Zinc in PDB 7duj: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1,3''Bz 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''Bz Bound, PDB code: 7duj 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)	39.80 / 3.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400, 400, 173, 90, 90, 90
R / Rfree (%)	18.9 / 23.5

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''Bz 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''Bz Bound (pdb code 7duj). 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''Bz Bound, PDB code: 7duj:
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''Bz 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''Bz Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:116.0 occ:1.00 SG D:CYS31 2.3 123.9 1.0 SG D:CYS26 2.3 117.2 1.0 SG D:CYS9 2.3 102.9 1.0 SG D:CYS12 2.3 130.2 1.0 O D:CYS31 3.2 153.5 1.0 O D:LEU19 3.4 199.2 1.0 CB D:CYS9 3.6 131.5 1.0 CB D:CYS31 3.6 154.7 1.0 CB D:CYS12 3.6 146.8 1.0 CB D:CYS26 3.6 157.2 1.0 CA D:CYS9 3.8 166.1 1.0 CA D:CYS31 3.8 174.0 1.0 C D:CYS31 4.0 175.2 1.0 CA D:CYS26 4.0 183.3 1.0 CB D:LYS22 4.3 164.0 1.0 C D:LEU19 4.4 191.3 1.0 N D:CYS9 4.7 188.9 1.0 CG D:LYS22 4.7 159.4 1.0 N D:CYS26 4.7 192.7 1.0 O D:CYS9 4.7 170.6 1.0 N D:LEU19 4.8 181.3 1.0 C D:CYS9 4.8 172.1 1.0 O D:ARG25 4.9 193.5 1.0 CG D:MET33 4.9 237.0 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''Bz 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''Bz Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:187.5 occ:1.00 SG N:CYS43 2.3 179.9 1.0 SG N:CYS40 2.3 170.8 1.0 SG N:CYS27 2.3 156.8 1.0 SG N:CYS24 2.3 193.1 1.0 CB N:CYS40 3.1 181.2 1.0 CB N:CYS27 3.1 167.8 1.0 CB N:CYS43 3.1 173.8 1.0 N N:CYS40 3.7 179.4 1.0 N N:CYS27 3.7 182.2 1.0 CB N:CYS24 3.7 200.4 1.0 CA N:CYS27 3.9 182.8 1.0 CA N:CYS40 3.9 180.4 1.0 N N:CYS43 3.9 150.2 1.0 CB N:ARG29 4.1 179.2 1.0 CA N:CYS43 4.1 165.2 1.0 N2 A:G1202 4.5 203.3 1.0 C N:CYS27 4.6 196.0 1.0 N N:ARG29 4.7 206.7 1.0 C N:CYS40 4.7 174.6 1.0 CB N:ARG26 4.8 155.8 1.0 C N:ARG26 4.8 176.4 1.0 C N:LEU39 4.8 178.8 1.0 N N:GLY28 4.8 201.4 1.0 N3 A:G1202 4.9 183.2 1.0 O N:CYS40 5.0 168.7 1.0

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