Zinc in PDB 5iwa: Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic, PDB code: 5iwa was solved by A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Chieko, K.Masahito, C.Takemoto, S.Yokoyama, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.03 / 3.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	413.140, 413.140, 173.630, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.8

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic also contains other interesting chemical elements:

Magnesium	(Mg)	204 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic (pdb code 5iwa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic, PDB code: 5iwa:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.7 occ:1.00 SG D:CYS12 2.1 97.0 1.0 SG D:CYS26 2.4 97.8 1.0 SG D:CYS31 2.6 83.3 1.0 SG D:CYS9 2.7 73.8 1.0 CB D:CYS26 3.9 63.5 1.0 CB D:CYS12 4.0 0.9 1.0 CB D:CYS31 4.2 66.8 1.0 CB D:CYS9 4.2 67.3 1.0 CB D:LYS22 4.2 0.9 1.0 CA D:CYS26 4.2 1.0 1.0 CA D:CYS9 4.3 0.9 1.0 CA D:CYS31 4.6 0.5 1.0 N D:LYS22 4.6 0.7 1.0 N D:LEU21 4.7 0.9 1.0 N D:TYR20 4.8 0.0 1.0 N D:CYS9 4.9 0.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.9 occ:1.00 SG N:CYS27 1.8 0.9 1.0 SG N:CYS43 1.9 0.0 1.0 SG N:CYS40 2.3 0.5 1.0 SG N:CYS24 2.3 0.2 1.0 CB N:CYS43 3.1 0.8 1.0 CB N:CYS24 3.2 0.6 1.0 CB N:CYS27 3.4 0.8 1.0 CB N:CYS40 3.7 0.0 1.0 N N:CYS27 3.7 0.8 1.0 N N:CYS40 3.9 0.1 1.0 CA N:CYS27 4.1 0.0 1.0 N N:CYS43 4.2 0.3 1.0 CA N:CYS43 4.3 0.8 1.0 CB N:ARG26 4.3 0.5 1.0 CA N:CYS40 4.3 0.3 1.0 CB N:ARG29 4.5 0.6 1.0 CA N:CYS24 4.6 0.9 1.0 N2 A:G1202 4.7 0.1 1.0 C N:ARG26 4.7 0.1 1.0 N N:GLY28 4.7 0.4 1.0 C N:CYS27 4.9 0.6 1.0 CA N:ARG26 4.9 0.7 1.0 N N:ARG29 4.9 0.0 1.0 C N:CYS40 5.0 0.2 1.0

A.Fabbretti, A.Schedlbauer, L.Brandi, T.Kaminishi, A.M.Giuliodori, R.Garofalo, B.Ochoa-Lizarralde, C.Takemoto, S.Yokoyama, S.R.Connell, C.O.Gualerzi, P.Fucini. Inhibition of Translation Initiation Complex Formation By GE81112 Unravels A 16S Rrna Structural Switch Involved in P-Site Decoding. Proc.Natl.Acad.Sci.Usa V. 113 E2286 2016.
ISSN: ESSN 1091-6490
PubMed: 27071098
DOI: 10.1073/PNAS.1521156113