Zinc in PDB 4dr3: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound, PDB code: 4dr3 was solved by H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.55 / 3.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	404.041, 404.041, 173.527, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.6

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound also contains other interesting chemical elements:

Magnesium

(Mg)

264 atoms

The binding sites of Zinc atom in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound (pdb code 4dr3). 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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound, PDB code: 4dr3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.5 occ:1.00 SG D:CYS26 2.3 0.3 1.0 SG D:CYS31 2.3 0.9 1.0 SG D:CYS9 2.3 0.8 1.0 SG D:CYS12 2.3 0.6 1.0 O D:CYS31 3.6 0.1 1.0 CB D:CYS12 3.8 0.5 1.0 CB D:CYS9 3.8 0.9 1.0 CB D:CYS31 3.8 0.0 1.0 CB D:CYS26 4.0 0.8 1.0 O D:LEU19 4.2 0.1 1.0 CA D:CYS31 4.2 1.0 1.0 CA D:CYS9 4.2 1.0 1.0 C D:CYS31 4.3 0.3 1.0 CA D:CYS26 4.5 0.7 1.0 CG D:LYS22 4.6 0.1 1.0 CB D:LYS22 4.9 0.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.2 occ:1.00 SG N:CYS43 2.3 0.7 1.0 SG N:CYS27 2.3 0.1 1.0 SG N:CYS24 2.3 0.4 1.0 SG N:CYS40 2.3 0.7 1.0 CB N:CYS43 3.3 0.7 1.0 CB N:CYS40 3.5 0.4 1.0 CB N:CYS27 3.7 0.2 1.0 N N:CYS27 3.8 0.0 1.0 N N:CYS40 3.8 0.6 1.0 CB N:CYS24 3.9 0.7 1.0 CA N:CYS40 4.2 1.0 1.0 CB N:ARG29 4.2 0.0 1.0 CA N:CYS27 4.2 0.7 1.0 N N:CYS43 4.4 0.8 1.0 CA N:CYS43 4.4 0.8 1.0 N N:ARG29 4.6 0.1 1.0 N N:GLY28 4.7 0.6 1.0 CB N:ARG26 4.7 0.7 1.0 C N:CYS27 4.7 1.0 1.0 C N:ARG26 4.8 0.5 1.0 C N:LEU39 4.9 0.8 1.0 C N:CYS40 4.9 0.1 1.0 N N:ARG26 4.9 0.6 1.0 O N:CYS24 5.0 0.2 1.0

H.Demirci, F.Murphy, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl. A Structural Basis For Streptomycin-Induced Misreading of the Genetic Code. Nat Commun V. 4 1355 2013.
ISSN: ESSN 2041-1723
PubMed: 23322043
DOI: 10.1038/NCOMMS2346