Fluorine in PDB 8g4v: Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol, PDB code: 8g4v was solved by B.V.Plapp, R.Subramanian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.17, 51.59, 92.77, 92.02, 102.89, 110.04
R / Rfree (%) 13.5 / 16.1

Other elements in 8g4v:

The structure of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol (pdb code 8g4v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol, PDB code: 8g4v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 8g4v

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Fluorine binding site 1 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:17.0
occ:1.00
 F2 A:PFB404 0.0 17.0 1.0
C2 A:PFB404 1.3 14.5 1.0
C3 A:PFB404 2.3 14.9 1.0
C1 A:PFB404 2.4 14.5 1.0
F3 A:PFB404 2.7 17.9 1.0
C7N A:NAJ403 2.9 10.8 1.0
C7 A:PFB404 2.9 13.6 1.0
O7N A:NAJ403 3.0 11.3 1.0
C3N A:NAJ403 3.1 10.5 1.0
C2N A:NAJ403 3.5 10.2 1.0
N7N A:NAJ403 3.5 10.6 1.0
C4 A:PFB404 3.6 17.1 1.0
C6 A:PFB404 3.6 16.9 1.0
CG2 A:VAL294 3.7 14.8 1.0
CD1 A:ILE318 3.7 19.8 1.0
C4N A:NAJ403 3.7 12.3 1.0
O1 A:PFB404 3.9 12.8 1.0
C5 A:PFB404 4.0 16.5 1.0
CE1 A:PHE93 4.3 12.5 1.0
N1N A:NAJ403 4.3 10.2 1.0
CG2 A:ILE318 4.5 13.4 1.0
CZ A:PHE93 4.6 13.4 1.0
OG A:SER48 4.6 11.9 1.0
CD1 A:LEU116 4.7 21.1 0.3
F4 A:PFB404 4.7 21.7 1.0
F6 A:PFB404 4.7 17.2 1.0
C5N A:NAJ403 4.7 11.9 1.0
CD2 A:LEU116 4.8 22.1 0.7
C6N A:NAJ403 4.9 11.2 1.0
CD2 B:LEU309 5.0 18.3 1.0
CG1 A:ILE318 5.0 15.5 1.0

Fluorine binding site 2 out of 10 in 8g4v

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Fluorine binding site 2 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:17.9
occ:1.00
 F3 A:PFB404 0.0 17.9 1.0
C3 A:PFB404 1.3 14.9 1.0
C4 A:PFB404 2.3 17.1 1.0
C2 A:PFB404 2.4 14.5 1.0
F2 A:PFB404 2.7 17.0 1.0
F4 A:PFB404 2.7 21.7 1.0
CD2 A:LEU116 3.3 22.4 0.3
CG2 A:VAL294 3.5 14.8 1.0
CD1 A:ILE318 3.5 19.8 1.0
C5 A:PFB404 3.6 16.5 1.0
C1 A:PFB404 3.7 14.5 1.0
CD1 A:LEU116 3.7 21.1 0.3
CG A:LEU116 3.8 20.2 0.3
CD2 B:LEU309 3.8 18.3 1.0
CD2 A:LEU116 3.8 22.1 0.7
C6 A:PFB404 4.1 16.9 1.0
O A:HOH867 4.2 30.4 1.0
CG1 A:VAL294 4.4 19.8 1.0
CB A:VAL294 4.6 13.9 1.0
F5 A:PFB404 4.7 18.3 1.0
CG A:LEU116 4.8 19.4 0.7
CG1 A:ILE318 4.8 15.5 1.0
CG B:LEU309 4.9 15.1 1.0
C7 A:PFB404 5.0 13.6 1.0

