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Fluorine in PDB 6teq: Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose

Protein crystallography data

The structure of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose, PDB code: 6teq was solved by T.Keenan, F.Parmeggiani, C.Q.Fontenelle, J.Malassis, J.Vendeville, W.A.Offen, P.Both, K.Huang, A.Marchesi, A.Heyam, C.Young, S.Charnock, G.J.Davies, B.Linclau, S.L.Flitsch, M.A.Fascione, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.55 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.218, 164.386, 115.874, 90.00, 95.94, 90.00
R / Rfree (%) 16.9 / 20.3

Other elements in 6teq:

The structure of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose (pdb code 6teq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose, PDB code: 6teq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6teq

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Fluorine binding site 1 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:15.5
occ:0.60
 F2 A:GAF609 0.0 15.5 0.6
F2 A:2FG610 0.1 25.5 0.4
C2 A:2FG610 1.3 20.5 0.4
C2 A:GAF609 1.4 14.7 0.6
O A:HOH709 2.3 16.3 1.0
C1 A:GAF609 2.3 14.9 0.6
C3 A:GAF609 2.3 11.9 0.6
C3 A:2FG610 2.4 17.7 0.4
C1 A:2FG610 2.4 20.1 0.4
O1 A:GAF609 2.6 17.8 0.6
O1 A:2FG610 2.8 17.0 0.4
O3 A:GAF609 2.9 14.7 0.6
O3 A:2FG610 2.9 20.4 0.4
O A:HOH786 2.9 24.3 1.0
OD2 A:ASP191 3.2 15.8 1.0
OG1 A:THR187 3.2 22.5 1.0
O A:HOH874 3.3 16.0 1.0
O A:HOH902 3.5 39.4 1.0
O A:HOH804 3.5 31.2 1.0
O5 A:GAF609 3.6 15.6 0.6
O5 A:2FG610 3.6 20.2 0.4
C4 A:GAF609 3.7 13.5 0.6
C4 A:2FG610 3.7 18.8 0.4
CG A:ASP191 3.7 13.1 1.0
OD1 A:ASP191 4.0 13.1 1.0
CB A:THR187 4.1 20.1 1.0
C5 A:GAF609 4.1 12.3 0.6
C5 A:2FG610 4.1 18.4 0.4
OH A:TYR248 4.3 17.3 1.0
CA A:THR187 4.3 20.4 1.0
O4 A:2FG610 4.4 19.2 0.4
O4 A:GAF609 4.4 14.1 0.6
N A:GLY188 4.5 16.3 1.0
O A:HOH707 4.5 22.6 1.0
CZ A:TYR248 4.6 18.1 1.0
CE1 A:TYR248 4.8 16.6 1.0
CB A:ASP191 4.9 12.9 1.0
C A:THR187 4.9 16.8 1.0
O A:SER186 4.9 20.5 1.0
O A:HOH923 5.0 23.9 1.0

Fluorine binding site 2 out of 8 in 6teq

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Fluorine binding site 2 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F610

