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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 4aq7

Go back to Zinc Binding Sites List in 4aq7
Zinc 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 Zinc with other atoms in the Zn 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
A:Zn900

b:0.1
occ:1.00
SG A:CYS179 2.7 0.6 1.0
SG A:CYS159 2.9 84.5 1.0
SG A:CYS176 3.1 0.2 1.0
CB A:CYS176 3.4 0.1 1.0
OD2 A:ASP162 3.5 95.7 1.0
CB A:CYS159 3.8 77.8 1.0
N A:CYS179 4.0 0.8 1.0
NH1 A:ARG178 4.1 0.7 1.0
CB A:ARG178 4.2 0.5 1.0
CB A:CYS179 4.2 0.0 1.0
CG A:ASP162 4.3 89.8 1.0
CA A:CYS179 4.5 0.6 1.0
CG2 A:THR181 4.5 0.0 1.0
O A:CYS179 4.6 0.1 1.0
O A:THR181 4.7 0.0 1.0
C A:CYS179 4.8 0.3 1.0
CA A:CYS176 4.8 0.1 1.0
CG A:ARG178 4.9 0.7 1.0
CB A:ASP162 4.9 86.4 1.0
CA A:ARG178 4.9 0.7 1.0
N A:ARG178 4.9 0.1 1.0
C A:ARG178 4.9 0.6 1.0

Zinc binding site 2 out of 2 in 4aq7

Go back to Zinc Binding Sites List in 4aq7
Zinc 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 Zinc with other atoms in the Zn 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
D:Zn900

b:0.5
occ:1.00
SG D:CYS176 2.3 0.8 1.0
SG D:CYS179 2.7 0.4 1.0
OD2 D:ASP162 2.9 94.2 1.0
SG D:CYS159 3.3 0.6 1.0
CB D:CYS176 3.4 0.9 1.0
CG D:ASP162 4.0 95.1 1.0
OG1 D:THR181 4.0 0.6 1.0
CB D:CYS179 4.2 0.7 1.0
N D:CYS179 4.3 0.9 1.0
OD1 D:ASP162 4.4 94.9 1.0
ND2 D:ASN161 4.5 0.1 1.0
O D:CYS179 4.5 0.5 1.0
CB D:CYS159 4.6 0.8 1.0
CD1 D:LEU166 4.7 82.7 1.0
CB D:ARG178 4.7 0.1 1.0
CA D:CYS179 4.7 0.8 1.0
N D:ARG178 4.8 0.0 1.0
CA D:CYS176 4.8 1.0 1.0
CB D:ASN161 4.9 0.4 1.0
CG D:ARG178 4.9 0.3 1.0
C D:CYS179 5.0 0.3 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: Wed Dec 16 05:03:24 2020

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