Zinc in PDB 4dr7: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound, PDB code: 4dr7 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)	48.91 / 3.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.490, 402.490, 174.790, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 20.1

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound also contains other interesting chemical elements:

Magnesium

(Mg)

344 atoms

The binding sites of Zinc atom in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound (pdb code 4dr7). 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 Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound, PDB code: 4dr7:
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 Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and 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 Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.1 occ:1.00 SG D:CYS31 2.3 0.5 1.0 SG D:CYS26 2.3 0.5 1.0 SG D:CYS9 2.3 1.0 1.0 SG D:CYS12 2.3 1.0 1.0 CB D:CYS31 3.7 0.1 1.0 CB D:LYS22 3.8 0.7 1.0 O D:CYS31 3.8 0.7 1.0 CB D:CYS9 3.8 1.0 1.0 CB D:CYS12 3.8 0.8 1.0 CB D:CYS26 3.9 0.3 1.0 O D:LEU19 4.0 0.8 1.0 CG D:LYS22 4.0 0.6 1.0 CA D:CYS9 4.2 0.9 1.0 CA D:CYS31 4.2 0.7 1.0 CA D:CYS26 4.4 0.4 1.0 C D:CYS31 4.5 0.3 1.0 N D:CYS9 4.9 0.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and 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 Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.1 occ:1.00 SG N:CYS43 2.3 0.6 1.0 SG N:CYS27 2.3 0.8 1.0 SG N:CYS24 2.3 0.6 1.0 SG N:CYS40 2.3 0.7 1.0 CB N:CYS27 2.9 0.5 1.0 CB N:CYS43 3.0 0.6 1.0 CB N:CYS24 3.1 0.6 1.0 CB N:CYS40 3.4 0.8 1.0 CB N:ARG29 3.6 0.0 1.0 N N:CYS27 3.8 0.7 1.0 N N:CYS40 3.8 0.8 1.0 CA N:CYS27 3.9 0.2 1.0 CA N:CYS43 4.1 0.1 1.0 N N:CYS43 4.1 0.8 1.0 CA N:CYS40 4.1 0.4 1.0 CG N:ARG29 4.3 0.5 1.0 C N:CYS27 4.5 0.1 1.0 CA N:CYS24 4.6 0.2 1.0 N N:ARG29 4.6 0.7 1.0 CD N:ARG29 4.7 0.5 1.0 O N:CYS40 4.7 0.7 1.0 C N:CYS40 4.8 0.8 1.0 CA N:ARG29 4.8 0.2 1.0 CB N:ARG26 4.9 0.9 1.0 N2 A:G1202 4.9 0.1 1.0 CG N:ARG26 4.9 0.5 1.0 O2' A:G1202 4.9 0.4 1.0 N N:GLY28 5.0 0.1 1.0 C N:ARG26 5.0 0.6 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