Zinc in PDB 2byt: Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation

The structure of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation, PDB code: 2byt was solved by S.Cusack, M.Tukalo, A.Yaremchuk, R.Fukunaga, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.45 / 3.3
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.869, 125.578, 172.979, 90.00, 118.44, 90.00
R / Rfree (%)	24.3 / 28.2

The structure of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation also contains other interesting chemical elements:

Mercury

(Hg)

2 atoms

The binding sites of Zinc atom in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation (pdb code 2byt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation, PDB code: 2byt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:0.2 occ:1.00 SG A:CYS484 2.3 0.1 1.0 SG A:CYS442 2.3 0.9 1.0 SG A:CYS439 2.4 0.5 1.0 SG A:CYS487 2.4 0.7 1.0 CB A:CYS442 3.2 0.1 1.0 CB A:CYS484 3.2 0.3 1.0 CB A:CYS439 3.2 0.5 1.0 CB A:CYS487 3.3 0.6 1.0 N A:CYS487 3.7 0.3 1.0 N A:CYS442 4.0 0.8 1.0 CA A:CYS487 4.1 0.8 1.0 CA A:CYS442 4.2 0.7 1.0 CB A:LYS486 4.2 0.5 1.0 CG A:LYS486 4.6 0.7 1.0 N A:GLY488 4.6 0.1 1.0 CA A:CYS484 4.7 0.3 1.0 CA A:CYS439 4.7 0.8 1.0 C A:LYS486 4.8 0.2 1.0 CD A:LYS486 4.8 0.4 1.0 CA A:LYS486 4.9 0.5 1.0 C A:CYS487 4.9 0.6 1.0 C A:ALA441 5.0 0.4 1.0

Zinc binding site 2 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:85.7 occ:1.00 ND1 A:HIS179 2.1 0.8 1.0 SG A:CYS162 2.3 98.2 1.0 SG A:CYS176 2.3 98.6 1.0 SG A:CYS159 2.3 92.3 1.0 CE1 A:HIS179 2.4 0.5 1.0 CB A:CYS162 3.2 99.9 1.0 CG A:HIS179 3.5 0.9 1.0 CB A:CYS176 3.5 0.4 1.0 CB A:CYS159 3.6 95.4 1.0 NE2 A:HIS179 3.7 0.6 1.0 N A:CYS162 3.8 98.5 1.0 CA A:CYS162 4.1 98.3 1.0 CD2 A:HIS179 4.2 0.6 1.0 CB A:HIS179 4.3 0.4 1.0 CD1 A:LEU166 4.4 79.0 1.0 CB A:LYS161 4.6 0.2 1.0 N A:HIS179 4.8 0.3 1.0 CA A:CYS176 4.8 0.4 1.0 C A:LYS161 4.9 99.2 1.0 CA A:CYS159 5.0 96.6 1.0

Zinc binding site 3 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1602 b:0.1 occ:1.00 SG D:CYS484 2.3 0.5 1.0 SG D:CYS439 2.3 0.5 1.0 SG D:CYS442 2.4 0.7 1.0 SG D:CYS487 2.4 0.5 1.0 CB D:CYS484 3.2 0.9 1.0 CB D:CYS442 3.2 0.9 1.0 CB D:CYS439 3.3 1.0 1.0 CB D:CYS487 3.3 0.4 1.0 N D:CYS487 3.7 0.3 1.0 N D:CYS442 4.0 0.8 1.0 CA D:CYS487 4.1 1.0 1.0 CB D:LYS486 4.2 0.8 1.0 CA D:CYS442 4.2 0.2 1.0 CG D:LYS486 4.6 0.3 1.0 N D:GLY488 4.6 0.0 1.0 CA D:CYS484 4.6 0.3 1.0 CA D:CYS439 4.7 0.8 1.0 C D:LYS486 4.7 0.7 1.0 CD D:LYS486 4.8 0.0 1.0 CA D:LYS486 4.9 0.3 1.0 C D:CYS487 4.9 0.0 1.0 N D:LYS486 5.0 0.8 1.0

Zinc binding site 4 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1603 b:0.1 occ:1.00 ND1 D:HIS179 2.1 0.8 1.0 SG D:CYS162 2.3 0.3 1.0 SG D:CYS176 2.3 0.9 1.0 SG D:CYS159 2.4 0.2 1.0 CE1 D:HIS179 2.4 0.6 1.0 CB D:CYS162 3.2 0.4 1.0 CG D:HIS179 3.4 1.0 1.0 CB D:CYS176 3.5 0.5 1.0 CB D:CYS159 3.6 0.1 1.0 NE2 D:HIS179 3.7 0.1 1.0 N D:CYS162 3.8 0.0 1.0 CA D:CYS162 4.1 0.7 1.0 CD2 D:HIS179 4.2 0.5 1.0 CB D:HIS179 4.3 0.1 1.0 CD1 D:LEU166 4.4 0.9 1.0 CB D:LYS161 4.6 0.2 1.0 N D:HIS179 4.8 0.5 1.0 CA D:CYS176 4.8 0.8 1.0 C D:LYS161 4.9 0.0 1.0 CA D:CYS159 5.0 0.2 1.0

M.Tukalo, A.Yaremchuk, R.Fukunaga, S.Yokoyama, S.Cusack. The Crystal Structure of Leucyl-Trna Synthetase Complexed with Trna(Leu) in the Post-Transfer- Editing Conformation. Nat.Struct.Mol.Biol. V. 12 923 2005.
ISSN: ISSN 1545-9993
PubMed: 16155583
DOI: 10.1038/NSMB986