b:25.5
occ:0.40
 F2 A:2FG610 0.0 25.5 0.4
F2 A:GAF609 0.1 15.5 0.6
C2 A:2FG610 1.4 20.5 0.4
C2 A:GAF609 1.4 14.7 0.6
C1 A:GAF609 2.3 14.9 0.6
O A:HOH709 2.3 16.3 1.0
C1 A:2FG610 2.3 20.1 0.4
C3 A:GAF609 2.4 11.9 0.6
C3 A:2FG610 2.4 17.7 0.4
O1 A:GAF609 2.4 17.8 0.6
O1 A:2FG610 2.7 17.0 0.4
O A:HOH786 2.9 24.3 1.0
O3 A:GAF609 2.9 14.7 0.6
O3 A:2FG610 3.0 20.4 0.4
OD2 A:ASP191 3.1 15.8 1.0
O A:HOH874 3.3 16.0 1.0
O A:HOH804 3.3 31.2 1.0
OG1 A:THR187 3.3 22.5 1.0
O A:HOH902 3.5 39.4 1.0
O5 A:GAF609 3.6 15.6 0.6
O5 A:2FG610 3.6 20.2 0.4
CG A:ASP191 3.7 13.1 1.0
C4 A:GAF609 3.7 13.5 0.6
C4 A:2FG610 3.8 18.8 0.4
OD1 A:ASP191 3.9 13.1 1.0
C5 A:GAF609 4.0 12.3 0.6
C5 A:2FG610 4.1 18.4 0.4
CB A:THR187 4.2 20.1 1.0
OH A:TYR248 4.4 17.3 1.0
CA A:THR187 4.4 20.4 1.0
O4 A:2FG610 4.4 19.2 0.4
O4 A:GAF609 4.4 14.1 0.6
O A:HOH707 4.5 22.6 1.0
N A:GLY188 4.6 16.3 1.0
CZ A:TYR248 4.7 18.1 1.0
CB A:ASP191 4.9 12.9 1.0
O A:HOH923 4.9 23.9 1.0
CE1 A:TYR248 4.9 16.6 1.0
NH1 A:ARG40 4.9 14.5 1.0
O A:HOH702 4.9 23.2 0.5

Fluorine binding site 3 out of 8 in 6teq

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Fluorine binding site 3 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F609

b:26.1
occ:0.60
 F2 B:2FG609 0.0 26.1 0.6
F2 B:GAF610 0.0 17.1 0.4
C2 B:GAF610 1.4 14.0 0.4
C2 B:2FG609 1.4 22.4 0.6
C1 B:GAF610 2.3 13.4 0.4
C1 B:2FG609 2.3 21.9 0.6
O B:HOH706 2.4 16.3 1.0
C3 B:GAF610 2.5 13.6 0.4
C3 B:2FG609 2.5 20.4 0.6
O1 B:2FG609 2.7 22.6 0.6
O1 B:GAF610 2.7 13.5 0.4
O B:HOH829 2.9 25.5 1.0
O B:HOH905 2.9 36.5 1.0
O3 B:GAF610 3.0 12.3 0.4
O3 B:2FG609 3.0 18.8 0.6
OD2 B:ASP191 3.1 17.0 1.0
OG1 B:THR187 3.2 23.8 1.0
O B:HOH739 3.4 29.8 1.0
O B:HOH896 3.4 15.3 1.0
O5 B:GAF610 3.5 13.1 0.4
O5 B:2FG609 3.5 23.9 0.6
C4 B:GAF610 3.8 12.6 0.4
CG B:ASP191 3.8 13.1 1.0
C4 B:2FG609 3.8 19.1 0.6
OD1 B:ASP191 3.9 13.6 1.0
C5 B:GAF610 4.0 13.0 0.4
C5 B:2FG609 4.1 19.4 0.6
CB B:THR187 4.1 22.1 1.0
OH B:TYR248 4.2 18.2 1.0
CA B:THR187 4.4 17.1 1.0
O4 B:GAF610 4.4 14.3 0.4
O4 B:2FG609 4.4 22.2 0.6
O B:HOH774 4.5 25.1 1.0
N B:GLY188 4.5 17.4 1.0
CZ B:TYR248 4.5 17.6 1.0
CE1 B:TYR248 4.7 17.0 1.0
O B:HOH701 4.9 20.6 0.5
O B:HOH881 4.9 25.0 1.0
CB B:ASP191 4.9 14.0 1.0
NH1 B:ARG40 5.0 15.7 1.0