Fluorine binding site 3 out of 10 in 8g4v

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Fluorine binding site 3 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:21.7
occ:1.00
 F4 A:PFB404 0.0 21.7 1.0
C4 A:PFB404 1.4 17.1 1.0
C5 A:PFB404 2.3 16.5 1.0
C3 A:PFB404 2.4 14.9 1.0
F3 A:PFB404 2.7 17.9 1.0
F5 A:PFB404 2.7 18.3 1.0
CD1 A:LEU57 3.2 12.4 0.3
CG A:LEU116 3.4 20.2 0.3
CD2 A:LEU116 3.5 22.4 0.3
C2 A:PFB404 3.6 14.5 1.0
O A:HOH867 3.6 30.4 1.0
C6 A:PFB404 3.6 16.9 1.0
CD2 A:LEU57 3.7 13.0 0.3
CD2 A:LEU57 3.7 14.4 0.7
CD1 A:LEU57 3.8 14.4 0.7
CD1 A:LEU116 3.9 21.1 0.3
CG A:LEU57 4.0 14.9 0.7
CG A:LEU57 4.1 11.9 0.3
C1 A:PFB404 4.2 14.5 1.0
CD2 A:LEU116 4.2 22.1 0.7
CG A:LEU116 4.3 19.4 0.7
CB A:LEU116 4.6 17.8 0.7
F2 A:PFB404 4.7 17.0 1.0
CG1 A:VAL294 4.7 19.8 1.0
F6 A:PFB404 4.7 17.2 1.0
CB A:LEU116 4.7 18.6 0.3
CG2 A:VAL294 4.8 14.8 1.0
CD2 A:LEU141 4.9 20.4 1.0
O A:LEU116 5.0 22.3 1.0

Fluorine binding site 4 out of 10 in 8g4v

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Fluorine binding site 4 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:18.3
occ:1.00
 F5 A:PFB404 0.0 18.3 1.0
C5 A:PFB404 1.4 16.5 1.0
C4 A:PFB404 2.3 17.1 1.0
C6 A:PFB404 2.4 16.9 1.0
F4 A:PFB404 2.7 21.7 1.0
F6 A:PFB404 2.7 17.2 1.0
CD2 A:LEU57 2.8 13.0 0.3
CZ A:PHE140 3.3 14.0 1.0
CD1 A:LEU57 3.3 14.4 0.7
CD1 A:LEU141 3.4 17.0 1.0
CD2 A:LEU57 3.5 14.4 0.7
C3 A:PFB404 3.6 14.9 1.0
C1 A:PFB404 3.7 14.5 1.0
CE1 A:PHE140 3.7 13.8 1.0
CD2 A:LEU141 3.8 20.4 1.0
CG A:LEU57 3.9 11.9 0.3
CG A:LEU141 4.0 15.8 1.0
CG A:LEU57 4.0 14.9 0.7
C2 A:PFB404 4.1 14.5 1.0
CD1 A:LEU57 4.1 12.4 0.3
CE2 A:PHE140 4.3 15.4 1.0
CB A:SER48 4.5 11.7 1.0
F3 A:PFB404 4.7 17.9 1.0
CD1 A:LEU116 4.9 21.1 0.3
CG A:LEU116 4.9 20.2 0.3
C7 A:PFB404 4.9 13.6 1.0
OG A:SER48 5.0 11.9 1.0
CD1 A:PHE140 5.0 12.4 1.0

Fluorine binding site 5 out of 10 in 8g4v

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Fluorine binding site 5 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:17.2
occ:1.00
 F6 A:PFB404 0.0 17.2 1.0
C6 A:PFB404 1.3 16.9 1.0
C5 A:PFB404 2.3 16.5 1.0
C1 A:PFB404 2.3 14.5 1.0
F5 A:PFB404 2.7 18.3 1.0
C7 A:PFB404 2.8 13.6 1.0
O1 A:PFB404 3.1 12.8 1.0
CB A:SER48 3.2 11.7 1.0
CD1 A:LEU141 3.3 17.0 1.0
NE2 A:HIS67 3.4 12.6 1.0
CE1 A:HIS67 3.4 11.3 1.0
CD2 A:HIS67 3.6 11.7 1.0
C2 A:PFB404 3.6 14.5 1.0
C4 A:PFB404 3.6 17.1 1.0
OG A:SER48 3.6 11.9 1.0
ND1 A:HIS67 3.7 11.7 1.0
CG A:HIS67 3.8 10.9 1.0
CZ A:PHE140 4.0 14.0 1.0
C3 A:PFB404 4.1 14.9 1.0
ZN A:ZN401 4.1 12.9 1.0
CE2 A:PHE140 4.2 15.4 1.0
CD2 A:LEU57 4.6 13.0 0.3
CA A:SER48 4.6 11.1 1.0
CG A:LEU141 4.6 15.8 1.0
F4 A:PFB404 4.7 21.7 1.0
F2 A:PFB404 4.7 17.0 1.0
CD1 A:LEU57 4.8 14.4 0.7
CB A:HIS67 4.8 11.1 1.0
C A:SER48 4.8 11.6 1.0
CD1 A:PHE93 4.9 11.6 1.0
CE1 A:PHE93 5.0 12.5 1.0

