Chlorine in PDB 8ke5: Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp

Enzymatic activity of Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp

All present enzymatic activity of Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp:
6.1.1.26;

Protein crystallography data

The structure of Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp, PDB code: 8ke5 was solved by J.H.Weng, M.D.Tsai, Y.S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.27 / 1.90
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 104.685, 104.685, 71.338, 90, 90, 120
R / Rfree (%) 18.4 / 18.6

Other elements in 8ke5:

The structure of Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp (pdb code 8ke5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp, PDB code: 8ke5:

Chlorine binding site 1 out of 1 in 8ke5

Go back to Chlorine Binding Sites List in 8ke5
Chlorine binding site 1 out of 1 in the Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pylrs C-Terminus Domain Mutant Bound with D-3-Chlorophenylalanine and Ampnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:36.3
occ:0.56
 CL1 A:FXL504 0.0 36.3 0.6
CE1 A:FXL504 1.7 26.8 0.6
CD1 A:FXL504 2.7 24.1 0.6
O A:HOH629 2.7 29.9 1.0
CZ A:FXL504 2.7 24.1 0.6
O A:HOH668 2.7 22.1 1.0
CB A:ALA302 3.7 15.9 1.0
NE2 A:GLN348 3.8 16.9 1.0
CG A:FXL504 3.9 23.2 0.6
CE2 A:FXL504 3.9 23.8 0.6
CH2 A:TRP417 4.0 21.2 1.0
CZ A:TYR306 4.1 22.8 1.0
OH A:TYR306 4.2 22.7 1.0
CE2 A:TYR306 4.2 19.8 1.0
CD A:GLN348 4.3 20.2 1.0
CZ3 A:TRP417 4.3 17.9 1.0
OE1 A:GLN348 4.4 18.3 1.0
CD2 A:FXL504 4.4 24.1 0.6
CZ2 A:TRP417 4.4 20.8 1.0
CA A:ALA302 4.5 16.4 1.0
CE1 A:TYR306 4.7 20.6 1.0
CD2 A:TYR306 4.8 19.6 1.0

Reference:

H.K.Jiang, J.H.Weng, Y.H.Wang, J.C.Tsou, P.J.Chen, A.L.A.Ko, D.Soll, M.D.Tsai, Y.S.Wang. Rational Design of the Genetic Code Expansion Toolkit For in Vivo Encoding of D-Amino Acids Front Genet 2023.
DOI: 10.3389/FGENE.2023.1277489
Page generated: Tue Jul 30 11:05:40 2024

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