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Zinc in PDB 4gkk: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin, PDB code: 4gkk was solved by W.A.Cantara, F.V.Murphy Iv, J.L.Spears, H.Demirci, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.47 / 3.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.370, 402.370, 175.620, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.6

Other elements in 4gkk:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 186 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin (pdb code 4gkk). 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 Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin, PDB code: 4gkk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gkk

Go back to Zinc Binding Sites List in 4gkk
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:73.5
occ:1.00
SG D:CYS31 2.1 85.0 1.0
SG D:CYS9 2.3 83.1 1.0
SG D:CYS26 2.4 83.7 1.0
O D:CYS31 2.6 85.9 1.0
SG D:CYS12 2.8 71.0 1.0
CA D:CYS31 3.0 86.2 1.0
C D:CYS31 3.1 86.2 1.0
CB D:CYS31 3.1 85.2 1.0
CB D:CYS26 3.9 83.0 1.0
CB D:CYS9 4.0 83.6 1.0
N D:ALA32 4.3 0.5 1.0
CB D:CYS12 4.3 70.2 1.0
N D:CYS31 4.4 86.4 1.0
CA D:CYS26 4.5 83.3 1.0
CA D:CYS9 4.6 83.3 1.0
N D:TYR20 4.7 1.0 1.0
N D:LEU21 4.8 71.0 1.0
CA D:TYR20 4.8 0.6 1.0
CB D:LYS22 4.9 0.6 1.0

Zinc binding site 2 out of 2 in 4gkk

Go back to Zinc Binding Sites List in 4gkk
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:90.1
occ:1.00
SG N:CYS43 2.2 80.7 1.0
SG N:CYS27 2.2 91.1 1.0
SG N:CYS40 2.3 79.8 1.0
SG N:CYS24 2.4 83.5 1.0
CB N:CYS24 3.0 83.8 1.0
CB N:CYS27 3.2 90.6 1.0
CB N:CYS43 3.2 81.2 1.0
CB N:CYS40 3.3 80.9 1.0
N N:CYS27 3.7 90.8 1.0
N N:CYS40 3.9 82.8 1.0
CA N:CYS27 3.9 91.0 1.0
CA N:CYS40 4.1 81.6 1.0
N N:CYS43 4.2 78.9 1.0
CB N:ARG29 4.2 89.0 1.0
CA N:CYS43 4.3 80.0 1.0
C N:CYS27 4.5 91.8 1.0
CA N:CYS24 4.5 85.4 1.0
N N:GLY28 4.5 0.7 1.0
N N:ARG29 4.6 89.3 1.0
CB N:ARG26 4.7 84.6 1.0
C N:CYS40 4.7 80.5 1.0
C N:ARG26 4.8 84.3 1.0
O N:CYS40 4.8 80.7 1.0
N2 A:G1183 4.9 77.4 1.0
CG1 N:ILE42 4.9 76.3 1.0
N3 A:G1183 4.9 76.4 1.0

Reference:

W.A.Cantara, F.V.Murphy, H.Demirci, P.F.Agris. Expanded Use of Sense Codons Is Regulated By Modified Cytidines in Trna. Proc.Natl.Acad.Sci.Usa V. 110 10964 2013.
ISSN: ISSN 0027-8424
PubMed: 23781103
DOI: 10.1073/PNAS.1222641110
Page generated: Wed Dec 16 05:20:07 2020

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