Fluorine binding site 6 out of 10 in 8g4v

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Fluorine binding site 6 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:19.9
occ:1.00
 F2 B:PFB404 0.0 19.9 1.0
C2 B:PFB404 1.3 17.3 1.0
C3 B:PFB404 2.2 18.4 1.0
C1 B:PFB404 2.4 17.5 1.0
F3 B:PFB404 2.6 20.8 1.0
C7N B:NAJ403 2.9 12.6 1.0
C7 B:PFB404 2.9 17.8 1.0
O7N B:NAJ403 3.0 13.1 1.0
C3N B:NAJ403 3.1 12.0 1.0
C2N B:NAJ403 3.5 12.2 1.0
C4 B:PFB404 3.5 19.8 1.0
N7N B:NAJ403 3.5 12.7 1.0
C6 B:PFB404 3.6 17.6 1.0
CG2 B:VAL294 3.7 15.3 1.0
CD1 B:ILE318 3.8 24.4 1.0
O1 B:PFB404 3.8 15.5 1.0
C4N B:NAJ403 3.8 14.7 1.0
C5 B:PFB404 4.1 20.3 1.0
CE1 B:PHE93 4.3 14.1 1.0
N1N B:NAJ403 4.4 12.4 1.0
CD1 B:LEU116 4.4 21.6 0.4
CG2 B:ILE318 4.5 16.2 1.0
CZ B:PHE93 4.5 14.6 1.0
F4 B:PFB404 4.6 24.3 1.0
OG B:SER48 4.6 13.9 1.0
F6 B:PFB404 4.7 19.6 1.0
CD2 B:LEU116 4.8 21.6 0.6
C5N B:NAJ403 4.8 13.8 1.0
CD2 A:LEU309 4.9 20.2 1.0
CG1 B:ILE318 5.0 18.4 1.0
C6N B:NAJ403 5.0 13.2 1.0

Fluorine binding site 7 out of 10 in 8g4v

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Fluorine binding site 7 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:20.8
occ:1.00
 F3 B:PFB404 0.0 20.8 1.0
C3 B:PFB404 1.3 18.4 1.0
C4 B:PFB404 2.4 19.8 1.0
C2 B:PFB404 2.4 17.3 1.0
F2 B:PFB404 2.6 19.9 1.0
F4 B:PFB404 2.7 24.3 1.0
CD1 B:LEU116 3.4 21.6 0.4
CG2 B:VAL294 3.5 15.3 1.0
CD1 B:ILE318 3.5 24.4 1.0
C5 B:PFB404 3.6 20.3 1.0
C1 B:PFB404 3.6 17.5 1.0
CD2 B:LEU116 3.6 21.6 0.4
CD2 A:LEU309 3.7 20.2 1.0
CD2 B:LEU116 3.9 21.6 0.6
CG B:LEU116 3.9 20.8 0.4
C6 B:PFB404 4.1 17.6 1.0
CG1 B:VAL294 4.3 19.6 1.0
CE A:MET306 4.4 33.2 0.3
CB B:VAL294 4.5 16.0 1.0
F5 B:PFB404 4.7 20.8 1.0
CG A:LEU309 4.8 16.1 1.0
CG1 B:ILE318 4.9 18.4 1.0
CG B:LEU116 4.9 19.4 0.6
C7 B:PFB404 4.9 17.8 1.0

Fluorine binding site 8 out of 10 in 8g4v

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Fluorine binding site 8 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:24.3
occ:1.00
 F4 B:PFB404 0.0 24.3 1.0
C4 B:PFB404 1.3 19.8 1.0
C5 B:PFB404 2.3 20.3 1.0
C3 B:PFB404 2.4 18.4 1.0
F5 B:PFB404 2.7 20.8 1.0
F3 B:PFB404 2.7 20.8 1.0
CD1 B:LEU57 3.4 18.4 0.4
CG B:LEU116 3.4 20.8 0.4
C6 B:PFB404 3.6 17.6 1.0
C2 B:PFB404 3.6 17.3 1.0
CD1 B:LEU116 3.6 21.6 0.4
CD2 B:LEU116 3.6 21.6 0.4
CD2 B:LEU57 3.6 19.1 0.4
CD1 B:LEU57 3.7 19.7 0.6
CD2 B:LEU57 3.8 20.5 0.6
CG B:LEU57 4.0 18.8 0.6
C1 B:PFB404 4.1 17.5 1.0
CG B:LEU57 4.1 19.4 0.4
CD2 B:LEU116 4.2 21.6 0.6
CG B:LEU116 4.3 19.4 0.6
CG1 B:VAL294 4.6 19.6 1.0
F2 B:PFB404 4.6 19.9 1.0
F6 B:PFB404 4.6 19.6 1.0
CG2 B:VAL294 4.8 15.3 1.0
CB B:LEU116 4.8 20.1 0.4
CB B:LEU116 4.8 19.9 0.6
O B:LEU116 4.8 20.7 0.4
CD2 B:LEU141 4.9 22.7 1.0

