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Zinc in PDB 1n34: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position, PDB code: 1n34 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 / 3.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.844, 401.844, 173.854, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 31.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position (pdb code 1n34). 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 the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position, PDB code: 1n34:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1n34

Go back to Zinc Binding Sites List in 1n34
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position


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 the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn306

b:78.9
occ:2.42
CG D:LYS22 2.3 93.2 1.0
SG D:CYS26 2.3 96.5 1.0
SG D:CYS31 2.5 36.9 1.0
CE D:LYS22 2.6 93.2 1.0
CD D:LYS22 2.7 93.2 1.0
CB D:LYS22 2.7 93.2 1.0
SG D:CYS9 2.9 5.2 1.0
SG D:CYS12 3.0 87.5 1.0
CB D:CYS31 3.4 36.9 1.0
O D:LEU19 3.6 99.3 1.0
NZ D:LYS22 3.7 93.2 1.0
CB D:CYS26 3.9 96.5 1.0
CB D:CYS9 4.0 5.2 1.0
CA D:CYS31 4.1 87.6 1.0
O D:CYS31 4.1 87.6 1.0
CB D:CYS12 4.2 87.5 1.0
CA D:LYS22 4.3 75.8 1.0
CA D:CYS9 4.3 0.2 1.0
CA D:CYS26 4.4 0.5 1.0
C D:CYS31 4.6 87.6 1.0
C D:LEU19 4.7 99.3 1.0
O D:LYS22 4.8 75.8 1.0
N D:LYS22 4.9 75.8 1.0

Zinc binding site 2 out of 2 in 1n34

Go back to Zinc Binding Sites List in 1n34
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position


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 the Presence of Codon and Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn307

b:78.9
occ:1.20
CB N:CYS27 2.1 34.6 1.0
N N:CYS27 3.0 0.1 1.0
CA N:CYS27 3.0 0.1 1.0
SG N:CYS43 3.0 49.7 1.0
SG N:CYS24 3.1 68.9 1.0
CB N:CYS40 3.1 42.8 1.0
CB N:CYS43 3.3 49.7 1.0
N2 A:G1202 3.3 0.1 1.0
SG N:CYS27 3.4 34.6 1.0
N N:CYS43 3.9 0.7 1.0
N N:CYS40 4.0 0.3 1.0
C2 A:G1202 4.1 0.1 1.0
C N:ARG26 4.2 0.3 1.0
CA N:CYS43 4.2 0.7 1.0
CA N:CYS40 4.2 0.3 1.0
SG N:CYS40 4.3 42.8 1.0
C N:CYS27 4.3 0.1 1.0
CB N:ILE42 4.3 57.3 1.0
CB N:CYS24 4.5 68.9 1.0
CB N:ARG26 4.6 70.5 1.0
N3 A:G1202 4.6 0.1 1.0
CD1 N:ILE42 4.6 57.3 1.0
CG1 N:ILE42 4.7 57.3 1.0
CB N:LEU39 4.7 0.8 1.0
N N:GLY28 4.8 66.4 1.0
N1 A:G1202 4.8 0.1 1.0
NE N:ARG26 4.8 70.5 1.0
CA N:ARG26 4.8 0.3 1.0
C N:LEU39 4.9 0.2 1.0
C N:CYS40 5.0 0.3 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 16:10:24 2021

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