Zinc in PDB 8i9i: Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc

Enzymatic activity of Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc

All present enzymatic activity of Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc:
6.1.1.17;

Protein crystallography data

The structure of Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc, PDB code: 8i9i was solved by A.Dev, N.Chongdar, S.Dasgupta, G.Basu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 211.51, 61.29, 101.9, 90, 96.69, 90
R / Rfree (%) 25.3 / 29.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc (pdb code 8i9i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc, PDB code: 8i9i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8i9i

Go back to Zinc Binding Sites List in 8i9i
Zinc binding site 1 out of 2 in the Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:90.3
occ:1.00
OH A:TYR121 2.2 88.2 1.0
SG A:CYS98 2.3 77.3 1.0
SG A:CYS100 2.3 85.8 1.0
SG A:CYS125 2.3 92.9 1.0
CZ A:TYR121 3.0 85.5 1.0
CB A:CYS100 3.0 85.9 1.0
CE1 A:TYR121 3.2 85.3 1.0
CB A:CYS125 3.3 92.3 1.0
N A:CYS100 3.4 87.0 1.0
CA A:CYS100 3.8 88.6 1.0
CB A:CYS98 3.8 75.7 1.0
N A:TYR99 4.0 85.4 1.0
N A:CYS125 4.1 95.8 1.0
CE2 A:TYR121 4.2 83.9 1.0
CA A:CYS125 4.4 95.7 1.0
CA A:CYS98 4.4 78.5 1.0
NH1 A:ARG104 4.4 83.7 1.0
CD1 A:TYR121 4.5 83.5 1.0
C A:TYR99 4.5 89.8 1.0
C A:CYS98 4.6 82.0 1.0
CA A:TYR99 4.9 88.6 1.0
CB A:ARG124 4.9 98.9 1.0
CD2 A:LEU105 5.0 80.2 1.0
C A:CYS100 5.0 89.3 1.0

Zinc binding site 2 out of 2 in 8i9i

Go back to Zinc Binding Sites List in 8i9i
Zinc binding site 2 out of 2 in the Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glutamyl-Trna Synthetase From Escherichia Coli Bound to Glutamate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:152.8
occ:1.00
OH B:TYR121 2.2 115.6 1.0
SG B:CYS100 2.3 121.2 1.0
SG B:CYS98 2.3 113.5 1.0
SG B:CYS125 2.3 118.3 1.0
CB B:CYS100 3.0 120.2 1.0
N B:CYS100 3.1 118.7 1.0
CZ B:TYR121 3.4 114.6 1.0
N B:TYR99 3.6 115.9 1.0
CA B:CYS100 3.6 120.5 1.0
CB B:CYS98 3.7 111.5 1.0
CB B:CYS125 3.8 116.8 1.0
CE1 B:TYR121 3.9 115.6 1.0
C B:TYR99 4.1 119.1 1.0
CA B:CYS98 4.1 112.5 1.0
C B:CYS98 4.3 113.8 1.0
CA B:TYR99 4.4 117.5 1.0
CE2 B:TYR121 4.5 112.7 1.0
N B:CYS125 4.5 118.8 1.0
CA B:CYS125 4.8 118.2 1.0
C B:CYS100 4.9 120.0 1.0
CB B:ARG124 4.9 122.9 1.0

Reference:

A.Dev, N.Chongdar, S.Dasgupta, G.Basu. Escherichia Coli Glurs To Be Published.
Page generated: Wed Apr 26 00:48:03 2023

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