SG C:CYS11 2.4 98.6 1.0 SG C:CYS27 2.4 90.8 1.0 CE1 C:HIS33 3.2 103.6 1.0 CG C:HIS33 3.2 92.3 1.0 CB C:CYS27 3.4 91.8 1.0 CB C:HIS33 3.5 79.0 1.0 CB C:CYS14 3.5 84.2 1.0 CB C:CYS11 3.5 107.3 1.0 N C:CYS14 3.5 91.1 1.0 CA C:CYS14 3.8 85.3 1.0 N C:CYS11 3.8 106.5 1.0 CA C:CYS11 4.1 109.1 1.0 NE2 C:HIS33 4.3 107.0 1.0 CD2 C:HIS33 4.3 95.8 1.0 C C:ASN13 4.4 97.9 1.0 C C:CYS11 4.5 114.2 1.0 O C:CYS11 4.5 119.5 1.0 CA C:CYS27 4.7 89.7 1.0 CB C:LEU10 4.7 94.1 1.0 CB C:ASN13 4.7 112.9 1.0 C C:LEU10 4.8 101.0 1.0 N C:ASN13 4.9 106.3 1.0 CA C:ASN13 4.9 105.7 1.0 CB C:GLU30 4.9 124.5 1.0 N C:LEU10 5.0 85.7 1.0

P.V.Panteleev, E.B.Pichkur, R.N.Kruglikov, A.Paleskava, O.V.Shulenina, I.A.Bolosov, I.V.Bogdanov, V.N.Safronova, S.V.Balandin, V.I.Marina, T.I.Kombarova, O.V.Korobova, O.V.Shamova, A.G.Myasnikov, A.I.Borzilov, I.A.Osterman, P.V.Sergiev, A.A.Bogdanov, O.A.Dontsova, A.L.Konevega, T.V.Ovchinnikova. Rumicidins Are A Family of Mammalian Host-Defense Peptides Plugging the 70S Ribosome Exit Tunnel. Nat Commun V. 15 8925 2024.
ISSN: ESSN 2041-1723
PubMed: 39414793
DOI: 10.1038/S41467-024-53309-Y