Fluorine binding site 4 out of 8 in 6teq

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Fluorine binding site 4 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F610

b:17.1
occ:0.40
 F2 B:GAF610 0.0 17.1 0.4
F2 B:2FG609 0.0 26.1 0.6
C2 B:GAF610 1.4 14.0 0.4
C2 B:2FG609 1.4 22.4 0.6
C1 B:GAF610 2.3 13.4 0.4
C1 B:2FG609 2.3 21.9 0.6
O B:HOH706 2.4 16.3 1.0
C3 B:GAF610 2.5 13.6 0.4
C3 B:2FG609 2.5 20.4 0.6
O1 B:2FG609 2.7 22.6 0.6
O1 B:GAF610 2.8 13.5 0.4
O B:HOH829 2.9 25.5 1.0
O B:HOH905 2.9 36.5 1.0
O3 B:GAF610 3.0 12.3 0.4
O3 B:2FG609 3.0 18.8 0.6
OG1 B:THR187 3.2 23.8 1.0
OD2 B:ASP191 3.2 17.0 1.0
O B:HOH896 3.4 15.3 1.0
O B:HOH739 3.4 29.8 1.0
O5 B:GAF610 3.5 13.1 0.4
O5 B:2FG609 3.5 23.9 0.6
C4 B:GAF610 3.8 12.6 0.4
C4 B:2FG609 3.8 19.1 0.6
CG B:ASP191 3.8 13.1 1.0
OD1 B:ASP191 4.0 13.6 1.0
C5 B:GAF610 4.1 13.0 0.4
C5 B:2FG609 4.1 19.4 0.6
CB B:THR187 4.1 22.1 1.0
OH B:TYR248 4.2 18.2 1.0
CA B:THR187 4.3 17.1 1.0
O4 B:GAF610 4.4 14.3 0.4
O4 B:2FG609 4.4 22.2 0.6
O B:HOH774 4.5 25.1 1.0
N B:GLY188 4.5 17.4 1.0
CZ B:TYR248 4.5 17.6 1.0
CE1 B:TYR248 4.7 17.0 1.0
O B:HOH701 4.9 20.6 0.5
CB B:ASP191 4.9 14.0 1.0
O B:HOH881 4.9 25.0 1.0
C B:THR187 5.0 17.7 1.0
O B:SER186 5.0 23.6 1.0

Fluorine binding site 5 out of 8 in 6teq

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Fluorine binding site 5 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F615

b:20.9
occ:0.60
 F2 C:GAF615 0.0 20.9 0.6
F2 C:2FG616 0.0 17.0 0.4
C2 C:2FG616 1.4 17.2 0.4
C2 C:GAF615 1.4 19.0 0.6
O C:HOH711 2.3 14.4 1.0
C1 C:GAF615 2.3 16.8 0.6
C1 C:2FG616 2.4 16.6 0.4
C3 C:2FG616 2.4 16.1 0.4
C3 C:GAF615 2.4 17.7 0.6
O1 C:GAF615 2.7 20.6 0.6
O3 C:2FG616 2.8 14.6 0.4
O1 C:2FG616 2.9 22.3 0.4
O3 C:GAF615 2.9 18.0 0.6
O C:HOH834 2.9 23.7 1.0
O2 C:GOL608 3.1 30.8 0.5
OG1 C:THR187 3.1 21.6 1.0
O C:HOH845 3.2 16.9 1.0
OD2 C:ASP191 3.3 17.1 1.0
O C:HOH750 3.5 30.0 1.0
O5 C:GAF615 3.5 19.1 0.6
O5 C:2FG616 3.6 17.3 0.4
C4 C:2FG616 3.7 14.8 0.4
C4 C:GAF615 3.8 16.0 0.6
CG C:ASP191 3.8 15.1 1.0
C2 C:GOL608 3.9 24.7 0.5
OD1 C:ASP191 4.0 14.1 1.0
CB C:THR187 4.0 19.8 1.0
C5 C:GAF615 4.1 16.4 0.6
C5 C:2FG616 4.1 15.2 0.4
OH C:TYR248 4.2 16.1 1.0
CA C:THR187 4.3 19.3 1.0
C1 C:GOL608 4.3 21.2 0.5
O4 C:GAF615 4.3 15.5 0.6
O4 C:2FG616 4.3 14.7 0.4
N C:GLY188 4.4 18.2 1.0
O C:HOH710 4.5 20.1 1.0
CZ C:TYR248 4.6 15.9 1.0
O C:GLY188 4.7 19.1 1.0
CE1 C:TYR248 4.8 18.6 1.0
C C:THR187 4.9 17.8 1.0
CB C:ASP191 4.9 15.8 1.0
O C:HOH701 4.9 23.1 0.5
O C:SER186 5.0 21.9 1.0

