Zinc in PDB 1n33: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin, PDB code: 1n33 was solved by J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.54 / 3.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.599, 401.599, 176.025, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 28.4

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin also contains other interesting chemical elements:

Magnesium

(Mg)

106 atoms

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin (pdb code 1n33). 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin, PDB code: 1n33:
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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn306 b:34.6 occ:1.01 NZ D:LYS22 2.0 62.9 1.0 SG D:CYS9 2.1 86.8 1.0 SG D:CYS31 2.2 44.5 1.0 SG D:CYS26 2.2 40.1 1.0 SG D:CYS12 2.7 86.9 1.0 CE D:LYS22 2.8 62.9 1.0 CB D:CYS9 3.3 86.8 1.0 CA D:CYS9 3.5 0.6 1.0 CB D:CYS31 3.6 44.5 1.0 O D:CYS31 3.7 76.1 1.0 CB D:CYS26 3.8 40.1 1.0 CA D:CYS31 3.9 76.1 1.0 CB D:CYS12 4.0 86.9 1.0 CD D:LYS22 4.1 62.9 1.0 C D:CYS31 4.2 76.1 1.0 O D:CYS9 4.2 0.6 1.0 C D:CYS9 4.4 0.6 1.0 CA D:CYS26 4.4 0.6 1.0 N D:CYS9 4.6 0.6 1.0 N D:LEU21 4.8 0.8 1.0 CA D:TYR20 5.0 0.3 1.0

Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn307 b:34.6 occ:0.69 CB N:CYS43 2.2 0.2 1.0 SG N:CYS43 2.2 0.2 1.0 SG N:CYS27 2.5 52.2 1.0 SG N:CYS40 2.9 50.7 1.0 CA N:CYS43 3.2 52.8 1.0 CB N:CYS27 3.2 52.2 1.0 N N:CYS43 3.3 52.8 1.0 SG N:CYS24 3.3 88.5 1.0 N2 A:G1202 3.8 0.4 1.0 N N:CYS27 3.9 94.4 1.0 CD N:ARG26 3.9 73.9 1.0 CA N:CYS27 4.2 94.4 1.0 CB N:CYS40 4.4 50.7 1.0 C N:CYS43 4.5 52.8 1.0 CG N:ARG26 4.5 73.9 1.0 CB N:ARG26 4.5 73.9 1.0 N N:CYS40 4.5 90.7 1.0 NE N:ARG26 4.5 73.9 1.0 C N:ILE42 4.6 0.4 1.0 O N:CYS40 4.6 90.7 1.0 CB N:CYS24 4.8 88.5 1.0 C2 A:G1202 4.8 0.4 1.0 CB N:ILE42 4.8 93.3 1.0 N N:LEU44 4.9 0.4 1.0 CA N:CYS40 4.9 90.7 1.0 N3 A:G1202 5.0 0.4 1.0 NH1 N:ARG26 5.0 73.9 1.0

J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan. Selection of Trna By the Ribosome Requires A Transition From An Open to A Closed Form Cell(Cambridge,Mass.) V. 111 721 2002.
ISSN: ISSN 0092-8674
PubMed: 12464183
DOI: 10.1016/S0092-8674(02)01086-3