Fluorine binding site 9 out of 10 in 8g4v

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Fluorine binding site 9 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:20.8
occ:1.00
 F5 B:PFB404 0.0 20.8 1.0
C5 B:PFB404 1.4 20.3 1.0
C4 B:PFB404 2.3 19.8 1.0
C6 B:PFB404 2.4 17.6 1.0
F4 B:PFB404 2.7 24.3 1.0
F6 B:PFB404 2.7 19.6 1.0
CD2 B:LEU57 2.9 19.1 0.4
CZ B:PHE140 3.3 18.6 1.0
CD1 B:LEU141 3.4 18.6 1.0
CD1 B:LEU57 3.4 19.7 0.6
CD2 B:LEU57 3.6 20.5 0.6
C1 B:PFB404 3.6 17.5 1.0
C3 B:PFB404 3.7 18.4 1.0
CD2 B:LEU141 3.7 22.7 1.0
CE1 B:PHE140 3.8 16.7 1.0
CG B:LEU141 4.0 17.6 1.0
CG B:LEU57 4.0 19.4 0.4
CG B:LEU57 4.1 18.8 0.6
C2 B:PFB404 4.1 17.3 1.0
CE2 B:PHE140 4.3 18.2 1.0
CD1 B:LEU57 4.3 18.4 0.4
CB B:SER48 4.5 13.5 1.0
F3 B:PFB404 4.7 20.8 1.0
CD1 B:LEU116 4.7 21.6 0.4
CG B:LEU116 4.8 20.8 0.4
C7 B:PFB404 4.9 17.8 1.0

Fluorine binding site 10 out of 10 in 8g4v

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Fluorine binding site 10 out of 10 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:19.6
occ:1.00
 F6 B:PFB404 0.0 19.6 1.0
C6 B:PFB404 1.3 17.6 1.0
C5 B:PFB404 2.3 20.3 1.0
C1 B:PFB404 2.3 17.5 1.0
F5 B:PFB404 2.7 20.8 1.0
C7 B:PFB404 2.8 17.8 1.0
O1 B:PFB404 3.2 15.5 1.0
CD1 B:LEU141 3.2 18.6 1.0
CB B:SER48 3.3 13.5 1.0
NE2 B:HIS67 3.4 14.7 1.0
CE1 B:HIS67 3.5 13.4 1.0
C2 B:PFB404 3.5 17.3 1.0
C4 B:PFB404 3.5 19.8 1.0
CD2 B:HIS67 3.6 14.2 1.0
ND1 B:HIS67 3.7 14.4 1.0
OG B:SER48 3.7 13.9 1.0
CG B:HIS67 3.8 13.5 1.0
C3 B:PFB404 4.1 18.4 1.0
CZ B:PHE140 4.1 18.6 1.0
ZN B:ZN401 4.1 15.2 1.0
CE2 B:PHE140 4.2 18.2 1.0
CG B:LEU141 4.5 17.6 1.0
F4 B:PFB404 4.6 24.3 1.0
CA B:SER48 4.6 12.8 1.0
CD2 B:LEU57 4.7 19.1 0.4
F2 B:PFB404 4.7 19.9 1.0
CB B:HIS67 4.7 13.8 1.0
CD1 B:PHE93 4.8 13.5 1.0
CD1 B:LEU57 4.9 19.7 0.6
CE1 B:PHE93 4.9 14.1 1.0
C B:SER48 4.9 14.9 1.0

Reference:

B.V.Plapp, E.G.Kovaleva. Histidine-51 Facilitates Deprotonation of the Zinc-Bound Ligand During Catalysis By Horse Liver Alcohol Dehydrogenase To Be Published.
Page generated: Fri Aug 2 19:40:20 2024

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