Fluorine binding site 6 out of 8 in 6teq

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Fluorine binding site 6 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F616

b:17.0
occ:0.40
 F2 C:2FG616 0.0 17.0 0.4
F2 C:GAF615 0.0 20.9 0.6
C2 C:2FG616 1.4 17.2 0.4
C2 C:GAF615 1.4 19.0 0.6
O C:HOH711 2.3 14.4 1.0
C1 C:GAF615 2.3 16.8 0.6
C1 C:2FG616 2.3 16.6 0.4
C3 C:2FG616 2.4 16.1 0.4
C3 C:GAF615 2.4 17.7 0.6
O1 C:GAF615 2.6 20.6 0.6
O1 C:2FG616 2.8 22.3 0.4
O3 C:2FG616 2.9 14.6 0.4
O3 C:GAF615 2.9 18.0 0.6
O C:HOH834 2.9 23.7 1.0
O2 C:GOL608 3.1 30.8 0.5
OG1 C:THR187 3.2 21.6 1.0
O C:HOH845 3.2 16.9 1.0
OD2 C:ASP191 3.2 17.1 1.0
O C:HOH750 3.4 30.0 1.0
O5 C:GAF615 3.5 19.1 0.6
O5 C:2FG616 3.5 17.3 0.4
C4 C:2FG616 3.7 14.8 0.4
C4 C:GAF615 3.7 16.0 0.6
CG C:ASP191 3.8 15.1 1.0
C2 C:GOL608 4.0 24.7 0.5
OD1 C:ASP191 4.0 14.1 1.0
C5 C:GAF615 4.1 16.4 0.6
C5 C:2FG616 4.1 15.2 0.4
CB C:THR187 4.1 19.8 1.0
OH C:TYR248 4.2 16.1 1.0
C1 C:GOL608 4.3 21.2 0.5
CA C:THR187 4.3 19.3 1.0
O4 C:GAF615 4.3 15.5 0.6
O4 C:2FG616 4.3 14.7 0.4
N C:GLY188 4.4 18.2 1.0
O C:HOH710 4.5 20.1 1.0
CZ C:TYR248 4.6 15.9 1.0
O C:GLY188 4.8 19.1 1.0
CE1 C:TYR248 4.8 18.6 1.0
C C:THR187 4.9 17.8 1.0
CB C:ASP191 4.9 15.8 1.0
O C:HOH701 4.9 23.1 0.5
O1 C:GOL608 5.0 26.5 0.5
O C:HOH853 5.0 22.8 1.0

Fluorine binding site 7 out of 8 in 6teq

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Fluorine binding site 7 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F705

b:24.5
occ:0.60
 F2 D:2FG705 0.0 24.5 0.6
F2 D:GAF706 0.0 20.6 0.4
C2 D:GAF706 1.3 18.0 0.4
C2 D:2FG705 1.3 24.0 0.6
C1 D:2FG705 2.3 26.9 0.6
C1 D:GAF706 2.3 18.4 0.4
C3 D:GAF706 2.4 17.5 0.4
O D:HOH805 2.4 19.0 1.0
C3 D:2FG705 2.4 22.1 0.6
O1 D:2FG705 2.6 31.9 0.6
O1 D:GAF706 2.8 17.4 0.4
O3 D:GAF706 2.9 16.2 0.4
O3 D:2FG705 2.9 20.5 0.6
O D:HOH967 2.9 30.0 1.0
O D:HOH883 3.0 30.2 0.6
OG1 D:THR187 3.1 24.9 1.0
OD2 D:ASP191 3.2 21.2 1.0
O D:HOH909 3.4 18.3 1.0
O5 D:GAF706 3.5 16.8 0.4
O D:HOH871 3.5 22.5 0.5
O5 D:2FG705 3.6 25.2 0.6
C4 D:GAF706 3.7 16.0 0.4
C4 D:2FG705 3.8 19.5 0.6
CG D:ASP191 3.8 17.9 1.0
CB D:THR187 4.0 24.2 1.0
OD1 D:ASP191 4.0 16.7 1.0
C5 D:GAF706 4.1 17.4 0.4
C5 D:2FG705 4.1 22.2 0.6
OH D:TYR248 4.2 20.7 1.0
CA D:THR187 4.3 19.7 1.0
O4 D:GAF706 4.3 17.4 0.4
O4 D:2FG705 4.4 19.8 0.6
O D:HOH803 4.4 29.2 1.0
N D:GLY188 4.4 20.8 1.0
CZ D:TYR248 4.5 20.4 1.0
CE1 D:TYR248 4.7 21.2 1.0
C D:THR187 4.9 21.1 1.0
CB D:ASP191 4.9 16.9 1.0
O D:HOH891 5.0 29.6 1.0
O D:SER186 5.0 28.1 1.0

