Zinc in PDB 3t1y: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin, PDB code: 3t1y was solved by F.V.Murphy, F.A.P.Vendeix, W.Cantara, G.Leszczynska, E.M.Gustilo, B.Sproat, A.A.P.Malkiewicz, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.972, 400.972, 174.647, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 26.8

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin (pdb code 3t1y). 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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin, PDB code: 3t1y:
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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.2 occ:1.00 SG D:CYS31 2.4 81.8 1.0 SG D:CYS9 2.7 66.3 1.0 SG D:CYS26 2.8 75.0 1.0 SG D:CYS12 3.4 63.2 1.0 O D:CYS31 4.0 85.1 1.0 CB D:CYS9 4.1 66.3 1.0 CB D:CYS31 4.1 81.8 1.0 CB D:CYS26 4.3 75.0 1.0 CA D:CYS9 4.4 69.9 1.0 CB D:CYS12 4.5 63.2 1.0 CA D:CYS31 4.5 85.1 1.0 CA D:CYS26 4.6 78.2 1.0 C D:CYS31 4.7 85.1 1.0

Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:61.0 occ:1.00 SG N:CYS43 2.0 53.6 1.0 SG N:CYS27 2.1 60.7 1.0 SG N:CYS40 2.5 62.3 1.0 SG N:CYS24 2.7 65.9 1.0 CB N:CYS27 2.9 60.7 1.0 CB N:CYS43 3.4 53.6 1.0 CB N:CYS40 3.6 62.3 1.0 N N:CYS27 3.7 63.5 1.0 CB N:CYS24 3.7 65.9 1.0 CA N:CYS27 3.9 63.5 1.0 N N:CYS40 4.1 60.8 1.0 N N:CYS43 4.2 56.2 1.0 CB N:ARG29 4.3 70.7 1.0 C N:ARG26 4.4 63.2 1.0 CA N:CYS43 4.4 56.2 1.0 CA N:CYS40 4.5 60.8 1.0 N2 A:G1183 4.5 60.8 1.0 CB N:ARG26 4.6 61.1 1.0 C N:CYS27 4.7 63.5 1.0 N3 A:G1183 4.8 60.8 1.0 CA N:ARG26 4.9 63.2 1.0 N N:ARG29 4.9 67.9 1.0 NH1 N:ARG26 4.9 61.1 1.0 N N:GLY28 5.0 65.5 1.0

F.A.Vendeix, F.V.Murphy, W.A.Cantara, G.Leszczynska, E.M.Gustilo, B.Sproat, A.Malkiewicz, P.F.Agris. Human Trna(LYS3)(Uuu) Is Pre-Structured By Natural Modifications For Cognate and Wobble Codon Binding Through Keto-Enol Tautomerism. J.Mol.Biol. V. 416 467 2012.
ISSN: ISSN 0022-2836
PubMed: 22227389
DOI: 10.1016/J.JMB.2011.12.048