Zinc in PDB 1ibk: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin, PDB code: 1ibk was solved by J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	316.23 / 3.31
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.160, 401.160, 176.360, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.2

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

Magnesium

(Mg)

113 atoms

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

Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


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 Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn306 b:24.1 occ:1.23 SG D:CYS31 2.1 12.6 1.0 SG D:CYS9 2.3 35.2 1.0 SG D:CYS26 2.3 28.7 1.0 SG D:CYS12 2.9 38.1 1.0 CB D:CYS31 3.2 12.6 1.0 CB D:CYS26 3.4 28.7 1.0 CA D:CYS31 3.6 92.3 1.0 O D:CYS31 3.8 92.3 1.0 CB D:CYS9 3.8 35.2 1.0 CA D:CYS26 4.0 0.6 1.0 CB D:CYS12 4.1 38.1 1.0 CA D:CYS9 4.2 0.0 1.0 C D:CYS31 4.2 92.3 1.0 N D:CYS9 4.9 0.0 1.0 N D:CYS26 4.9 0.6 1.0 N D:CYS31 4.9 92.3 1.0

Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


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 Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn307 b:24.1 occ:0.80 SG N:CYS27 2.0 33.6 1.0 SG N:CYS43 2.1 23.7 1.0 CB N:CYS27 2.4 33.6 1.0 SG N:CYS40 2.5 44.9 1.0 SG N:CYS24 2.7 33.4 1.0 N N:CYS27 3.1 70.2 1.0 CB N:CYS43 3.3 23.7 1.0 CA N:CYS27 3.3 70.2 1.0 CB N:CYS24 3.5 33.4 1.0 CB N:CYS40 3.5 44.9 1.0 C N:CYS27 4.1 70.2 1.0 N N:CYS40 4.1 99.5 1.0 CB N:ARG26 4.3 59.9 1.0 N N:CYS43 4.3 52.8 1.0 N N:GLY28 4.3 75.1 1.0 C N:ARG26 4.3 80.5 1.0 CB N:ARG29 4.3 73.6 1.0 CA N:CYS43 4.4 52.8 1.0 CA N:CYS40 4.4 99.5 1.0 CG N:ARG26 4.4 59.9 1.0 N2 A:G1202 4.5 56.9 1.0 N N:ARG29 4.6 0.6 1.0 CA N:ARG26 4.8 80.5 1.0 N3 A:G1202 4.8 56.9 1.0 CA N:CYS24 4.9 82.3 1.0 O N:CYS27 5.0 70.2 1.0 O N:CYS40 5.0 99.5 1.0

J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan. Recognition of Cognate Transfer Rna By the 30S Ribosomal Subunit. Science V. 292 897 2001.
ISSN: ISSN 0036-8075
PubMed: 11340196
DOI: 10.1126/SCIENCE.1060612