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Iron in PDB 3l75: Cytochrome BC1 Complex From Chicken with Fenamidone Bound

Enzymatic activity of Cytochrome BC1 Complex From Chicken with Fenamidone Bound

All present enzymatic activity of Cytochrome BC1 Complex From Chicken with Fenamidone Bound:
1.10.2.2;

Protein crystallography data

The structure of Cytochrome BC1 Complex From Chicken with Fenamidone Bound, PDB code: 3l75 was solved by L.Huang, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.78 / 2.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 172.285, 182.141, 241.198, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 27.5

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound (pdb code 3l75). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound, PDB code: 3l75:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3l75

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Iron binding site 1 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:29.7
occ:1.00
FE C:HEM501 0.0 29.7 1.0
NB C:HEM501 1.9 30.0 1.0
NC C:HEM501 1.9 31.0 1.0
NA C:HEM501 2.0 30.4 1.0
ND C:HEM501 2.0 30.4 1.0
NE2 C:HIS183 2.0 30.4 1.0
NE2 C:HIS84 2.0 31.9 1.0
CE1 C:HIS183 2.8 34.0 1.0
CE1 C:HIS84 2.9 33.1 1.0
C4B C:HEM501 2.9 31.4 1.0
C1C C:HEM501 3.0 32.0 1.0
C4C C:HEM501 3.0 31.8 1.0
C4A C:HEM501 3.0 29.6 1.0
C1B C:HEM501 3.0 30.1 1.0
C1A C:HEM501 3.0 30.7 1.0
C1D C:HEM501 3.0 31.5 1.0
C4D C:HEM501 3.0 30.9 1.0
CD2 C:HIS84 3.1 32.2 1.0
CD2 C:HIS183 3.1 30.6 1.0
CHC C:HEM501 3.3 32.9 1.0
CHB C:HEM501 3.4 30.3 1.0
CHD C:HEM501 3.4 32.1 1.0
CHA C:HEM501 3.4 30.0 1.0
ND1 C:HIS183 4.0 32.6 1.0
ND1 C:HIS84 4.1 32.4 1.0
CG C:HIS84 4.2 32.6 1.0
CG C:HIS183 4.2 30.0 1.0
C3B C:HEM501 4.2 29.7 1.0
C2C C:HEM501 4.2 32.3 1.0
C2A C:HEM501 4.2 30.3 1.0
C3C C:HEM501 4.2 33.5 1.0
C3A C:HEM501 4.3 28.5 1.0
C2B C:HEM501 4.3 28.9 1.0
C2D C:HEM501 4.3 31.1 1.0
C3D C:HEM501 4.3 32.0 1.0
NE2 C:GLN45 4.9 37.3 1.0
CA C:GLY49 5.0 27.8 1.0
CA C:GLY131 5.0 30.8 1.0

Iron binding site 2 out of 10 in 3l75

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Iron binding site 2 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:25.8
occ:1.00
FE C:HEM502 0.0 25.8 1.0
NB C:HEM502 1.9 25.0 1.0
NA C:HEM502 1.9 26.5 1.0
ND C:HEM502 1.9 25.2 1.0
NC C:HEM502 2.0 26.1 1.0
NE2 C:HIS197 2.0 26.6 1.0
NE2 C:HIS98 2.0 27.3 1.0
C4B C:HEM502 2.9 27.6 1.0
CD2 C:HIS197 2.9 28.2 1.0
C1B C:HEM502 3.0 26.1 1.0
C1D C:HEM502 3.0 26.4 1.0
C1A C:HEM502 3.0 25.8 1.0
C4A C:HEM502 3.0 28.3 1.0
CE1 C:HIS98 3.0 25.6 1.0
C4D C:HEM502 3.0 27.0 1.0
CD2 C:HIS98 3.0 26.2 1.0
C4C C:HEM502 3.0 23.8 1.0
C1C C:HEM502 3.0 26.1 1.0
CE1 C:HIS197 3.1 27.4 1.0
CHC C:HEM502 3.4 26.7 1.0
CHA C:HEM502 3.4 26.9 1.0
CHD C:HEM502 3.4 24.9 1.0
CHB C:HEM502 3.4 25.5 1.0
CG C:HIS197 4.1 29.6 1.0
ND1 C:HIS98 4.1 24.5 1.0
ND1 C:HIS197 4.1 28.0 1.0
CG C:HIS98 4.2 25.6 1.0
C3B C:HEM502 4.2 27.0 1.0
C2B C:HEM502 4.2 25.8 1.0
C2A C:HEM502 4.2 27.6 1.0
C3A C:HEM502 4.2 27.4 1.0
C2C C:HEM502 4.3 25.4 1.0
C2D C:HEM502 4.3 26.6 1.0
C3C C:HEM502 4.3 25.1 1.0
C3D C:HEM502 4.3 26.9 1.0

