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Magnesium in PDB 4aq7: Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation

Enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation

All present enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation:
6.1.1.4;

Protein crystallography data

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation, PDB code: 4aq7 was solved by A.Palencia, T.Crepin, M.T.Vu, T.L.Lincecum Jr, S.A.Martinis, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.69 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.660, 69.200, 228.840, 90.00, 104.35, 90.00
R / Rfree (%) 18.752 / 25.031

Other elements in 4aq7:

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue 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 Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation (pdb code 4aq7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation, PDB code: 4aq7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4aq7

Go back to Magnesium Binding Sites List in 4aq7
Magnesium binding site 1 out of 2 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue 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 Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1077

b:55.8
occ:1.00
OP2 B:U8 2.0 33.5 1.0
OP2 B:G9 2.3 32.3 1.0
P B:U8 3.4 33.5 1.0
P B:G9 3.6 32.7 1.0
OP1 B:U11 4.0 36.6 1.0
O5' B:U8 4.1 33.9 1.0
OP1 B:U8 4.1 31.6 1.0
OP1 B:G9 4.3 34.2 1.0
C5' B:U8 4.3 32.5 1.0
O5' B:G9 4.5 32.7 1.0
OP2 B:G12 4.5 30.4 1.0
O3' B:A7 4.6 30.2 1.0
C5' B:G9 4.6 33.9 1.0
O3' B:U8 4.7 32.0 1.0
C3' B:U8 4.8 31.7 1.0

Magnesium binding site 2 out of 2 in 4aq7

Go back to Magnesium Binding Sites List in 4aq7
Magnesium binding site 2 out of 2 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue 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 Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Leucyl-Adenylate Analogue in the Aminoacylation Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1077

b:67.7
occ:1.00
OP2 E:G9 2.2 52.5 1.0
OP2 E:U8 2.6 52.6 1.0
P E:G9 3.4 55.0 1.0
OP1 E:G9 3.8 56.9 1.0
P E:U8 3.9 50.5 1.0
OP1 E:U11 3.9 58.6 1.0
O5' E:U8 4.1 50.2 1.0
O5' E:G9 4.5 54.1 1.0
O3' E:U8 4.6 52.5 1.0
C5' E:G9 4.7 54.6 1.0
O3' E:A7 4.9 51.6 1.0
OP2 E:U11 4.9 59.3 1.0
OP1 E:U8 5.0 50.1 1.0
C5' E:U8 5.0 50.3 1.0
P E:U11 5.0 59.6 1.0

Reference:

A.Palencia, T.Crepin, M.T.Vu, T.L.Lincecum Jr, S.A.Martinis, S.Cusack. Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-Trna Synthetase Nat.Struct.Mol.Biol. V. 19 677 2012.
ISSN: ISSN 1545-9993
PubMed: 22683997
DOI: 10.1038/NSMB.2317
Page generated: Mon Dec 14 09:08:33 2020

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