Mercury 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:

Zinc

(Zn)

4 atoms

The binding sites of Mercury 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 Mercury atom.
In total 2 binding sites of Mercury where determined in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with A Trnaleu Transcript in the Post-Editing Conformation, PDB code: 2byt:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 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 Mercury with other atoms in the Hg 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:Hg1304 b:86.6 occ:1.00 SG A:CYS128 2.5 68.3 1.0 O A:CYS128 3.3 58.8 1.0 OH A:TYR102 3.4 83.1 1.0 C A:CYS128 3.4 58.6 1.0 CE2 A:TYR102 3.5 73.5 1.0 CB A:CYS128 3.6 63.4 1.0 N A:GLU129 3.7 58.8 1.0 CG A:GLU129 3.7 66.8 1.0 CZ A:TYR102 3.9 78.4 1.0 CA A:GLU129 3.9 60.6 1.0 CA A:CYS128 4.1 58.5 1.0 CH2 A:TRP430 4.2 49.7 1.0 CZ2 A:TRP430 4.4 46.7 1.0 CB A:GLU129 4.4 63.7 1.0 CD2 A:TYR102 4.7 68.1 1.0 N A:CYS128 4.9 57.5 1.0 CD A:GLU129 5.0 74.4 1.0

Mercury binding site 2 out of 2 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 Mercury with other atoms in the Hg 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 D:Hg1604 b:0.1 occ:1.00 SG D:CYS128 2.5 0.8 1.0 OH D:TYR102 3.3 0.4 1.0 O D:CYS128 3.3 0.7 1.0 C D:CYS128 3.3 0.6 1.0 CG D:GLU129 3.5 0.1 1.0 CE2 D:TYR102 3.5 0.3 1.0 N D:GLU129 3.5 0.8 1.0 CB D:CYS128 3.7 0.7 1.0 CA D:GLU129 3.7 0.9 1.0 CZ D:TYR102 3.8 0.3 1.0 CA D:CYS128 4.1 0.2 1.0 CB D:GLU129 4.2 0.4 1.0 CH2 D:TRP430 4.4 86.1 1.0 CZ2 D:TRP430 4.6 87.4 1.0 CD2 D:TYR102 4.7 0.9 1.0 CD D:GLU129 4.8 0.8 1.0 N D:CYS128 4.9 0.4 1.0 OE1 D:GLU129 5.0 0.8 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