Zinc in PDB 1irx: Crystal Structure of Class I Lysyl-Trna Synthetase

All present enzymatic activity of Crystal Structure of Class I Lysyl-Trna Synthetase:
6.1.1.6;

The structure of Crystal Structure of Class I Lysyl-Trna Synthetase, PDB code: 1irx was solved by O.Nureki, T.Terada, R.Ishitani, A.Ambrogelly, M.Ibba, D.Soll, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.945, 74.767, 156.945, 90.00, 90.26, 90.00
R / Rfree (%)	22.5 / 29.2

The binding sites of Zinc atom in the Crystal Structure of Class I Lysyl-Trna Synthetase (pdb code 1irx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Class I Lysyl-Trna Synthetase, PDB code: 1irx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Class I Lysyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Class I Lysyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:47.7 occ:1.00 OD1 A:ASP95 2.0 44.8 1.0 ND1 A:HIS100 2.3 42.8 1.0 ND1 A:HIS106 2.3 43.7 1.0 SG A:CYS99 2.4 50.5 1.0 CG A:ASP95 3.0 44.8 1.0 CG A:HIS106 3.2 42.9 1.0 N A:HIS100 3.2 48.5 1.0 CB A:CYS99 3.2 48.3 1.0 CE1 A:HIS100 3.2 44.1 1.0 CG A:HIS100 3.3 44.6 1.0 CB A:HIS106 3.3 42.1 1.0 OD2 A:ASP95 3.3 43.4 1.0 CE1 A:HIS106 3.4 43.9 1.0 CB A:HIS100 3.5 43.8 1.0 C A:CYS99 3.6 49.0 1.0 CA A:CYS99 3.6 49.3 1.0 N A:CYS99 3.7 50.0 1.0 CA A:HIS106 3.9 41.3 1.0 CA A:HIS100 4.0 46.0 1.0 CD2 A:HIS106 4.3 45.5 1.0 CB A:ASP95 4.3 45.5 1.0 NE2 A:HIS100 4.4 45.0 1.0 CD2 A:HIS100 4.4 44.5 1.0 NE2 A:HIS106 4.4 46.9 1.0 O A:CYS99 4.4 49.8 1.0 C A:GLY98 4.7 50.3 1.0 N A:HIS106 4.7 42.7 1.0 CB A:TRP97 4.8 46.5 1.0 N A:GLY98 4.9 48.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Class I Lysyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Class I Lysyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.7 occ:1.00 SG A:CYS199 2.6 92.5 1.0 SG A:CYS177 2.7 71.2 1.0 ND1 A:HIS180 2.9 79.7 1.0 CB A:CYS199 3.0 91.8 1.0 ND1 A:HIS203 3.3 94.1 1.0 CB A:CYS177 3.4 65.6 1.0 CE1 A:HIS180 3.6 79.3 1.0 CG A:HIS180 3.8 79.0 1.0 CE1 A:HIS203 4.1 94.6 1.0 CB A:HIS180 4.2 76.2 1.0 CG A:HIS203 4.3 93.6 1.0 CA A:CYS199 4.4 91.7 1.0 CB A:HIS203 4.5 92.8 1.0 CE1 A:TYR197 4.5 67.7 1.0 NE2 A:HIS180 4.6 80.0 1.0 CD2 A:HIS180 4.7 78.9 1.0 OH A:TYR197 4.7 69.1 1.0 CA A:CYS177 4.9 65.2 1.0 N A:HIS180 4.9 74.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Class I Lysyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Class I Lysyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn600 b:82.9 occ:1.00 ND1 B:HIS100 2.3 82.3 1.0 N B:HIS100 2.6 85.3 1.0 OD1 B:ASP95 2.6 96.6 1.0 CB B:CYS99 2.8 86.4 1.0 SG B:CYS99 2.8 85.4 1.0 CB B:HIS100 2.8 83.5 1.0 CG B:HIS100 2.8 83.3 1.0 C B:CYS99 2.9 86.0 1.0 ND1 B:HIS106 3.0 73.4 1.0 CA B:HIS100 3.2 84.0 1.0 CA B:CYS99 3.3 86.8 1.0 CE1 B:HIS100 3.4 83.5 1.0 O B:CYS99 3.7 85.3 1.0 CA B:HIS106 3.7 71.3 1.0 CG B:HIS106 3.9 73.2 1.0 CB B:HIS106 3.9 72.5 1.0 CG B:ASP95 3.9 96.6 1.0 N B:CYS99 4.0 88.0 1.0 CE1 B:HIS106 4.0 73.7 1.0 CD2 B:HIS100 4.1 83.6 1.0 NE2 B:HIS100 4.3 84.4 1.0 C B:HIS100 4.4 83.1 1.0 N B:HIS106 4.6 72.3 1.0 OD2 B:ASP95 4.7 97.2 1.0 O B:HIS100 4.7 82.4 1.0 C B:HIS106 4.7 71.2 1.0 O B:HIS106 4.8 70.6 1.0 CB B:ASP95 4.8 95.7 1.0 C B:GLY98 4.8 88.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Class I Lysyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Class I Lysyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:0.1 occ:1.00 CE1 B:TYR197 3.0 86.1 1.0 SG B:CYS177 3.3 96.7 1.0 CD1 B:TYR197 3.3 86.2 1.0 SG B:CYS199 3.6 0.5 1.0 CB B:CYS177 3.7 94.8 1.0 ND1 B:HIS203 4.1 0.5 1.0 CB B:CYS199 4.1 0.1 1.0 CZ B:TYR197 4.2 86.2 1.0 CE1 B:HIS203 4.2 0.7 1.0 CB B:ALA184 4.3 89.1 1.0 N B:CYS199 4.6 98.3 1.0 OH B:TYR197 4.6 87.1 1.0 CG B:TYR197 4.6 86.1 1.0 CG B:HIS203 4.8 0.1 1.0 C B:LYS198 4.8 95.2 1.0 O B:GLU204 4.9 95.9 1.0 CA B:CYS177 4.9 94.2 1.0 NE2 B:HIS203 4.9 0.6 1.0 O B:HIS203 4.9 0.6 1.0

T.Terada, O.Nureki, R.Ishitani, A.Ambrogelly, M.Ibba, D.Soll, S.Yokoyama. Functional Convergence of Two Lysyl-Trna Synthetases with Unrelated Topologies. Nat.Struct.Biol. V. 9 257 2002.
ISSN: ISSN 1072-8368
PubMed: 11887185
DOI: 10.1038/NSB777