Atomistry » Zinc » PDB 4ad9-4arf » 4aq7
Atomistry »
  Zinc »
    PDB 4ad9-4arf »
      4aq7 »

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: Sat Oct 26 19:19:20 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy