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Fluorine in PDB 5oly: 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form

Enzymatic activity of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form

All present enzymatic activity of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form:
5.4.2.6;

Protein crystallography data

The structure of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form, PDB code: 5oly was solved by M.W.Bowler, J.Von Velsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.47 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.737, 36.714, 107.853, 90.00, 105.27, 90.00
R / Rfree (%) 20.4 / 25.5

Other elements in 5oly:

The structure of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form (pdb code 5oly). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form, PDB code: 5oly:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 5oly

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Fluorine binding site 1 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F24

b:18.8
occ:1.00
F A:FTR24 0.0 18.8 1.0
CZ3 A:FTR24 1.4 17.1 1.0
CH2 A:FTR24 2.3 12.6 1.0
CE3 A:FTR24 2.4 15.3 1.0
CD1 A:LEU53 3.4 14.1 1.0
CB A:LEU53 3.5 19.3 1.0
CZ2 A:FTR24 3.6 17.0 1.0
CD1 A:LEU27 3.6 18.9 1.0
CD2 A:FTR24 3.7 14.9 1.0
CG A:LEU53 3.9 11.9 1.0
CB A:LYS76 3.9 16.1 1.0
CG A:LEU27 3.9 16.1 1.0
CA A:LEU53 4.0 14.4 1.0
CE2 A:FTR24 4.1 12.4 1.0
O A:LEU72 4.2 19.4 1.0
CG A:LYS76 4.3 12.9 1.0
CD2 A:LEU53 4.3 11.9 1.0
CA A:ALA73 4.5 18.3 1.0
N A:LEU53 4.5 19.5 1.0
C A:LEU72 4.5 11.1 1.0
N A:ALA73 4.6 18.5 1.0
CB A:LEU27 4.7 16.4 1.0
CD1 A:ILE56 4.9 5.6 1.0
CG A:FTR24 4.9 16.3 1.0
CD A:LYS76 5.0 13.0 1.0

Fluorine binding site 2 out of 10 in 5oly

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Fluorine binding site 2 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F216

b:29.3
occ:1.00
F A:FTR216 0.0 29.3 1.0
CZ3 A:FTR216 1.4 28.2 1.0
CE3 A:FTR216 2.4 22.8 1.0
CH2 A:FTR216 2.4 24.4 1.0
CD2 A:LEU217 2.9 29.8 1.0
CD2 A:FTR216 3.6 27.3 1.0
CZ2 A:FTR216 3.7 22.5 1.0
CE A:MET1 3.8 27.6 1.0
CG A:LEU217 3.8 33.5 1.0
CA A:MET1 3.9 22.2 1.0
N A:MET1 4.0 19.7 1.0
CE2 A:FTR216 4.1 20.6 1.0
SD A:MET1 4.3 17.8 1.0
CA A:LEU217 4.4 20.9 1.0
CB A:LEU217 4.6 17.3 1.0
CB A:MET1 4.6 12.5 1.0
N A:LEU217 4.6 18.4 1.0
CD A:LYS219 4.7 28.9 1.0
CG A:FTR216 4.8 15.9 1.0

Fluorine binding site 3 out of 10 in 5oly

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Fluorine binding site 3 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F24

b:12.5
occ:1.00
F G:FTR24 0.0 12.5 1.0
CZ3 G:FTR24 1.3 13.2 1.0
CH2 G:FTR24 2.3 11.1 1.0
CE3 G:FTR24 2.3 9.7 1.0
CD2 G:FTR24 3.5 8.6 1.0
CD1 G:LEU53 3.5 9.2 1.0
CZ2 G:FTR24 3.6 8.8 1.0
CD1 G:LEU27 3.6 19.4 1.0
CG G:LEU27 3.6 11.7 1.0
CB G:LEU53 3.7 12.9 1.0
CB G:LYS76 3.9 15.3 1.0
CA G:LEU53 4.0 12.5 1.0
CE2 G:FTR24 4.1 9.4 1.0
CG G:LEU53 4.1 10.6 1.0
CB G:LEU27 4.2 7.8 1.0
CG G:LYS76 4.2 13.2 1.0
N G:LEU53 4.5 10.4 1.0
O G:LEU72 4.5 24.8 1.0
CD2 G:LEU53 4.5 12.6 1.0
CA G:ALA73 4.8 9.3 1.0
CD1 G:ILE56 4.8 6.6 1.0
CG G:FTR24 4.8 6.9 1.0
CD G:LYS76 4.9 11.5 1.0
C G:LEU72 4.9 20.7 1.0
CD2 G:LEU27 4.9 25.1 1.0

