Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5onh

Go back to Magnesium Binding Sites List in 5onh
Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg101

b:37.9
occ:1.00
 OP1 B:U8 2.0 55.9 1.0
OP2 B:G9 2.5 55.9 1.0
P B:U8 3.4 55.6 1.0
P B:G9 3.9 56.2 1.0
O5' B:U8 4.0 54.9 1.0
OP1 B:U11 4.3 61.0 1.0
OP2 B:U8 4.3 55.8 1.0
C5' B:U8 4.3 55.1 1.0
O3' B:A7 4.4 54.9 1.0
OP1 B:G9 4.6 56.2 1.0
OP2 B:G12 4.6 55.1 1.0
O5' B:G9 4.8 57.7 1.0
OP2 B:U11 4.9 59.8 1.0
O3' B:U8 5.0 55.7 1.0
C5' B:G9 5.0 59.5 1.0

Magnesium binding site 2 out of 2 in 5onh

Go back to Magnesium Binding Sites List in 5onh
Magnesium 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 Magnesium with other atoms in the Mg 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
E:Mg101

b:53.1
occ:1.00
 OP2 E:G9 2.0 67.5 1.0
OP1 E:U8 2.9 68.0 1.0
P E:G9 3.2 67.8 1.0
OP2 E:U11 3.7 71.7 1.0
OP1 E:U11 3.8 72.7 1.0
O5' E:G9 3.8 69.0 1.0
C5' E:G9 3.9 69.8 1.0
OP1 E:G9 3.9 67.9 1.0
P E:U8 4.2 68.0 1.0
P E:U11 4.3 73.2 1.0
OP2 E:G12 4.4 66.8 1.0
O5' E:U8 4.4 66.2 1.0
O3' E:U8 4.5 66.4 1.0
C5' E:U8 4.7 65.9 1.0
C3' E:U8 4.8 65.5 1.0
OP2 E:U8 4.9 68.3 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: Mon Dec 14 21:00:28 2020

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