Zinc in PDB 7dui: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound, PDB code: 7dui was solved by H.Demirci, E.Destan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.73 / 3.62
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400, 400, 173, 90, 90, 90
R / Rfree (%)	17.7 / 21.3

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound also contains other interesting chemical elements:

Magnesium

(Mg)

249 atoms

The binding sites of Zinc atom in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound (pdb code 7dui). 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 Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound, PDB code: 7dui:
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 Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs 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 Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:204.9 occ:1.00 SG D:CYS31 2.3 150.6 1.0 SG D:CYS9 2.3 99.9 1.0 SG D:CYS26 2.3 124.9 1.0 SG D:CYS12 2.3 132.7 1.0 O D:LEU19 3.2 210.1 1.0 O D:CYS31 3.2 175.9 1.0 CB D:CYS31 3.6 163.6 1.0 CB D:CYS26 3.6 152.3 1.0 CB D:CYS12 3.6 145.5 1.0 CB D:CYS9 3.7 130.7 1.0 CA D:CYS31 3.9 177.7 1.0 CA D:CYS9 4.0 158.2 1.0 C D:CYS31 4.0 182.3 1.0 CA D:CYS26 4.1 167.3 1.0 C D:LEU19 4.4 202.7 1.0 CB D:LYS22 4.4 176.3 1.0 N D:CYS26 4.8 168.8 1.0 CG D:LYS22 4.8 167.1 1.0 N D:CYS9 4.9 155.5 1.0 O D:CYS9 4.9 169.7 1.0 CG D:MET33 5.0 190.5 1.0 C D:CYS9 5.0 164.6 1.0 O D:ARG25 5.0 169.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs 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 Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Pyrs Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:163.8 occ:1.00 SG N:CYS27 2.3 135.0 1.0 SG N:CYS43 2.3 145.0 1.0 SG N:CYS40 2.3 163.0 1.0 SG N:CYS24 2.3 194.2 1.0 CB N:CYS40 3.1 164.7 1.0 CB N:CYS43 3.2 142.3 1.0 CB N:CYS27 3.2 149.8 1.0 N N:CYS40 3.6 139.7 1.0 CB N:CYS24 3.7 191.6 1.0 N N:CYS27 3.8 169.0 1.0 CA N:CYS40 3.9 152.7 1.0 N N:CYS43 4.0 132.3 1.0 CB N:ARG29 4.0 163.6 1.0 CA N:CYS27 4.0 160.6 1.0 CA N:CYS43 4.2 135.8 1.0 N N:ARG29 4.6 180.5 1.0 N2 A:G1202 4.6 169.8 1.0 C N:CYS27 4.6 161.2 1.0 C N:CYS40 4.6 146.1 1.0 C N:LEU39 4.8 143.3 1.0 CB N:ARG26 4.8 143.4 1.0 O N:CYS40 4.9 145.2 1.0 N N:GLY28 4.9 171.7 1.0 C N:ARG26 4.9 162.2 1.0 N3 A:G1202 4.9 163.0 1.0 CG N:ARG29 5.0 160.8 1.0 CA N:ARG29 5.0 171.5 1.0

H.Demirci, H.Demirci, E.Destan. N/A N/A.