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Mercury in PDB 2v0g: Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site.

Protein crystallography data

The structure of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site., PDB code: 2v0g was solved by F.Rock, W.Mao, A.Yaremchuk, M.Tukalo, T.Crepin, H.Zhou, Y.Zhang, V.Hernandez, T.Akama, S.Baker, J.Plattner, L.Shapiro, S.A.Martinis, S.J.Benkovic, S.Cusack, M.R.K.Alley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 152.50 / 3.5
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.050, 125.800, 173.200, 90.00, 118.71, 90.00
R / Rfree (%) 24.5 / 31.4

Other elements in 2v0g:

The structure of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site. also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site. (pdb code 2v0g). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site., PDB code: 2v0g:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 2v0g

Go back to Mercury Binding Sites List in 2v0g
Mercury binding site 1 out of 2 in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site.


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1879

b:79.3
occ:1.00
SG A:CYS128 2.2 44.9 1.0
OH A:TYR102 3.0 61.6 1.0
CE2 A:TYR102 3.2 61.4 1.0
CB A:CYS128 3.4 44.5 1.0
CZ A:TYR102 3.5 61.8 1.0
C A:CYS128 3.5 44.5 1.0
N A:GLU129 3.7 44.9 1.0
O A:CYS128 3.7 44.4 1.0
CA A:GLU129 4.0 45.4 1.0
CA A:CYS128 4.1 44.6 1.0
CD2 A:TYR102 4.3 61.5 1.0
CG A:GLU129 4.4 45.9 1.0
CZ2 A:TRP430 4.5 59.7 1.0
CH2 A:TRP430 4.5 59.4 1.0
CE1 A:TYR102 4.8 61.7 1.0
CB A:GLU129 4.8 45.5 1.0
N A:CYS128 4.9 44.4 1.0

Mercury binding site 2 out of 2 in 2v0g

Go back to Mercury Binding Sites List in 2v0g
Mercury binding site 2 out of 2 in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site.


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Trna(Leu) Transcript with 5-Fluoro-1,3-Dihydro-1- Hydroxy-2,1-Benzoxaborole (AN2690) Forming An Adduct to the Ribose of Adenosine-76 in the Enzyme Editing Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1882

b:0.9
occ:1.00
SG D:CYS128 1.6 83.0 1.0
O D:CYS128 2.4 83.3 1.0
C D:CYS128 2.6 83.4 1.0
CB D:CYS128 2.8 83.3 1.0
N D:GLU129 3.2 83.8 1.0
CA D:CYS128 3.3 83.2 1.0
OH D:TYR102 3.7 0.6 1.0
CE2 D:TYR102 3.8 0.6 1.0
CA D:GLU129 3.8 84.1 1.0
CZ D:TYR102 4.2 0.7 1.0
CG D:GLU129 4.3 84.0 1.0
CH2 D:TRP430 4.3 93.6 1.0
N D:CYS128 4.3 82.8 1.0
CZ2 D:TRP430 4.5 93.7 1.0
CB D:GLU129 4.7 84.1 1.0
CG D:LYS98 4.8 0.9 1.0
CD2 D:TYR102 4.9 0.7 1.0
C D:GLU129 5.0 84.4 1.0

Reference:

F.Rock, W.Mao, A.Yaremchuk, M.Tukalo, T.Crepin, H.Zhou, Y.Zhang, V.Hernandez, T.Akama, S.Baker, J.Plattner, L.Shapiro, S.A.Martinis, S.J.Benkovic, S.Cusack, M.R.K.Alley. An Antifungal Agent Inhibits An Aminoacyl-Trna Synthetase By Trapping Trna in the Editing Site. Science V. 316 1759 2007.
ISSN: ISSN 0036-8075
PubMed: 17588934
DOI: 10.1126/SCIENCE.1142189
Page generated: Wed Oct 28 18:42:00 2020

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