Zinc in PDB 5o60: Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis

The structure of Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis also contains other interesting chemical elements:

Magnesium

(Mg)

408 atoms

The binding sites of Zinc atom in the Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis (pdb code 5o60). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis, PDB code: 5o60:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ Y:Zn101 b:73.7 occ:1.00 SG Y:CYS8 2.4 60.9 1.0 SG Y:CYS55 2.4 76.5 1.0 SG Y:CYS52 2.5 59.6 1.0 SG Y:CYS5 2.5 53.4 1.0 CB Y:CYS55 3.4 47.0 1.0 CB Y:CYS5 3.4 39.6 1.0 CB Y:CYS8 3.5 68.7 1.0 CB Y:CYS52 3.6 33.4 1.0 N Y:CYS8 3.8 61.9 1.0 N Y:CYS52 4.0 27.2 1.0 CA Y:CYS8 4.2 66.9 1.0 N Y:CYS55 4.3 36.7 1.0 CA Y:CYS52 4.3 26.4 1.0 CA Y:CYS55 4.4 39.4 1.0 CB Y:ILE7 4.6 56.5 1.0 O Y:CYS52 4.6 30.4 1.0 C Y:CYS52 4.8 29.6 1.0 CA Y:CYS5 4.9 38.4 1.0 CB Y:LYS10 4.9 33.6 1.0 C Y:ILE7 4.9 58.2 1.0 C Y:CYS8 4.9 62.0 1.0 CD Y:LYS10 5.0 28.6 1.0

Zinc binding site 2 out of 4 in the Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ c:Zn101 b:77.2 occ:1.00 SG c:CYS18 2.3 71.5 1.0 SG c:CYS42 2.4 65.0 1.0 SG c:CYS45 2.4 73.3 1.0 SG c:CYS15 2.4 64.9 1.0 CB c:CYS15 3.3 41.3 1.0 OD1 c:ASN44 3.3 66.6 1.0 CB c:CYS42 3.4 49.8 1.0 CB c:CYS18 3.6 73.0 1.0 CB c:CYS45 3.7 66.9 1.0 N c:CYS18 4.0 62.6 1.0 CA c:CYS18 4.4 66.8 1.0 N c:CYS45 4.4 60.1 1.0 CG c:ASN44 4.5 71.3 1.0 CG c:GLN49 4.6 39.5 1.0 CA c:CYS45 4.6 61.7 1.0 CB c:VAL17 4.7 60.3 1.0 CA c:CYS15 4.8 38.3 1.0 CA c:CYS42 4.8 40.0 1.0 ND2 c:ASN44 4.9 66.2 1.0

Zinc binding site 3 out of 4 in the Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn101 b:78.0 occ:1.00 ND1 f:HIS32 2.1 68.8 1.0 SG f:CYS14 2.2 69.0 1.0 SG f:CYS11 2.3 81.8 1.0 SG f:CYS27 2.4 86.1 1.0 CE1 f:HIS32 3.0 68.3 1.0 CG f:HIS32 3.1 50.3 1.0 CB f:HIS32 3.4 43.6 1.0 CB f:CYS11 3.6 69.7 1.0 CB f:CYS27 3.7 59.7 1.0 CB f:CYS14 3.8 53.5 1.0 N f:CYS14 3.9 64.9 1.0 N f:CYS11 4.1 59.9 1.0 NE2 f:HIS32 4.1 62.1 1.0 CA f:CYS14 4.2 54.9 1.0 CD2 f:HIS32 4.2 46.6 1.0 CA f:CYS11 4.3 60.6 1.0 C f:CYS11 4.7 68.1 1.0 CB f:ASP29 4.7 66.8 1.0 C f:LYS13 4.7 63.6 1.0 CB f:LYS13 4.8 75.0 1.0 N f:LYS13 4.8 67.1 1.0 CA f:HIS32 4.9 35.7 1.0 C f:ILE10 4.9 55.8 1.0 O f:CYS11 5.0 72.0 1.0

Zinc binding site 4 out of 4 in the Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the 50S Large Ribosomal Subunit From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ g:Zn101 b:0.3 occ:1.00 SG g:CYS41 2.2 0.7 1.0 SG g:CYS18 2.3 0.7 1.0 SG g:CYS16 2.4 0.2 1.0 SG g:CYS38 2.4 0.2 1.0 CB g:CYS18 3.4 0.3 1.0 CB g:CYS41 3.5 0.3 1.0 CB g:CYS16 3.5 0.0 1.0 CB g:CYS38 3.6 1.0 1.0 N g:CYS41 3.8 0.7 1.0 N g:CYS18 4.0 0.2 1.0 N g:CYS38 4.1 0.5 1.0 CA g:CYS41 4.2 0.8 1.0 CA g:CYS18 4.3 0.2 1.0 CA g:CYS38 4.4 0.8 1.0 O g:GLU36 4.5 0.5 1.0 CB g:GLN40 4.5 99.9 1.0 CB g:HIS20 4.7 0.9 1.0 C g:VAL37 4.7 0.4 1.0 C g:GLN40 4.7 0.1 1.0 N g:GLY17 4.7 0.6 1.0 CA g:CYS16 4.9 0.4 1.0 CA g:VAL37 4.9 0.0 1.0 C g:CYS16 5.0 0.8 1.0 C g:CYS18 5.0 0.7 1.0 C g:CYS38 5.0 0.2 1.0

J.Hentschel, C.Burnside, I.Mignot, M.Leibundgut, D.Boehringer, N.Ban. The Complete Structure of the Mycobacterium Smegmatis 70S Ribosome. Cell Rep V. 20 149 2017.
ISSN: ESSN 2211-1247
PubMed: 28683309
DOI: 10.1016/J.CELREP.2017.06.029