Zinc in PDB 8a5i: Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit.

The structure of Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. also contains other interesting chemical elements:

Potassium	(K)	1 atom
Magnesium	(Mg)	165 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. (pdb code 8a5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit., PDB code: 8a5i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ 5:Zn101 b:177.5 occ:1.00 OD1 5:ASN32 2.0 193.9 1.0 SG 5:CYS33 2.3 177.8 1.0 SG 5:CYS30 2.3 155.7 1.0 SG 5:CYS43 2.3 171.8 1.0 SG 5:CYS46 2.3 184.6 1.0 CG 5:ASN32 2.8 203.2 1.0 ND2 5:ASN32 3.1 202.7 1.0 CB 5:CYS46 3.4 200.6 1.0 CB 5:CYS30 3.4 156.9 1.0 CB 5:CYS43 3.4 170.5 1.0 CB 5:CYS33 3.4 173.7 1.0 N 5:CYS33 3.5 186.4 1.0 CA 5:CYS33 4.0 174.7 1.0 CA 5:ASP50 4.1 308.8 1.0 NE2 5:GLN48 4.1 235.2 1.0 CB 5:ASP50 4.2 294.8 1.0 CB 5:ASN32 4.2 202.0 1.0 C 5:ASN32 4.4 198.7 1.0 N 5:CYS46 4.5 224.5 1.0 CA 5:CYS46 4.5 218.6 1.0 N 5:ASN32 4.6 197.6 1.0 CA 5:ASN32 4.6 199.7 1.0 N 5:ASP50 4.8 301.0 1.0 CA 5:CYS30 4.8 160.0 1.0 CA 5:CYS43 4.8 167.7 1.0 CD 5:ARG37 4.9 84.8 1.0 O 5:GLN48 5.0 249.6 1.0 O 5:CYS43 5.0 193.0 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ 9:Zn101 b:64.6 occ:1.00 ND1 9:HIS32 2.0 62.3 1.0 SG 9:CYS14 2.3 71.8 1.0 SG 9:CYS11 2.3 77.0 1.0 SG 9:CYS27 2.3 65.0 1.0 CE1 9:HIS32 3.0 64.1 1.0 CG 9:HIS32 3.1 62.0 1.0 CB 9:CYS27 3.4 70.4 1.0 CB 9:HIS32 3.4 58.6 1.0 CB 9:CYS11 3.5 77.8 1.0 N 9:CYS14 3.6 79.8 1.0 CB 9:CYS14 3.6 72.8 1.0 N 9:CYS11 3.6 77.9 1.0 CA 9:CYS14 3.8 75.5 1.0 CA 9:CYS11 4.0 78.9 1.0 NE2 9:HIS32 4.2 65.5 1.0 CD2 9:HIS32 4.2 61.9 1.0 C 9:CYS11 4.4 82.5 1.0 O 9:CYS11 4.4 88.2 1.0 C 9:MET10 4.4 75.5 1.0 C 9:LYS13 4.4 90.6 1.0 CB 9:ASN29 4.6 71.5 1.0 CB 9:MET10 4.6 73.2 1.0 CB 9:LYS13 4.7 108.7 1.0 N 9:MET10 4.7 68.7 1.0 N 9:LYS13 4.7 90.9 1.0 CA 9:CYS27 4.8 69.8 1.0 CA 9:MET10 4.8 72.5 1.0 CA 9:LYS13 4.8 97.7 1.0 CA 9:HIS32 5.0 57.7 1.0

T.O.Koller, K.J.Turnbull, K.Vaitkevicius, C.Crowe-Mcauliffe, M.Roghanian, O.Bulvas, J.A.Nakamoto, T.Kurata, C.Julius, G.C.Atkinson, J.Johansson, V.Hauryliuk, D.N.Wilson. Structural Basis For Hflxr-Mediated Antibiotic Resistance in Listeria Monocytogenes. Nucleic Acids Res. V. 50 11285 2022.
ISSN: ESSN 1362-4962
PubMed: 36300626
DOI: 10.1093/NAR/GKAC934