Iron binding site 3 out of 10 in 3l75

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Iron binding site 3 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:32.0
occ:1.00
FE D:HEC501 0.0 32.0 1.0
ND D:HEC501 1.9 26.6 1.0
NA D:HEC501 1.9 27.2 1.0
NC D:HEC501 2.0 30.2 1.0
NB D:HEC501 2.0 29.9 1.0
NE2 D:HIS41 2.0 31.6 1.0
SD D:MET160 2.2 35.3 1.0
C1D D:HEC501 2.9 29.0 1.0
CE1 D:HIS41 3.0 34.5 1.0
C4D D:HEC501 3.0 29.0 1.0
C4A D:HEC501 3.0 27.7 1.0
C1B D:HEC501 3.0 31.2 1.0
C4C D:HEC501 3.0 30.4 1.0
C1A D:HEC501 3.0 28.5 1.0
CD2 D:HIS41 3.0 33.9 1.0
C1C D:HEC501 3.0 31.8 1.0
C4B D:HEC501 3.0 31.9 1.0
CHD D:HEC501 3.3 30.4 1.0
CHA D:HEC501 3.4 27.7 1.0
CHB D:HEC501 3.4 29.6 1.0
CE D:MET160 3.4 25.8 1.0
CHC D:HEC501 3.4 31.6 1.0
CG D:MET160 3.6 30.1 1.0
ND1 D:HIS41 4.1 36.0 1.0
CG D:HIS41 4.1 35.3 1.0
C3A D:HEC501 4.2 27.1 1.0
C2B D:HEC501 4.2 32.9 1.0
C2D D:HEC501 4.2 28.8 1.0
C2A D:HEC501 4.2 27.6 1.0
CB D:MET160 4.3 32.8 1.0
C3B D:HEC501 4.3 32.5 1.0
C3C D:HEC501 4.3 32.2 1.0
C2C D:HEC501 4.3 31.9 1.0
C3D D:HEC501 4.3 29.9 1.0

Iron binding site 4 out of 10 in 3l75

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Iron binding site 4 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:86.1
occ:0.91
FE1 E:FES501 0.0 86.1 0.9
S2 E:FES501 2.2 85.4 0.9
S1 E:FES501 2.2 84.5 0.9
SG E:CYS139 2.2 82.0 0.9
SG E:CYS158 2.3 84.7 0.9
FE2 E:FES501 2.7 83.4 0.9
CB E:CYS139 3.0 81.1 0.9
CB E:CYS158 3.1 87.4 0.9
CB E:HIS141 3.9 76.7 0.9
OG E:SER163 4.1 89.6 0.9
CB E:SER163 4.3 93.3 0.9
CB E:CYS144 4.3 75.2 0.9
CB E:CYS160 4.3 84.7 0.9
ND1 E:HIS141 4.4 79.7 0.9
CA E:CYS139 4.4 79.9 0.9
CA E:CYS158 4.5 87.8 0.9
N E:CYS144 4.6 73.6 0.9
ND1 E:HIS161 4.6 86.2 0.9
N E:HIS161 4.6 89.8 0.9
CG E:HIS141 4.6 78.0 0.9
N E:LEU142 4.7 72.2 0.9
SG E:CYS144 4.8 77.4 0.9
O E:CYS158 4.8 87.0 0.9
C E:CYS158 4.8 87.2 0.9
N E:HIS141 4.9 76.0 0.9
O E:CYS144 4.9 74.8 0.9
CA E:CYS144 4.9 74.7 0.9
CA E:HIS141 4.9 75.2 0.9
N E:CYS160 5.0 87.2 0.9
C E:CYS139 5.0 78.5 0.9
N E:SER163 5.0 95.4 0.9

Iron binding site 5 out of 10 in 3l75

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Iron binding site 5 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:83.4
occ:0.91
FE2 E:FES501 0.0 83.4 0.9
ND1 E:HIS161 2.1 86.2 0.9
ND1 E:HIS141 2.1 79.7 0.9
S1 E:FES501 2.2 84.5 0.9
S2 E:FES501 2.2 85.4 0.9
FE1 E:FES501 2.7 86.1 0.9
CG E:HIS161 3.1 87.8 0.9
CG E:HIS141 3.1 78.0 0.9
CE1 E:HIS161 3.2 85.7 0.9
CE1 E:HIS141 3.2 78.6 0.9
CB E:HIS161 3.3 89.5 0.9
CB E:HIS141 3.3 76.7 0.9
N E:HIS161 3.7 89.8 0.9
CB E:CYS160 4.0 84.7 0.9
N E:LEU142 4.0 72.2 0.9
CA E:HIS161 4.1 90.9 0.9
CD2 E:HIS161 4.2 87.2 0.9
CD2 E:HIS141 4.2 77.7 0.9
NE2 E:HIS161 4.2 85.8 0.9
NE2 E:HIS141 4.3 78.0 0.9
SG E:CYS139 4.3 82.0 0.9
CB E:LEU142 4.4 70.0 0.9
C E:CYS160 4.5 88.2 0.9
CG E:LEU142 4.5 69.2 0.9
SG E:CYS158 4.6 84.7 0.9
CA E:HIS141 4.7 75.2 0.9
OG E:SER163 4.7 89.6 0.9
CA E:LEU142 4.8 71.4 0.9
CA E:CYS160 4.8 86.8 0.9
C E:HIS141 4.8 73.8 0.9
C E:HIS161 4.8 92.3 0.9
CD1 E:LEU142 4.9 69.3 0.9

