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Zinc in PDB 6mpi: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin, PDB code: 6mpi was solved by W.A.Cantara, H.Demirci, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.77 / 3.33
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 403.960, 403.960, 176.770, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.7

Other elements in 6mpi:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 96 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin (pdb code 6mpi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin, PDB code: 6mpi:

Zinc binding site 1 out of 1 in 6mpi

Go back to Zinc Binding Sites List in 6mpi
Zinc binding site 1 out of 1 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with A 2-Thiocytidine (S2C32) and Inosine (I34) Modified Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 1 (TRNAARG1) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.5
occ:1.00
SG D:CYS31 2.2 0.0 1.0
SG D:CYS26 2.4 0.5 1.0
SG D:CYS12 2.5 0.1 1.0
SG D:CYS9 2.7 0.8 1.0
O D:LEU19 3.3 0.5 1.0
O D:CYS31 3.4 0.3 1.0
CB D:CYS31 3.8 0.4 1.0
CB D:CYS12 4.0 0.8 1.0
CB D:CYS26 4.0 0.3 1.0
CA D:CYS31 4.2 0.7 1.0
C D:CYS31 4.3 0.6 1.0
CB D:CYS9 4.3 0.3 1.0
C D:LEU19 4.5 0.0 1.0
CA D:CYS26 4.6 0.3 1.0
CB D:LYS22 4.6 1.0 1.0
CA D:CYS9 4.7 0.5 1.0
CG D:LYS22 4.9 0.6 1.0
N D:LYS22 5.0 0.4 1.0

Reference:

W.A.Cantara, S.Vangaveti, K.L.Sarachan, J.L.Spears, H.Demirci, F.V.Murphy Iv, S.V.Ranganathan, P.F.Agris. A Structural Basis For Restricted Codon Recognition Mediated By 2-Thiocytidine in Trna Containing A Wobble Position Inosine To Be Published.
Page generated: Wed Dec 16 12:20:25 2020

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