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

Protein crystallography data

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

Other elements in 2byt:

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

Mercury Binding Sites:

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 2byt

Go back to Mercury Binding Sites List in 2byt
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 2byt

Go back to Mercury Binding Sites List in 2byt
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

Reference:

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
Page generated: Wed Oct 28 18:41:19 2020

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