Fluorine binding site 4 out of 10 in 5oly

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Fluorine binding site 4 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F216

b:25.9
occ:1.00
F G:FTR216 0.0 25.9 1.0
CZ3 G:FTR216 1.3 21.2 1.0
CH2 G:FTR216 2.3 22.9 1.0
CE3 G:FTR216 2.3 18.4 1.0
O G:SER165 3.1 14.4 1.0
CB G:LEU184 3.5 10.4 1.0
CZ2 G:FTR216 3.5 19.9 1.0
CD2 G:FTR216 3.5 17.6 1.0
O G:SER163 3.5 16.9 1.0
C G:SER165 3.8 12.3 1.0
N G:SER165 3.9 12.0 1.0
CD2 G:LEU184 4.0 16.6 1.0
CE2 G:FTR216 4.1 14.8 1.0
N G:LEU184 4.3 10.0 1.0
C G:GLU164 4.3 10.9 1.0
CG G:LEU184 4.4 14.9 1.0
CA G:SER165 4.4 10.0 1.0
CG1 G:ILE166 4.4 6.0 1.0
CB G:PHE2 4.4 13.0 1.0
C G:SER163 4.4 13.4 1.0
CA G:LEU184 4.5 14.1 1.0
N G:ILE166 4.6 16.8 1.0
CA G:GLU164 4.6 11.0 1.0
NE2 G:GLN220 4.7 24.4 1.0
CG G:FTR216 4.9 14.6 1.0
O G:GLU164 4.9 13.4 1.0
N G:GLU164 5.0 15.9 1.0
CA G:ILE166 5.0 11.8 1.0

Fluorine binding site 5 out of 10 in 5oly

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Fluorine binding site 5 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:13.8
occ:1.00
F1 A:MGF301 0.0 13.8 1.0
MG A:MGF301 1.7 10.9 1.0
O1 A:G6P303 2.3 7.6 1.0
NZ A:LYS145 2.8 8.5 1.0
OD1 A:ASP8 2.9 10.9 1.0
N A:ALA115 2.9 13.2 1.0
F2 A:MGF301 3.3 7.7 1.0
F3 A:MGF301 3.4 14.6 1.0
C1 A:G6P303 3.5 16.1 1.0
CB A:ALA115 3.5 14.2 1.0
CE A:LYS145 3.6 13.3 1.0
CA A:ALA115 3.8 13.8 1.0
O2 A:G6P303 3.8 10.1 1.0
O5 A:G6P303 3.8 10.3 1.0
CA A:SER114 3.8 11.8 1.0
C A:SER114 3.8 9.4 1.0
CD A:LYS145 4.0 11.3 1.0
CA A:GLY46 4.0 10.8 1.0
CG A:ASP8 4.0 10.7 1.0
O A:GLY46 4.1 9.0 1.0
C2 A:G6P303 4.2 7.0 1.0
OG A:SER114 4.2 14.3 1.0
N A:SER116 4.4 9.0 1.0
O A:ALA113 4.4 10.3 1.0
C A:GLY46 4.5 8.7 1.0
C A:ALA115 4.5 10.3 1.0
OE2 A:GLU169 4.6 12.2 1.0
MG A:MG302 4.6 9.2 1.0
CB A:SER114 4.6 5.2 1.0
OD2 A:ASP8 4.6 10.6 1.0
C5 A:G6P303 4.9 8.4 1.0
N A:GLY46 4.9 10.4 1.0
N A:SER114 5.0 11.8 1.0

Fluorine binding site 6 out of 10 in 5oly

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Fluorine binding site 6 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:7.7
occ:1.00
F2 A:MGF301 0.0 7.7 1.0
MG A:MGF301 1.9 10.9 1.0
OG A:SER114 2.7 14.3 1.0
N A:ASP10 2.7 9.7 1.0
OD1 A:ASP8 2.8 10.9 1.0
O1 A:G6P303 2.8 7.6 1.0
N A:LEU9 2.9 9.8 1.0
F3 A:MGF301 3.1 14.6 1.0
CB A:LEU9 3.1 7.2 1.0
CA A:LEU9 3.3 9.5 1.0
OD2 A:ASP10 3.3 9.3 1.0
F1 A:MGF301 3.3 13.8 1.0
CB A:SER114 3.3 5.2 1.0
C A:LEU9 3.4 9.4 1.0
CG A:ASP10 3.5 11.0 1.0
CG A:ASP8 3.6 10.7 1.0
CA A:SER114 3.8 11.8 1.0
CB A:ASP10 3.8 9.8 1.0
CA A:ASP10 3.8 15.0 1.0
OD2 A:ASP8 3.9 10.6 1.0
C1 A:G6P303 4.0 16.1 1.0
C A:ASP8 4.1 9.3 1.0
OD1 A:ASP10 4.2 12.7 1.0
MG A:MG302 4.4 9.2 1.0
CG A:LEU9 4.5 15.8 1.0
N A:ALA115 4.5 13.2 1.0
CA A:ASP8 4.5 6.0 1.0
C A:SER114 4.6 9.4 1.0
CB A:SER116 4.6 7.8 1.0
O A:ASP10 4.6 9.4 1.0
CB A:ASP8 4.6 9.9 1.0
O A:LEU9 4.7 10.2 1.0
C A:ASP10 4.7 10.1 1.0
O5 A:G6P303 4.8 10.3 1.0
N A:SER116 4.8 9.0 1.0
O2 A:G6P303 4.8 10.1 1.0
CD2 A:LEU9 4.9 13.6 1.0
C2 A:G6P303 4.9 7.0 1.0
N A:SER114 5.0 11.8 1.0

