Zinc in PDB 1hnz: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B, PDB code: 1hnz was solved by D.E.Brodersen, W.M.Clemons Jr., A.P.Carter, R.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.063, 402.063, 175.263, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.1

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B also contains other interesting chemical elements:

Magnesium

(Mg)

96 atoms

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B (pdb code 1hnz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B, PDB code: 1hnz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn190 b:67.0 occ:0.81 SG N:CYS27 2.1 56.3 1.0 SG N:CYS43 2.1 65.3 1.0 SG N:CYS24 2.3 0.8 1.0 SG N:CYS40 2.6 73.5 1.0 CB N:CYS27 3.1 56.3 1.0 CB N:CYS43 3.3 65.3 1.0 CB N:CYS24 3.3 0.8 1.0 CB N:CYS40 3.3 73.5 1.0 N N:CYS27 3.5 70.0 1.0 CA N:CYS27 3.8 70.0 1.0 N N:CYS40 4.0 0.3 1.0 CB N:ARG29 4.1 0.6 1.0 C N:ARG26 4.2 90.7 1.0 N N:CYS43 4.3 80.1 1.0 CA N:CYS40 4.3 0.3 1.0 CB N:ARG26 4.3 84.6 1.0 CA N:CYS43 4.4 80.1 1.0 C N:CYS27 4.6 70.0 1.0 N N:ARG29 4.6 0.9 1.0 N2 A:G1202 4.6 0.5 1.0 CA N:ARG26 4.6 90.7 1.0 N N:GLY28 4.6 96.5 1.0 CA N:CYS24 4.7 0.5 1.0 CG N:ARG26 4.7 84.6 1.0 N N:ARG26 4.8 90.7 1.0 N3 A:G1202 4.9 0.5 1.0 CA N:ARG29 5.0 0.9 1.0

Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:67.0 occ:1.29 SG D:CYS31 2.1 49.3 1.0 SG D:CYS9 2.1 56.4 1.0 SG D:CYS26 2.5 62.2 1.0 SG D:CYS12 2.7 69.8 1.0 CB D:CYS31 3.4 49.3 1.0 O D:LEU19 3.5 1.0 1.0 CB D:CYS9 3.7 56.4 1.0 CA D:CYS31 3.8 0.5 1.0 O D:CYS31 3.9 0.5 1.0 CB D:CYS26 4.1 62.2 1.0 CB D:CYS12 4.2 69.8 1.0 CA D:CYS9 4.3 0.5 1.0 C D:CYS31 4.3 0.5 1.0 CA D:CYS26 4.5 0.6 1.0 CD D:LYS22 4.6 71.7 1.0 C D:LEU19 4.8 1.0 1.0 CB D:LYS22 4.9 71.7 1.0

D.E.Brodersen, W.M.Clemons Jr., A.P.Carter, R.J.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan. The Structural Basis For the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit. Cell(Cambridge,Mass.) V. 103 1143 2000.
ISSN: ISSN 0092-8674
PubMed: 11163189
DOI: 10.1016/S0092-8674(00)00216-6