Zinc in PDB 1ile: Isoleucyl-Trna Synthetase

The structure of Isoleucyl-Trna Synthetase, PDB code: 1ile was solved by O.Nureki, D.G.Vassylyev, M.Tateno, A.Shimada, T.Nakama, S.Fukai, M.Konno, P.Schimmel, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.100, 94.800, 126.500, 90.00, 126.30, 90.00
R / Rfree (%)	22.2 / 29.8

The binding sites of Zinc atom in the Isoleucyl-Trna Synthetase (pdb code 1ile). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Isoleucyl-Trna Synthetase, PDB code: 1ile:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Isoleucyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Isoleucyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:74.0 occ:1.00 SG A:CYS392 1.3 74.6 1.0 SG A:CYS389 1.4 84.2 1.0 SG A:CYS184 1.7 49.7 1.0 SG A:CYS181 2.1 78.8 1.0 O A:HOH1327 2.4 20.6 1.0 CB A:CYS389 2.6 58.9 1.0 CB A:CYS392 2.9 41.8 1.0 CB A:CYS184 3.1 36.0 1.0 O A:HOH1366 3.3 52.2 1.0 CB A:CYS181 3.4 52.8 1.0 N A:CYS392 3.5 42.2 1.0 CA A:CYS389 3.6 46.7 1.0 CA A:CYS392 3.8 39.5 1.0 O A:CYS392 4.0 46.0 1.0 C A:CYS392 4.2 40.2 1.0 C A:CYS389 4.3 46.2 1.0 CA A:CYS184 4.4 33.0 1.0 N A:CYS184 4.5 30.9 1.0 CB A:ARG391 4.5 39.9 1.0 OG1 A:THR394 4.5 47.7 1.0 N A:ARG391 4.5 40.1 1.0 C A:ARG391 4.6 43.8 1.0 N A:TRP390 4.7 45.9 1.0 CG A:ARG183 4.8 41.4 1.0 CA A:CYS181 4.8 44.8 1.0 CA A:ARG391 4.9 40.0 1.0 N A:CYS389 4.9 45.4 1.0 CD1 A:LEU89 4.9 34.4 1.0 CD2 A:LEU93 4.9 35.1 1.0 CG A:ARG391 5.0 43.3 1.0

Zinc binding site 2 out of 2 in the Isoleucyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Isoleucyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:0.0 occ:1.00 SG A:CYS504 1.2 0.0 1.0 SG A:CYS502 1.5 0.0 1.0 SG A:CYS464 1.7 0.0 1.0 SG A:CYS461 1.9 0.0 1.0 CB A:CYS504 2.4 98.4 1.0 O A:HOH1179 2.7 66.2 1.0 CB A:CYS502 3.0 89.6 1.0 CB A:CYS461 3.0 79.3 1.0 CB A:CYS464 3.0 91.7 1.0 N A:CYS504 3.5 96.5 1.0 CA A:CYS504 3.5 96.2 1.0 CA A:CYS502 3.6 87.2 1.0 N A:GLY465 3.9 79.5 1.0 C A:CYS502 3.9 86.8 1.0 N A:ALA503 4.2 90.0 1.0 CA A:CYS461 4.3 71.9 1.0 CA A:CYS464 4.3 86.3 1.0 C A:CYS464 4.5 83.5 1.0 O A:CYS502 4.5 84.1 1.0 C A:CYS504 4.5 95.6 1.0 O A:HOH1367 4.6 84.0 1.0 CA A:GLY465 4.7 81.1 1.0 C A:ALA503 4.7 94.5 1.0 C A:GLY465 4.8 82.0 1.0 N A:CYS464 4.8 84.7 1.0 O A:GLY465 4.9 83.4 1.0 N A:GLY505 4.9 94.4 1.0

O.Nureki, D.G.Vassylyev, M.Tateno, A.Shimada, T.Nakama, S.Fukai, M.Konno, T.L.Hendrickson, P.Schimmel, S.Yokoyama. Enzyme Structure with Two Catalytic Sites For Double-Sieve Selection of Substrate. Science V. 280 578 1998.
ISSN: ISSN 0036-8075
PubMed: 9554847
DOI: 10.1126/SCIENCE.280.5363.578