Fluorine binding site 7 out of 10 in 5oly

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Fluorine binding site 7 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:14.6
occ:1.00
F3 A:MGF301 0.0 14.6 1.0
MG A:MG302 1.8 9.2 1.0
MG A:MGF301 2.1 10.9 1.0
O2 A:G6P303 2.6 10.1 1.0
O1 A:G6P303 2.7 7.6 1.0
O A:ASP10 2.8 9.4 1.0
OD2 A:ASP8 2.9 10.6 1.0
F2 A:MGF301 3.1 7.7 1.0
CB A:ASP10 3.1 9.8 1.0
OD1 A:ASP8 3.1 10.9 1.0
CG A:ASP8 3.4 10.7 1.0
F1 A:MGF301 3.4 13.8 1.0
N A:ASP10 3.5 9.7 1.0
C2 A:G6P303 3.5 7.0 1.0
CA A:ASP10 3.5 15.0 1.0
C A:ASP10 3.6 10.1 1.0
C1 A:G6P303 3.6 16.1 1.0
OD2 A:ASP10 3.7 9.3 1.0
OD1 A:ASP170 3.8 11.0 1.0
CG A:ASP10 3.9 11.0 1.0
O A:HOH490 4.3 9.7 1.0
C A:LEU9 4.5 9.4 1.0
N A:GLY46 4.5 10.4 1.0
CA A:GLY46 4.6 10.8 1.0
N A:LEU9 4.7 9.8 1.0
CG A:ASP170 4.8 11.4 1.0
C3 A:G6P303 4.8 15.4 1.0
N A:GLY11 4.8 9.2 1.0
OD2 A:ASP170 4.9 9.1 1.0
O5 A:G6P303 4.9 10.3 1.0
CB A:ASP8 4.9 9.9 1.0

Fluorine binding site 8 out of 10 in 5oly

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Fluorine binding site 8 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F304

b:12.1
occ:1.00
F1 G:MGF304 0.0 12.1 1.0
MG G:MGF304 1.8 7.9 1.0
O1 G:G6P303 2.4 5.3 1.0
N G:ALA115 2.6 13.2 1.0
OD1 G:ASP8 2.8 7.3 1.0
NZ G:LYS145 3.0 12.3 1.0
F2 G:MGF304 3.2 11.2 1.0
F3 G:MGF304 3.3 11.2 1.0
CB G:ALA115 3.3 24.5 1.0
CA G:ALA115 3.5 14.2 1.0
C1 G:G6P303 3.6 8.0 1.0
C G:SER114 3.6 15.3 1.0
CA G:SER114 3.6 9.2 1.0
CE G:LYS145 3.8 18.2 1.0
O5 G:G6P303 3.8 15.1 1.0
O2 G:G6P303 3.9 10.0 1.0
CG G:ASP8 4.0 7.4 1.0
OG G:SER114 4.1 10.0 1.0
CA G:GLY46 4.1 10.6 1.0
O G:GLY46 4.1 14.4 1.0
CD G:LYS145 4.2 8.3 1.0
N G:SER116 4.3 7.6 1.0
C2 G:G6P303 4.3 12.2 1.0
C G:ALA115 4.3 8.0 1.0
O G:ALA113 4.4 10.9 1.0
CB G:SER114 4.4 6.6 1.0
C G:GLY46 4.5 11.3 1.0
OD2 G:ASP8 4.6 8.7 1.0
OE2 G:GLU169 4.7 10.8 1.0
O G:SER114 4.7 12.2 1.0
N G:SER114 4.8 13.1 1.0
MG G:MG301 4.8 8.2 1.0
OD2 G:ASP10 4.9 10.9 1.0
C5 G:G6P303 5.0 9.4 1.0
N G:GLY46 5.0 11.2 1.0

