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Zinc in PDB 5onh: Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation

Enzymatic activity of Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation

All present enzymatic activity of Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation:
6.1.1.4;

Protein crystallography data

The structure of Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation, PDB code: 5onh was solved by A.Palencia, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 222.54 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.110, 70.380, 229.830, 90.00, 104.47, 90.00
R / Rfree (%) 22.3 / 25.7

Other elements in 5onh:

The structure of Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation (pdb code 5onh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation, PDB code: 5onh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5onh

Go back to Zinc Binding Sites List in 5onh
Zinc binding site 1 out of 2 in the Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn900

b:0.9
occ:1.00
 SG A:CYS176 2.3 0.6 1.0
SG A:CYS159 2.3 0.2 1.0
SG A:CYS179 2.3 0.4 1.0
OD2 A:ASP162 3.2 0.1 1.0
CB A:CYS176 3.3 0.9 1.0
CB A:CYS179 3.5 0.8 1.0
CB A:CYS159 3.5 0.3 1.0
N A:CYS179 3.7 0.7 1.0
O A:CYS179 4.0 0.0 1.0
NH1 A:ARG178 4.0 0.5 1.0
CA A:CYS179 4.0 0.3 1.0
C A:CYS179 4.4 0.7 1.0
CG A:ASP162 4.4 0.4 1.0
CG2 A:THR181 4.5 0.0 1.0
CB A:ARG178 4.5 0.1 1.0
CA A:CYS176 4.7 0.2 1.0
C A:ARG178 4.8 0.4 1.0
CA A:CYS159 4.9 0.9 1.0
N A:ARG178 5.0 0.4 1.0
C A:CYS176 5.0 0.7 1.0

Zinc binding site 2 out of 2 in 5onh

Go back to Zinc Binding Sites List in 5onh
Zinc binding site 2 out of 2 in the Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Quaternary Complex of Wild Type E. Coli Leucyl-Trna Synthetase with Trna(Leu), Leucyl-Adenylate Analogue, and Post-Transfer Editing Analogue of Norvaline in the Aminoacylation Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn900

b:0.0
occ:1.00
 SG D:CYS176 2.3 0.0 1.0
SG D:CYS179 2.3 1.0 1.0
SG D:CYS159 2.3 0.7 1.0
OD2 D:ASP162 2.9 0.0 1.0
CB D:CYS176 3.4 0.2 1.0
CB D:CYS179 3.5 0.7 1.0
CB D:CYS159 3.5 0.9 1.0
CG D:ASP162 3.9 0.3 1.0
N D:CYS179 4.2 0.6 1.0
CA D:CYS179 4.4 0.6 1.0
CB D:ASN161 4.6 0.8 1.0
CB D:ASP162 4.6 0.6 1.0
OG1 D:THR181 4.7 0.5 1.0
OD1 D:ASP162 4.8 0.4 1.0
CA D:CYS176 4.8 0.5 1.0
N D:ASP162 4.8 0.1 1.0
CA D:CYS159 4.9 0.2 1.0
CD1 D:LEU166 4.9 0.3 1.0
C D:CYS179 4.9 0.4 1.0
ND2 D:ASN161 5.0 0.3 1.0

Reference:

M.Dulic, N.Cvetesic, I.Zivkovic, A.Palencia, S.Cusack, B.Bertosa, I.Gruic-Sovulj. Kinetic Origin of Substrate Specificity in Post-Transfer Editing By Leucyl-Trna Synthetase. J. Mol. Biol. V. 430 1 2018.
ISSN: ESSN 1089-8638
PubMed: 29111343
DOI: 10.1016/J.JMB.2017.10.024
Page generated: Wed Dec 16 06:39:06 2020

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