Zinc in PDB 6mpf: 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 Cgc-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 Cgc-Codon in the A-Site and Paromomycin, PDB code: 6mpf 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) 49.56 / 3.33
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.330, 402.330, 176.030, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.9

Other elements in 6mpf:

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 Cgc-Codon in the A-Site and Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 103 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 Cgc-Codon in the A-Site and Paromomycin (pdb code 6mpf). 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 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 Cgc-Codon in the A-Site and Paromomycin, PDB code: 6mpf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6mpf

Go back to Zinc Binding Sites List in 6mpf
Zinc binding site 1 out of 2 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 Cgc-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 Cgc-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.1
occ:1.00
SG D:CYS26 2.1 0.6 1.0
SG D:CYS31 2.4 0.1 1.0
SG D:CYS9 2.5 0.3 1.0
SG D:CYS12 2.6 0.7 1.0
CB D:CYS26 3.8 0.0 1.0
CB D:CYS31 3.9 0.7 1.0
CG D:LYS22 4.0 0.7 1.0
CB D:CYS12 4.1 0.8 1.0
CB D:CYS9 4.1 0.4 1.0
CD D:LYS22 4.2 0.5 1.0
CA D:CYS26 4.4 0.3 1.0
CA D:CYS9 4.6 0.9 1.0
N D:TYR20 4.7 0.8 1.0
CA D:CYS31 4.7 0.4 1.0

Zinc binding site 2 out of 2 in 6mpf

Go back to Zinc Binding Sites List in 6mpf
Zinc binding site 2 out of 2 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 Cgc-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 2 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 Cgc-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:0.5
occ:1.00
SG N:CYS27 2.3 0.3 1.0
SG N:CYS24 2.3 0.6 1.0
SG N:CYS40 2.4 0.6 1.0
SG N:CYS43 2.4 0.2 1.0
CB N:CYS24 2.8 0.7 1.0
CB N:CYS40 3.1 0.2 1.0
CB N:CYS43 3.4 0.5 1.0
CB N:CYS27 3.6 0.4 1.0
CB N:ARG29 3.6 0.7 1.0
N N:CYS40 3.7 0.8 1.0
N N:CYS27 3.8 0.3 1.0
CA N:CYS40 4.0 0.5 1.0
CA N:CYS27 4.1 0.1 1.0
CA N:CYS24 4.3 0.6 1.0
N N:CYS43 4.3 0.6 1.0
N N:ARG29 4.4 0.2 1.0
C N:CYS27 4.5 0.7 1.0
CG N:ARG29 4.5 0.0 1.0
CA N:CYS43 4.5 0.3 1.0
N2 A:G1183 4.6 0.3 1.0
CA N:ARG29 4.6 0.5 1.0
C N:CYS40 4.6 0.5 1.0
N N:GLY28 4.7 0.8 1.0
CB N:ARG26 4.7 0.9 1.0
O N:CYS40 4.8 0.8 1.0
C N:ARG26 4.8 0.3 1.0
C N:CYS24 4.9 0.8 1.0
N3 A:G1183 4.9 0.6 1.0
C N:LEU39 4.9 0.9 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 12:20:24 2020

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