Zinc in PDB 1ibm: 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

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, PDB code: 1ibm 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 / 3.31
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.574, 401.574, 176.110, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.6

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 also contains other interesting chemical elements:

Magnesium

(Mg)

120 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 (pdb code 1ibm). 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, PDB code: 1ibm:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn506 b:27.0 occ:1.30 SG D:CYS9 2.2 39.6 1.0 SG D:CYS31 2.2 17.6 1.0 SG D:CYS26 2.4 21.1 1.0 SG D:CYS12 2.9 28.2 1.0 CA D:CYS31 2.9 59.7 1.0 CB D:CYS31 3.0 17.6 1.0 O D:CYS31 3.1 59.7 1.0 C D:CYS31 3.4 59.7 1.0 CB D:CYS9 3.8 39.6 1.0 O D:LEU19 3.9 0.1 1.0 CB D:CYS26 3.9 21.1 1.0 CD D:LYS22 3.9 58.2 1.0 CB D:CYS12 4.1 28.2 1.0 CA D:CYS26 4.2 0.0 1.0 N D:CYS31 4.3 59.7 1.0 CA D:CYS9 4.3 0.9 1.0 CE D:LYS22 4.6 58.2 1.0 O D:LYS30 4.6 0.3 1.0 N D:ALA32 4.7 92.0 1.0 C D:LYS30 4.9 0.3 1.0 N D:CYS9 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 A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site


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 within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn507 b:27.0 occ:0.83 SG N:CYS27 2.0 41.4 1.0 SG N:CYS43 2.1 21.1 1.0 SG N:CYS40 2.3 38.9 1.0 SG N:CYS24 2.6 41.6 1.0 CB N:CYS27 2.7 41.4 1.0 CB N:CYS40 3.3 38.9 1.0 CB N:CYS43 3.3 21.1 1.0 N N:CYS27 3.5 67.7 1.0 CB N:CYS24 3.5 41.6 1.0 CA N:CYS27 3.7 67.7 1.0 N N:CYS40 4.1 86.0 1.0 CA N:CYS40 4.3 86.0 1.0 CB N:ARG29 4.3 84.7 1.0 N N:CYS43 4.3 47.5 1.0 CB N:ARG26 4.4 61.6 1.0 CA N:CYS43 4.4 47.5 1.0 C N:ARG26 4.4 0.7 1.0 N N:GLY28 4.5 79.3 1.0 C N:CYS27 4.5 67.7 1.0 N2 A:G1202 4.7 61.5 1.0 N N:ARG29 4.7 89.5 1.0 CA N:ARG26 4.9 0.7 1.0 O N:CYS40 4.9 86.0 1.0 CG N:ARG26 4.9 61.6 1.0 C N:CYS40 4.9 86.0 1.0 NH1 N:ARG26 4.9 61.6 1.0 N3 A:G1202 4.9 61.5 1.0 CA N:CYS24 5.0 77.2 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