Zinc in PDB 4ji8: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4ji8 was solved by H.Demirci, L.Wang, F.Murphy Iv, E.Murphy, J.Carr, S.Blanchard, G.Jogl, A.E.Dahlberg, S.T.Gregory, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.85 / 3.74
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.305, 400.305, 214.785, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 18.7

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium

(Mg)

414 atoms

The binding sites of Zinc atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 4ji8). 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 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4ji8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.3 occ:1.00 SG D:CYS9 2.1 87.0 1.0 SG D:CYS31 2.2 0.4 1.0 SG D:CYS26 2.2 90.5 1.0 SG D:CYS12 2.3 93.0 1.0 O D:CYS31 3.1 0.6 1.0 CG D:LYS22 3.4 0.7 1.0 CB D:CYS9 3.6 0.1 1.0 CD D:LYS22 3.6 0.4 1.0 O D:LEU19 3.7 1.0 1.0 CB D:CYS31 3.8 0.9 1.0 CA D:CYS9 3.8 0.6 1.0 CB D:CYS26 3.9 1.0 1.0 CB D:CYS12 3.9 0.5 1.0 C D:CYS31 4.0 0.8 1.0 CD1 D:LEU21 4.0 0.2 1.0 CA D:CYS31 4.1 1.0 1.0 CB D:LYS22 4.3 0.7 1.0 CA D:CYS26 4.4 1.0 1.0 N D:CYS9 4.7 0.1 1.0 C D:CYS9 5.0 0.2 1.0 C D:LEU19 5.0 0.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.3 occ:1.00 SG N:CYS40 2.3 0.6 1.0 SG N:CYS27 2.3 0.2 1.0 SG N:CYS24 2.3 0.3 1.0 SG N:CYS43 2.3 0.6 1.0 CB N:CYS43 3.0 0.6 1.0 CB N:CYS27 3.4 0.8 1.0 CB N:CYS40 3.5 0.6 1.0 N N:CYS27 3.5 0.2 1.0 CB N:CYS24 3.5 0.4 1.0 CA N:CYS27 3.9 0.6 1.0 N N:CYS40 4.0 0.5 1.0 CB N:ARG29 4.0 0.1 1.0 CB N:ARG26 4.0 0.8 1.0 N N:CYS43 4.1 0.7 1.0 CA N:CYS43 4.2 0.9 1.0 CA N:CYS40 4.3 0.6 1.0 N2 A:G1202 4.4 0.4 1.0 C N:CYS27 4.5 0.8 1.0 O N:CYS24 4.5 0.2 1.0 C N:ARG26 4.6 0.3 1.0 N N:GLY28 4.6 0.5 1.0 N N:ARG29 4.7 0.6 1.0 C N:CYS24 4.7 0.9 1.0 CA N:CYS24 4.7 0.9 1.0 CA N:ARG26 4.8 0.8 1.0 CD2 N:LEU39 4.9 0.9 1.0 CG N:ARG26 4.9 0.0 1.0 CG N:ARG29 4.9 0.8 1.0 N N:ARG26 4.9 0.0 1.0 C N:CYS40 5.0 0.2 1.0

H.Demirci, L.Wang, F.V.Murphy, E.L.Murphy, J.F.Carr, S.C.Blanchard, G.Jogl, A.E.Dahlberg, S.T.Gregory. The Central Role of Protein S12 in Organizing the Structure of the Decoding Site of the Ribosome. Rna V. 19 1791 2013.
ISSN: ISSN 1355-8382
PubMed: 24152548
DOI: 10.1261/RNA.040030.113