Zinc in PDB 4dr2: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Multiple Copies of Paromomycin Molecules Bound

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Multiple Copies of Paromomycin Molecules Bound, PDB code: 4dr2 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)	44.39 / 3.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.596, 402.596, 177.577, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.1

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

Magnesium

(Mg)

327 atoms

The binding sites of Zinc atom in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Multiple Copies of Paromomycin Molecules Bound (pdb code 4dr2). 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 Multiple Copies of Paromomycin Molecules Bound, PDB code: 4dr2:
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 Multiple Copies of Paromomycin Molecules 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 Multiple Copies of Paromomycin Molecules Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.6 occ:1.00 SG D:CYS9 2.2 53.4 1.0 SG D:CYS31 2.2 77.7 1.0 SG D:CYS26 2.3 77.6 1.0 SG D:CYS12 2.3 73.6 1.0 CB D:CYS9 3.7 0.7 1.0 CB D:CYS12 3.8 1.0 1.0 CA D:CYS9 4.0 0.2 1.0 CB D:CYS26 4.0 94.0 1.0 CB D:CYS31 4.1 0.3 1.0 O D:LEU19 4.3 0.3 1.0 O D:CYS31 4.4 0.9 1.0 N D:CYS9 4.7 86.8 1.0 CA D:CYS26 4.8 0.5 1.0 CA D:CYS31 4.8 0.3 1.0 N D:LEU21 4.9 0.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Multiple Copies of Paromomycin Molecules 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 Multiple Copies of Paromomycin Molecules Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.4 occ:1.00 SG N:CYS43 2.3 70.9 1.0 SG N:CYS27 2.3 69.8 1.0 SG N:CYS40 2.3 99.3 1.0 SG N:CYS24 2.3 0.9 1.0 CB N:CYS43 3.1 75.8 1.0 CB N:CYS24 3.3 92.7 1.0 CB N:CYS40 3.4 0.6 1.0 CB N:CYS27 3.4 90.2 1.0 N N:CYS40 3.8 0.3 1.0 N N:CYS27 3.9 94.3 1.0 N N:CYS43 4.1 83.1 1.0 CA N:CYS40 4.1 0.7 1.0 CB N:ARG29 4.1 89.1 1.0 CA N:CYS43 4.2 79.4 1.0 CA N:CYS27 4.2 87.6 1.0 C N:CYS40 4.8 0.7 1.0 N N:ARG29 4.8 99.1 1.0 C N:LEU39 4.8 98.9 1.0 CA N:CYS24 4.8 93.3 1.0 C N:CYS27 4.8 80.6 1.0 N N:GLY28 4.8 84.3 1.0 CB N:ARG26 4.9 81.1 1.0 O N:CYS40 5.0 0.1 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