Zinc in PDB 1ibl: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin, PDB code: 1ibl was solved by J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	316.23 / 3.11
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.800, 400.800, 175.885, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.5

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin also contains other interesting chemical elements:

Magnesium

(Mg)

125 atoms

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin (pdb code 1ibl). 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 A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin, PDB code: 1ibl:
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 A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin


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 A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn306 b:20.0 occ:0.86 SG D:CYS9 2.1 51.7 1.0 SG D:CYS31 2.2 32.2 1.0 SG D:CYS26 2.4 42.3 1.0 SG D:CYS12 2.9 59.0 1.0 O D:CYS31 3.3 0.4 1.0 CB D:CYS9 3.5 51.7 1.0 CB D:CYS31 3.6 32.2 1.0 CA D:CYS31 3.8 0.4 1.0 CB D:CYS26 3.9 42.3 1.0 CA D:CYS9 4.0 94.8 1.0 C D:CYS31 4.0 0.4 1.0 O D:LEU19 4.0 0.0 1.0 CB D:CYS12 4.2 59.0 1.0 CA D:CYS26 4.3 0.7 1.0 N D:CYS9 4.7 94.8 1.0

Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin


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 A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn307 b:20.0 occ:0.68 SG N:CYS43 2.3 41.9 1.0 SG N:CYS27 2.3 39.7 1.0 CB N:CYS27 2.5 39.7 1.0 SG N:CYS40 2.6 36.0 1.0 SG N:CYS24 2.7 46.0 1.0 CB N:CYS43 2.9 41.9 1.0 N N:CYS27 3.2 48.4 1.0 CA N:CYS27 3.5 48.4 1.0 CB N:CYS40 3.8 36.0 1.0 N N:CYS43 3.9 65.1 1.0 CB N:CYS24 4.0 46.0 1.0 N2 A:G1202 4.0 67.3 1.0 CA N:CYS43 4.0 65.1 1.0 CG N:ARG26 4.1 71.5 1.0 CB N:ARG26 4.2 71.5 1.0 N N:CYS40 4.3 79.7 1.0 C N:ARG26 4.4 88.7 1.0 C N:CYS27 4.5 48.4 1.0 CA N:CYS40 4.6 79.7 1.0 CB N:ARG29 4.7 79.0 1.0 N N:GLY28 4.7 76.5 1.0 O N:CYS40 4.8 79.7 1.0 N3 A:G1202 4.8 67.3 1.0 CA N:ARG26 4.8 88.7 1.0 C2 A:G1202 4.8 67.3 1.0 NE N:ARG26 4.9 71.5 1.0 C N:CYS40 5.0 79.7 1.0

J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan. Recognition of Cognate Transfer Rna By the 30S Ribosomal Subunit. Science V. 292 897 2001.
ISSN: ISSN 0036-8075
PubMed: 11340196
DOI: 10.1126/SCIENCE.1060612