Zinc in PDB 7dul: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N3''Ms 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 N3''Ms Bound, PDB code: 7dul 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)	39.88 / 3.62
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.83, 400.83, 174.67, 90, 90, 90
R / Rfree (%)	18.3 / 22

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 N3''Ms 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 N3''Ms Bound (pdb code 7dul). 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 N3''Ms Bound, PDB code: 7dul:
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 N3''Ms 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 N3''Ms Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:183.7 occ:1.00 SG D:CYS31 2.3 151.0 1.0 SG D:CYS26 2.3 131.6 1.0 SG D:CYS9 2.3 103.9 1.0 SG D:CYS12 2.3 148.9 1.0 O D:CYS31 3.3 179.7 1.0 O D:LEU19 3.3 204.6 1.0 CB D:CYS31 3.6 159.2 1.0 CB D:CYS12 3.6 153.5 1.0 CB D:CYS9 3.7 133.4 1.0 CB D:CYS26 3.7 156.4 1.0 CA D:CYS9 3.9 167.9 1.0 CA D:CYS31 3.9 179.6 1.0 C D:CYS31 4.0 195.6 1.0 CA D:CYS26 4.1 176.1 1.0 CB D:LYS22 4.3 165.6 1.0 C D:LEU19 4.5 199.4 1.0 CG D:LYS22 4.7 152.8 1.0 N D:CYS26 4.8 179.6 1.0 N D:CYS9 4.8 166.6 1.0 O D:CYS9 4.9 187.6 1.0 O D:ARG25 4.9 181.0 1.0 C D:CYS9 4.9 175.4 1.0 CG D:MET33 5.0 200.8 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 N3''Ms 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 N3''Ms Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:168.7 occ:1.00 SG N:CYS27 2.3 144.3 1.0 SG N:CYS43 2.3 155.2 1.0 SG N:CYS40 2.3 183.3 1.0 SG N:CYS24 2.3 179.3 1.0 CB N:CYS40 3.1 185.8 1.0 CB N:CYS43 3.2 152.0 1.0 CB N:CYS27 3.2 152.3 1.0 N N:CYS40 3.7 167.6 1.0 CB N:CYS24 3.7 178.7 1.0 N N:CYS27 3.8 163.4 1.0 N N:CYS43 3.9 139.8 1.0 CA N:CYS40 4.0 176.0 1.0 CB N:ARG29 4.0 170.6 1.0 CA N:CYS27 4.0 158.2 1.0 CA N:CYS43 4.2 144.7 1.0 N N:ARG29 4.6 177.2 1.0 C N:CYS27 4.6 160.3 1.0 C N:CYS40 4.7 173.2 1.0 N2 A:G1202 4.7 183.4 1.0 C N:LEU39 4.8 164.0 1.0 N N:GLY28 4.8 166.9 1.0 CB N:ARG26 4.9 144.9 1.0 C N:ARG26 4.9 168.3 1.0 CA N:ARG29 5.0 173.6 1.0 CG N:ARG29 5.0 174.3 1.0 O N:CYS40 5.0 173.7 1.0

H.Demirci, E.Destan. Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N3''Ms Bound To Be Published.