Zinc in PDB 7duk: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1,3''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 N1,3''Ms Bound, PDB code: 7duk 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 / 3.60
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 (%)	18.6 / 22.8

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 N1,3''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 N1,3''Ms Bound (pdb code 7duk). 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 N1,3''Ms Bound, PDB code: 7duk:
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 N1,3''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 N1,3''Ms Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:209.8 occ:1.00 SG D:CYS31 2.3 147.2 1.0 SG D:CYS26 2.3 108.4 1.0 SG D:CYS9 2.3 89.2 1.0 SG D:CYS12 2.3 111.2 1.0 O D:CYS31 3.3 191.2 1.0 O D:LEU19 3.3 197.9 1.0 CB D:CYS31 3.6 162.0 1.0 CB D:CYS26 3.7 136.9 1.0 CB D:CYS9 3.7 127.7 1.0 CB D:CYS12 3.7 124.5 1.0 CA D:CYS31 3.9 180.2 1.0 CA D:CYS9 4.0 152.7 1.0 C D:CYS31 4.0 190.1 1.0 CA D:CYS26 4.1 152.2 1.0 CB D:LYS22 4.5 157.3 1.0 C D:LEU19 4.5 191.0 1.0 N D:CYS26 4.8 157.4 1.0 CG D:LYS22 4.8 148.4 1.0 O D:CYS9 4.9 155.4 1.0 N D:CYS9 4.9 147.1 1.0 O D:ARG25 4.9 164.2 1.0 C D:CYS9 5.0 150.4 1.0 CG D:MET33 5.0 165.7 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 N1,3''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 N1,3''Ms Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:159.5 occ:1.00 SG N:CYS27 2.3 129.3 1.0 SG N:CYS43 2.3 131.7 1.0 SG N:CYS40 2.3 161.2 1.0 SG N:CYS24 2.3 186.8 1.0 CB N:CYS27 3.2 140.5 1.0 CB N:CYS40 3.2 153.9 1.0 CB N:CYS43 3.3 130.4 1.0 CB N:CYS24 3.7 183.9 1.0 N N:CYS40 3.7 148.0 1.0 N N:CYS27 3.8 148.2 1.0 N N:CYS43 4.0 129.0 1.0 CA N:CYS27 4.0 147.7 1.0 CA N:CYS40 4.0 145.6 1.0 CB N:ARG29 4.0 159.5 1.0 CA N:CYS43 4.3 129.7 1.0 C N:CYS27 4.6 150.5 1.0 N N:ARG29 4.6 166.5 1.0 C N:CYS40 4.7 136.2 1.0 N2 A:G1202 4.7 164.1 1.0 N N:GLY28 4.8 157.8 1.0 C N:LEU39 4.9 152.8 1.0 O N:CYS40 4.9 128.4 1.0 C N:ARG26 4.9 142.8 1.0 CB N:ARG26 4.9 124.9 1.0 CA N:ARG29 5.0 163.2 1.0

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