Fluorine binding site 8 out of 8 in 6teq

Go back to Fluorine Binding Sites List in 6teq
Fluorine binding site 8 out of 8 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with 2-Deoxy-2-Fluoro-Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F706

b:20.6
occ:0.40
 F2 D:GAF706 0.0 20.6 0.4
F2 D:2FG705 0.0 24.5 0.6
C2 D:GAF706 1.3 18.0 0.4
C2 D:2FG705 1.4 24.0 0.6
C1 D:2FG705 2.3 26.9 0.6
C1 D:GAF706 2.3 18.4 0.4
O D:HOH805 2.4 19.0 1.0
C3 D:GAF706 2.4 17.5 0.4
C3 D:2FG705 2.5 22.1 0.6
O1 D:2FG705 2.7 31.9 0.6
O1 D:GAF706 2.8 17.4 0.4
O3 D:GAF706 2.9 16.2 0.4
O3 D:2FG705 2.9 20.5 0.6
O D:HOH967 2.9 30.0 1.0
O D:HOH883 2.9 30.2 0.6
OG1 D:THR187 3.1 24.9 1.0
OD2 D:ASP191 3.2 21.2 1.0
O D:HOH909 3.4 18.3 1.0
O D:HOH871 3.5 22.5 0.5
O5 D:GAF706 3.6 16.8 0.4
O5 D:2FG705 3.6 25.2 0.6
C4 D:GAF706 3.7 16.0 0.4
C4 D:2FG705 3.8 19.5 0.6
CG D:ASP191 3.8 17.9 1.0
CB D:THR187 4.0 24.2 1.0
OD1 D:ASP191 4.1 16.7 1.0
C5 D:GAF706 4.1 17.4 0.4
C5 D:2FG705 4.1 22.2 0.6
OH D:TYR248 4.2 20.7 1.0
CA D:THR187 4.3 19.7 1.0
O4 D:GAF706 4.4 17.4 0.4
O4 D:2FG705 4.4 19.8 0.6
O D:HOH803 4.4 29.2 1.0
N D:GLY188 4.4 20.8 1.0
CZ D:TYR248 4.5 20.4 1.0
CE1 D:TYR248 4.7 21.2 1.0
C D:THR187 4.9 21.1 1.0
CB D:ASP191 4.9 16.9 1.0
O D:SER186 4.9 28.1 1.0
O D:HOH891 5.0 29.6 1.0

Reference:

T.Keenan, F.Parmeggiani, C.Q.Fontenelle, J.Malassis, J.Vendeville, W.A.Offen, P.Both, K.Huang, A.Marchesi, A.Heyam, C.Young, S.Charnock, G.J.Davies, B.Linclau, S.L.Flitsch, M.A.Fascione. Substrate Promiscuity of Wild-Type Sugar Kinases: Chemo-Enzymatic Synthesis of Multi-Fluorinated Monosaccharide-1-Phosphates. To Be Published.
Page generated: Tue Jul 15 15:55:21 2025

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