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Zinc in PDB 3zgz: Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation

Enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation

All present enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation:
6.1.1.4;

Protein crystallography data

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation, PDB code: 3zgz was solved by S.Chopra, A.Palencia, C.Virus, A.Tripathy, B.R.Temple, A.Velazquez-Campoy, S.Cusack, J.S.Reader, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.59 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.580, 68.190, 226.220, 90.00, 105.53, 90.00
R / Rfree (%) 18.681 / 23.822

Other elements in 3zgz:

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation (pdb code 3zgz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation, PDB code: 3zgz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3zgz

Go back to Zinc Binding Sites List in 3zgz
Zinc binding site 1 out of 2 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1861

b:0.3
occ:1.00
 SG A:CYS159 2.5 85.6 1.0
SG A:CYS179 2.8 0.7 1.0
CB A:CYS176 2.9 99.8 1.0
OD2 A:ASP162 3.1 81.0 1.0
SG A:CYS176 3.1 97.1 1.0
O A:CYS179 3.7 0.1 1.0
CB A:CYS159 3.9 74.7 1.0
CG A:ASP162 3.9 84.6 1.0
N A:CYS179 4.3 0.9 1.0
C A:CYS179 4.3 0.3 1.0
OD1 A:ASP162 4.3 89.7 1.0
CB A:CYS179 4.4 0.4 1.0
CA A:CYS176 4.4 98.1 1.0
N A:THR181 4.6 0.8 1.0
O A:THR181 4.7 91.4 1.0
CG2 A:THR181 4.8 94.7 1.0
CB A:ARG178 4.8 0.5 1.0
CA A:CYS179 4.8 0.5 1.0
N A:CYS176 4.8 99.8 1.0
CB A:ASP162 4.9 82.4 1.0

Zinc binding site 2 out of 2 in 3zgz

Go back to Zinc Binding Sites List in 3zgz
Zinc binding site 2 out of 2 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1861

b:1.0
occ:1.00
 SG D:CYS179 2.5 0.8 1.0
SG D:CYS176 2.8 0.8 1.0
CB D:CYS176 2.9 0.2 1.0
SG D:CYS159 3.0 0.7 1.0
OD2 D:ASP162 3.0 0.7 1.0
CG D:ASP162 3.5 0.9 1.0
OD1 D:ASP162 3.5 0.7 1.0
O D:CYS179 3.6 0.6 1.0
OG1 D:THR181 3.6 0.1 1.0
CB D:CYS159 3.9 1.0 1.0
CB D:CYS179 4.1 0.3 1.0
N D:CYS179 4.1 0.0 1.0
CA D:CYS176 4.4 0.1 1.0
C D:CYS179 4.4 1.0 1.0
CA D:CYS179 4.5 0.7 1.0
ND2 D:ASN161 4.6 0.9 1.0
CB D:ASN161 4.7 0.9 1.0
CB D:ASP162 4.7 0.2 1.0
CB D:THR181 4.9 1.0 1.0

Reference:

S.Chopra, A.Palencia, C.Virus, A.Tripathy, B.R.Temple, A.Velazquez-Campoy, S.Cusack, J.S.Reader. Plant Tumour Biocontrol Agent Employs A Trna-Dependent Mechanism to Inhibit Leucyl-Trna Synthetase Nat.Commun. V. 4 1417 2013.
ISSN: ISSN 2041-1723
PubMed: 23361008
DOI: 10.1038/NCOMMS2421
Page generated: Wed Aug 20 15:29:21 2025

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