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Zinc 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
Mercury (Hg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2v0g

Go back to Zinc Binding Sites List in 2v0g
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn1877

b:0.5
occ:1.00
SG A:CYS487 2.6 86.3 1.0
CB A:CYS484 2.8 87.7 1.0
SG A:CYS484 2.8 87.2 1.0
SG A:CYS439 3.3 83.1 1.0
SG A:CYS442 3.6 85.0 1.0
N A:CYS487 3.7 86.6 1.0
CB A:LYS486 3.9 87.6 1.0
CB A:CYS487 3.9 86.2 1.0
CB A:CYS442 4.1 85.0 1.0
N A:GLY488 4.2 84.8 1.0
CB A:CYS439 4.3 82.8 1.0
CA A:CYS484 4.3 87.8 1.0
CA A:CYS487 4.3 86.1 1.0
N A:LYS486 4.4 87.5 1.0
C A:LYS486 4.4 87.1 1.0
N A:GLY489 4.5 82.8 1.0
CA A:LYS486 4.5 87.4 1.0
CG A:LYS486 4.7 87.6 1.0
CG2 A:VAL445 4.8 83.1 1.0
C A:CYS487 4.9 85.6 1.0
N A:CYS442 4.9 85.0 1.0
C A:CYS484 4.9 87.8 1.0

Zinc binding site 2 out of 4 in 2v0g

Go back to Zinc Binding Sites List in 2v0g
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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
A:Zn1878

b:25.6
occ:1.00
SG A:CYS159 1.9 68.4 1.0
SG A:CYS176 2.1 80.3 1.0
SG A:CYS162 2.1 69.1 1.0
ND1 A:HIS179 2.8 83.2 1.0
CE1 A:HIS179 3.1 83.3 1.0
CB A:CYS162 3.3 70.1 1.0
CB A:CYS159 3.3 69.4 1.0
CB A:CYS176 3.5 80.4 1.0
N A:CYS162 3.9 70.1 1.0
CG A:HIS179 4.1 82.8 1.0
CA A:CYS162 4.2 70.1 1.0
NE2 A:HIS179 4.5 83.7 1.0
CB A:LYS161 4.5 70.1 1.0
CD1 A:LEU166 4.5 69.9 1.0
CD2 A:LEU166 4.6 70.1 1.0
CA A:CYS159 4.6 69.6 1.0
CA A:CYS176 4.8 80.4 1.0
CB A:HIS179 4.8 82.0 1.0
C A:LYS161 4.8 70.0 1.0
CD2 A:HIS179 4.9 83.5 1.0

Zinc binding site 3 out of 4 in 2v0g

Go back to Zinc Binding Sites List in 2v0g
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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:Zn1880

b:0.3
occ:1.00
SG D:CYS439 3.0 0.1 1.0
SG D:CYS487 3.4 0.4 1.0
CB D:CYS484 3.6 0.2 1.0
SG D:CYS484 3.7 0.5 1.0
N D:GLY489 3.9 0.3 1.0
CA D:GLY489 4.0 0.6 1.0
SG D:CYS442 4.4 0.3 1.0
C D:GLY489 4.5 0.8 1.0
N D:CYS487 4.5 0.4 1.0
CB D:LYS486 4.5 0.5 1.0
N D:GLY488 4.6 0.7 1.0
CB D:CYS487 4.7 0.0 1.0
O D:GLY489 4.8 0.7 1.0
CD D:LYS486 4.8 0.4 1.0
CB D:CYS439 4.8 0.0 1.0
O D:CYS484 4.8 0.8 1.0
CA D:CYS484 4.8 0.2 1.0
O D:PRO490 5.0 1.0 1.0
CA D:CYS487 5.0 0.9 1.0

Zinc binding site 4 out of 4 in 2v0g

Go back to Zinc Binding Sites List in 2v0g
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn1881

b:70.4
occ:1.00
SG D:CYS162 1.8 0.5 1.0
SG D:CYS159 2.1 0.5 1.0
SG D:CYS176 2.7 0.2 1.0
CB D:CYS162 2.9 0.9 1.0
CB D:CYS159 3.5 0.7 1.0
ND1 D:HIS179 3.5 0.5 1.0
N D:CYS162 3.5 1.0 1.0
CA D:CYS162 3.7 0.9 1.0
CB D:CYS176 3.9 0.4 1.0
CG D:HIS179 4.4 0.8 1.0
CB D:HIS179 4.4 0.2 1.0
CD1 D:LEU166 4.4 0.3 1.0
CE1 D:HIS179 4.4 0.3 1.0
O D:CYS159 4.6 0.9 1.0
C D:LYS161 4.6 0.9 1.0
CB D:LYS161 4.6 0.8 1.0
ND2 D:ASN88 4.7 0.7 1.0
N D:HIS179 4.8 0.9 1.0
CA D:CYS159 4.8 0.7 1.0
CD1 D:LEU84 4.9 90.5 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 Dec 16 03:54:17 2020

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