Fluorine binding site 9 out of 10 in 5oly

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Fluorine binding site 9 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F304

b:11.2
occ:1.00
F2 G:MGF304 0.0 11.2 1.0
MG G:MGF304 1.8 7.9 1.0
N G:ASP10 2.7 5.7 1.0
OG G:SER114 2.7 10.0 1.0
O1 G:G6P303 2.8 5.3 1.0
OD1 G:ASP8 2.8 7.3 1.0
N G:LEU9 3.0 7.0 1.0
F3 G:MGF304 3.0 11.2 1.0
OD2 G:ASP10 3.1 10.9 1.0
F1 G:MGF304 3.2 12.1 1.0
CB G:LEU9 3.3 5.2 1.0
CB G:SER114 3.4 6.6 1.0
CA G:LEU9 3.4 6.4 1.0
CG G:ASP10 3.4 6.7 1.0
C G:LEU9 3.4 5.6 1.0
CG G:ASP8 3.5 7.4 1.0
CB G:ASP10 3.6 11.4 1.0
CA G:ASP10 3.7 6.4 1.0
CA G:SER114 3.7 9.2 1.0
OD2 G:ASP8 3.9 8.7 1.0
C1 G:G6P303 4.0 8.0 1.0
C G:ASP8 4.1 5.3 1.0
OD1 G:ASP10 4.2 4.8 1.0
N G:ALA115 4.3 13.2 1.0
MG G:MG301 4.4 8.2 1.0
O G:ASP10 4.4 10.0 1.0
C G:SER114 4.5 15.3 1.0
CA G:ASP8 4.5 7.2 1.0
C G:ASP10 4.5 9.6 1.0
O G:LEU9 4.6 6.2 1.0
CB G:ASP8 4.6 9.9 1.0
CG G:LEU9 4.6 5.7 1.0
O2 G:G6P303 4.7 10.0 1.0
CB G:SER116 4.7 4.5 1.0
N G:SER116 4.8 7.6 1.0
O5 G:G6P303 4.8 15.1 1.0
CD2 G:LEU9 4.9 6.3 1.0
C2 G:G6P303 4.9 12.2 1.0
N G:SER114 4.9 13.1 1.0

Fluorine binding site 10 out of 10 in 5oly

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Fluorine binding site 10 out of 10 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F304

b:11.2
occ:1.00
F3 G:MGF304 0.0 11.2 1.0
MG G:MG301 1.9 8.2 1.0
MG G:MGF304 1.9 7.9 1.0
O2 G:G6P303 2.5 10.0 1.0
OD2 G:ASP8 2.7 8.7 1.0
OD1 G:ASP8 2.9 7.3 1.0
O G:ASP10 2.9 10.0 1.0
O1 G:G6P303 2.9 5.3 1.0
F2 G:MGF304 3.0 11.2 1.0
CG G:ASP8 3.1 7.4 1.0
F1 G:MGF304 3.3 12.1 1.0
CB G:ASP10 3.3 11.4 1.0
C2 G:G6P303 3.6 12.2 1.0
N G:ASP10 3.7 5.7 1.0
C G:ASP10 3.7 9.6 1.0
C1 G:G6P303 3.7 8.0 1.0
CA G:ASP10 3.8 6.4 1.0
OD1 G:ASP170 3.9 6.7 1.0
OD2 G:ASP10 4.0 10.9 1.0
CG G:ASP10 4.1 6.7 1.0
N G:GLY46 4.2 11.2 1.0
CA G:GLY46 4.2 10.6 1.0
O G:HOH538 4.4 10.4 1.0
CB G:ASP8 4.7 9.9 1.0
C G:LEU9 4.7 5.6 1.0
N G:LEU9 4.8 7.0 1.0
CG G:ASP170 4.9 9.1 1.0
C3 G:G6P303 4.9 7.9 1.0
OE2 G:GLU169 4.9 10.8 1.0
O5 G:G6P303 5.0 15.1 1.0
OD2 G:ASP170 5.0 8.3 1.0
NZ G:LYS145 5.0 12.3 1.0

Reference:

A.Ampaw, M.Carroll, J.Von Velsen, D.Bhattasali, A.Cohen, M.W.Bowler, D.L.Jakeman. Observing Enzyme Ternary Transition State Analogue Complexes BY19F uc(Nmr) Spectroscopy. Chem Sci V. 8 8427 2017.
ISSN: ISSN 2041-6520
PubMed: 29619190
DOI: 10.1039/C7SC04204C
Page generated: Thu Aug 1 12:31:17 2024

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