Zinc in PDB 1hnx: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Pactamycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Pactamycin, PDB code: 1hnx 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)	95.34 / 3.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.719, 401.719, 177.002, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 28

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Pactamycin 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 Pactamycin (pdb code 1hnx). 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 Pactamycin, PDB code: 1hnx:
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 Pactamycin


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 Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn190 b:53.9 occ:0.81 SG N:CYS27 2.0 40.1 1.0 SG N:CYS43 2.3 39.9 1.0 SG N:CYS40 2.3 63.1 1.0 SG N:CYS24 2.4 95.2 1.0 CB N:CYS40 2.9 63.1 1.0 CB N:CYS24 3.1 95.2 1.0 CB N:CYS27 3.1 40.1 1.0 CB N:CYS43 3.3 39.9 1.0 N N:CYS27 3.5 74.0 1.0 N N:CYS40 3.7 88.5 1.0 CA N:CYS27 3.8 74.0 1.0 CB N:ARG29 3.9 0.7 1.0 CA N:CYS40 3.9 88.5 1.0 N N:CYS43 4.2 55.0 1.0 CA N:CYS43 4.3 55.0 1.0 N N:ARG29 4.5 0.1 1.0 N N:GLY28 4.5 70.6 1.0 C N:CYS27 4.5 74.0 1.0 CA N:CYS24 4.5 0.2 1.0 C N:ARG26 4.6 91.5 1.0 O N:CYS40 4.6 88.5 1.0 C N:CYS40 4.6 88.5 1.0 CB N:ARG26 4.6 78.5 1.0 N2 A:G1202 4.8 89.1 1.0 CA N:ARG29 4.8 0.1 1.0 CG N:ARG29 4.9 0.7 1.0 CA N:ARG26 4.9 91.5 1.0 N N:ARG26 4.9 91.5 1.0 C N:LEU39 4.9 0.5 1.0

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


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 Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:53.9 occ:1.40 SG D:CYS9 2.0 27.6 1.0 SG D:CYS31 2.2 27.9 1.0 SG D:CYS26 2.3 46.1 1.0 SG D:CYS12 2.9 55.1 1.0 CB D:CYS9 3.0 27.6 1.0 CB D:CYS31 3.2 27.9 1.0 CA D:CYS31 3.5 87.6 1.0 O D:LEU19 3.7 0.5 1.0 O D:CYS31 3.9 87.6 1.0 CA D:CYS9 3.9 0.1 1.0 CB D:CYS26 4.0 46.1 1.0 C D:CYS31 4.1 87.6 1.0 CB D:CYS12 4.4 55.1 1.0 CA D:CYS26 4.4 0.4 1.0 N D:CYS9 4.8 0.1 1.0 N D:CYS31 4.8 87.6 1.0 CB D:LYS22 4.9 60.0 1.0 CD D:LYS22 4.9 60.0 1.0 C D:LEU19 4.9 0.5 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