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Zinc in PDB 1n32: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin

Protein crystallography data

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 First Codon Position at the A Site with Paromomycin, PDB code: 1n32 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) 141.42 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.296, 400.296, 175.483, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27

Other elements in 1n32:

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 First Codon Position at the A Site with Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 158 atoms

Zinc Binding Sites:

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 First Codon Position at the A Site with Paromomycin (pdb code 1n32). 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 First Codon Position at the A Site with Paromomycin, PDB code: 1n32:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1n32

Go back to Zinc Binding Sites List in 1n32
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 First 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 First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn306

b:24.8
occ:0.68
SG D:CYS31 2.0 44.5 1.0
SG D:CYS9 2.1 45.9 1.0
SG D:CYS26 2.3 59.4 1.0
SG D:CYS12 2.9 60.8 1.0
O D:LEU19 3.6 0.2 1.0
CB D:CYS31 3.6 44.5 1.0
CB D:CYS9 3.8 45.9 1.0
O D:CYS31 3.8 0.3 1.0
CB D:CYS26 3.9 59.4 1.0
CA D:CYS31 4.2 0.3 1.0
CA D:CYS9 4.2 0.8 1.0
CB D:CYS12 4.4 60.8 1.0
CA D:CYS26 4.5 82.0 1.0
C D:CYS31 4.5 0.3 1.0
C D:LEU19 4.8 0.2 1.0

Zinc binding site 2 out of 2 in 1n32

Go back to Zinc Binding Sites List in 1n32
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 First 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 First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn307

b:24.8
occ:0.55
SG N:CYS43 1.9 41.6 1.0
SG N:CYS27 2.1 55.0 1.0
SG N:CYS24 2.4 66.3 1.0
SG N:CYS40 2.5 56.1 1.0
CB N:CYS27 2.7 55.0 1.0
N N:CYS27 3.4 68.1 1.0
CB N:CYS24 3.6 66.3 1.0
CA N:CYS27 3.6 68.1 1.0
CB N:CYS43 3.6 41.6 1.0
CB N:CYS40 3.7 56.1 1.0
N2 A:G1202 4.0 66.2 1.0
CB N:ARG26 4.2 63.2 1.0
N N:CYS43 4.3 52.1 1.0
N N:CYS40 4.4 0.7 1.0
C N:ARG26 4.4 86.5 1.0
CB N:ARG29 4.5 98.2 1.0
C N:CYS27 4.6 68.1 1.0
N N:GLY28 4.6 85.3 1.0
CA N:CYS40 4.6 0.7 1.0
CA N:CYS43 4.6 52.1 1.0
N3 A:G1202 4.7 66.2 1.0
CG N:ARG26 4.7 63.2 1.0
CD N:ARG26 4.7 63.2 1.0
CA N:ARG26 4.8 86.5 1.0
C2 A:G1202 4.9 66.2 1.0
N N:ARG29 4.9 88.1 1.0
O N:CYS40 4.9 0.7 1.0
N N:ARG26 5.0 86.5 1.0
CA N:CYS24 5.0 76.6 1.0

Reference:

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
Page generated: Mon Jan 25 16:10:23 2021

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