Fluorine in PDB 6afc: Dj-1 with Compound 4

Enzymatic activity of Dj-1 with Compound 4

All present enzymatic activity of Dj-1 with Compound 4:
3.5.1.124;

Protein crystallography data

The structure of Dj-1 with Compound 4, PDB code: 6afc was solved by J.M.M.Caaveiro, S.Tashiro, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.80 / 1.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.430, 75.430, 75.890, 90.00, 90.00, 120.00
R / Rfree (%) 13.3 / 16

Other elements in 6afc:

The structure of Dj-1 with Compound 4 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dj-1 with Compound 4 (pdb code 6afc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Dj-1 with Compound 4, PDB code: 6afc:

Fluorine binding site 1 out of 1 in 6afc

Go back to Fluorine Binding Sites List in 6afc
Fluorine binding site 1 out of 1 in the Dj-1 with Compound 4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dj-1 with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:28.1
occ:0.75
F10 A:72R201 0.0 28.1 0.8
C3 A:72R201 1.3 24.4 0.8
C4 A:72R201 2.3 31.3 0.8
C2 A:72R201 2.4 25.4 0.8
O A:HOH437 3.5 23.4 0.2
C1 A:72R201 3.6 28.9 0.8
C5 A:72R201 3.6 27.6 0.8
NE2 A:HIS126 3.9 15.6 1.0
C6 A:72R201 4.1 24.6 0.8
O A:HOH432 4.2 14.3 0.2
CD2 A:HIS126 4.5 15.2 1.0
CD A:PRO158 4.5 14.3 1.0
CE1 A:HIS126 4.7 15.0 1.0
CG A:PRO158 4.7 15.5 1.0
C9 A:72R201 4.9 25.5 0.8

Reference:

S.Tashiro, J.M.M.Caaveiro, M.Nakakido, A.Tanabe, S.Nagatoishi, Y.Tamura, N.Matsuda, D.Liu, Q.Q.Hoang, K.Tsumoto. Discovery and Optimization of Inhibitors of the Parkinson'S Disease Associated Protein Dj-1. Acs Chem. Biol. V. 13 2783 2018.
ISSN: ESSN 1554-8937
PubMed: 30063823
DOI: 10.1021/ACSCHEMBIO.8B00701
Page generated: Sun Dec 13 12:44:12 2020

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