Zinc in PDB 4gkj: 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 Aug-Codon in the A-Site and Paromomycin.

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 Aug-Codon in the A-Site and Paromomycin., PDB code: 4gkj 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)	97.15 / 3.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.550, 400.550, 176.190, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

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

Magnesium

(Mg)

186 atoms

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 Aug-Codon in the A-Site and Paromomycin. (pdb code 4gkj). 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 Aug-Codon in the A-Site and Paromomycin., PDB code: 4gkj:
Jump to Zinc binding site number: 1; 2;

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 Aug-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 Aug-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:64.9 occ:1.00 SG D:CYS31 2.1 65.8 1.0 SG D:CYS26 2.3 86.5 1.0 SG D:CYS9 2.3 64.8 1.0 SG D:CYS12 2.6 62.8 1.0 CB D:CYS31 3.6 67.4 1.0 CB D:CYS26 4.0 86.2 1.0 CB D:CYS9 4.1 64.0 1.0 CB D:CYS12 4.1 62.0 1.0 CA D:CYS31 4.5 68.1 1.0 CG D:LYS22 4.6 89.4 1.0 CD D:LYS22 4.6 90.0 1.0 CA D:CYS9 4.7 62.7 1.0 CA D:CYS26 4.7 86.4 1.0 N D:TYR20 4.8 95.4 1.0 N D:LEU21 5.0 62.9 1.0 CA D:TYR20 5.0 95.9 1.0

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 Aug-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 Aug-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn102 b:73.0 occ:1.00 SG N:CYS27 2.2 71.4 1.0 SG N:CYS43 2.2 71.7 1.0 SG N:CYS40 2.3 71.0 1.0 SG N:CYS24 2.3 74.2 1.0 CB N:CYS27 3.1 71.7 1.0 CB N:CYS24 3.1 74.4 1.0 CB N:CYS40 3.2 72.0 1.0 CB N:CYS43 3.3 72.2 1.0 N N:CYS27 3.8 74.0 1.0 N N:CYS40 4.0 73.9 1.0 CB N:ARG29 4.0 99.2 1.0 CA N:CYS27 4.0 73.0 1.0 N N:CYS43 4.0 70.3 1.0 CA N:CYS40 4.2 72.8 1.0 CA N:CYS43 4.3 71.2 1.0 N2 A:G1183 4.6 68.8 1.0 CA N:CYS24 4.6 75.8 1.0 C N:CYS27 4.6 73.1 1.0 N N:ARG29 4.6 99.3 1.0 N N:GLY28 4.7 74.5 1.0 C N:CYS40 4.7 72.0 1.0 CB N:ARG26 4.8 75.2 1.0 C N:ARG26 4.8 74.7 1.0 N3 A:G1183 4.9 68.1 1.0 O N:CYS40 4.9 72.3 1.0 CG N:ARG29 4.9 99.3 1.0 CA N:ARG29 5.0 99.6 1.0

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