Zinc in PDB 8ana: Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit

The structure of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium

(Mg)

216 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit (pdb code 8ana). 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 the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit, PDB code: 8ana:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 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 the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 3:Zn101 b:40.2 occ:1.00 ND1 3:HIS33 2.1 37.6 1.0 SG 3:CYS27 2.3 41.0 1.0 SG 3:CYS14 2.3 41.4 1.0 SG 3:CYS11 2.3 44.1 1.0 CE1 3:HIS33 3.0 37.6 1.0 CG 3:HIS33 3.1 36.8 1.0 CB 3:HIS33 3.4 35.8 1.0 CB 3:CYS27 3.4 42.1 1.0 CB 3:CYS11 3.5 45.2 1.0 N 3:CYS14 3.5 45.8 1.0 CB 3:CYS14 3.5 43.2 1.0 N 3:CYS11 3.6 45.5 1.0 CA 3:CYS14 3.7 44.6 1.0 CA 3:CYS11 4.0 46.3 1.0 NE2 3:HIS33 4.2 37.5 1.0 CD2 3:HIS33 4.2 37.0 1.0 C 3:ASN13 4.3 47.6 1.0 C 3:CYS11 4.3 48.4 1.0 O 3:CYS11 4.4 49.1 1.0 C 3:LEU10 4.5 44.9 1.0 CB 3:LEU10 4.6 43.4 1.0 CA 3:CYS27 4.6 42.5 1.0 CB 3:GLU30 4.7 51.5 1.0 N 3:ASN13 4.7 50.0 1.0 N 3:LEU10 4.7 42.6 1.0 CB 3:ASN13 4.8 50.1 1.0 CA 3:ASN13 4.8 49.5 1.0 CA 3:LEU10 4.9 43.8 1.0 CA 3:HIS33 4.9 35.2 1.0 O 3:GLU30 4.9 47.3 1.0 O 3:ASN13 5.0 47.2 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 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 the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn101 b:288.2 occ:1.00 SG 4:CYS18 2.3 289.7 1.0 SG 4:CYS37 2.3 281.8 1.0 SG 4:CYS40 2.3 293.0 1.0 SG 4:CYS16 2.3 286.9 1.0 CB 4:CYS18 3.4 290.2 1.0 CB 4:CYS37 3.4 280.2 1.0 CB 4:CYS16 3.4 286.4 1.0 CB 4:CYS40 3.4 293.0 1.0 N 4:CYS37 3.9 278.0 1.0 N 4:CYS18 3.9 291.6 1.0 CA 4:CYS37 4.2 278.7 1.0 CA 4:CYS18 4.3 291.0 1.0 N 4:CYS40 4.5 290.4 1.0 CA 4:CYS40 4.6 293.1 1.0 N 4:SER17 4.6 291.1 1.0 C 4:VAL36 4.6 277.4 1.0 CA 4:CYS16 4.7 286.2 1.0 C 4:CYS37 4.9 278.3 1.0 CA 4:VAL36 4.9 278.0 1.0 C 4:CYS16 5.0 288.9 1.0 O 4:ASP35 5.0 281.7 1.0

T.O.Koller, M.Morici, M.J.Berger, H.Safdari, D.S.Lele, B.Beckert, K.J.Kaur, D.N.Wilson. Structural Basis For Translation Inhibition By the Glycosylated Antimicrobial Peptide Drosocin From Drosophila Melanogaster To Be Published 2023.
DOI: 10.1038/S41589-023-01293-7