Iron binding site 6 out of 10 in 3l75

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Iron binding site 6 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe501

b:40.2
occ:1.00
FE P:HEM501 0.0 40.2 1.0
NA P:HEM501 1.9 43.9 1.0
NB P:HEM501 1.9 41.9 1.0
NC P:HEM501 2.0 42.3 1.0
ND P:HEM501 2.0 44.7 1.0
NE2 P:HIS84 2.0 39.6 1.0
NE2 P:HIS183 2.0 40.2 1.0
CE1 P:HIS183 2.9 40.7 1.0
CE1 P:HIS84 2.9 39.6 1.0
C4B P:HEM501 3.0 41.4 1.0
C1C P:HEM501 3.0 42.9 1.0
C1A P:HEM501 3.0 46.0 1.0
C4C P:HEM501 3.0 42.1 1.0
C4A P:HEM501 3.0 44.6 1.0
C1D P:HEM501 3.0 44.2 1.0
C1B P:HEM501 3.0 42.6 1.0
C4D P:HEM501 3.0 46.2 1.0
CD2 P:HIS84 3.0 40.8 1.0
CD2 P:HIS183 3.1 37.5 1.0
CHC P:HEM501 3.3 42.2 1.0
CHD P:HEM501 3.4 43.4 1.0
CHB P:HEM501 3.4 42.5 1.0
CHA P:HEM501 3.4 45.8 1.0
ND1 P:HIS183 4.0 38.8 1.0
ND1 P:HIS84 4.1 39.4 1.0
CG P:HIS84 4.2 42.6 1.0
CG P:HIS183 4.2 37.0 1.0
C3B P:HEM501 4.2 41.9 1.0
C2A P:HEM501 4.2 46.7 1.0
C2C P:HEM501 4.2 42.5 1.0
C3C P:HEM501 4.2 42.8 1.0
C3A P:HEM501 4.2 44.7 1.0
C2D P:HEM501 4.3 44.8 1.0
C2B P:HEM501 4.3 42.9 1.0
C3D P:HEM501 4.3 46.8 1.0
NE2 P:GLN45 4.9 42.0 1.0
CA P:GLY49 4.9 37.9 1.0

Iron binding site 7 out of 10 in 3l75

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Iron binding site 7 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe502

b:42.2
occ:1.00
FE P:HEM502 0.0 42.2 1.0
NC P:HEM502 1.9 40.0 1.0
ND P:HEM502 1.9 41.7 1.0
NB P:HEM502 1.9 40.5 1.0
NA P:HEM502 2.0 39.6 1.0
NE2 P:HIS98 2.0 43.4 1.0
NE2 P:HIS197 2.0 41.3 1.0
C4C P:HEM502 3.0 40.5 1.0
C4B P:HEM502 3.0 40.7 1.0
C1C P:HEM502 3.0 40.5 1.0
C1D P:HEM502 3.0 42.1 1.0
CE1 P:HIS98 3.0 44.5 1.0
CE1 P:HIS197 3.0 41.3 1.0
C4D P:HEM502 3.0 43.9 1.0
CD2 P:HIS197 3.0 41.4 1.0
CD2 P:HIS98 3.0 44.0 1.0
C1B P:HEM502 3.0 39.6 1.0
C1A P:HEM502 3.0 39.9 1.0
C4A P:HEM502 3.0 39.0 1.0
CHC P:HEM502 3.3 40.6 1.0
CHD P:HEM502 3.3 40.7 1.0
CHA P:HEM502 3.4 41.8 1.0
CHB P:HEM502 3.4 38.0 1.0
ND1 P:HIS98 4.1 46.6 1.0
ND1 P:HIS197 4.1 40.6 1.0
CG P:HIS197 4.1 43.5 1.0
CG P:HIS98 4.1 46.3 1.0
C2C P:HEM502 4.2 39.4 1.0
C3C P:HEM502 4.2 40.2 1.0
C3B P:HEM502 4.2 41.3 1.0
C2D P:HEM502 4.2 43.4 1.0
C2B P:HEM502 4.3 40.7 1.0
C3D P:HEM502 4.3 45.9 1.0
C2A P:HEM502 4.3 40.9 1.0
C3A P:HEM502 4.3 39.8 1.0
O P:HOH383 4.9 33.1 1.0

Iron binding site 8 out of 10 in 3l75

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Iron binding site 8 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe501

b:60.2
occ:1.00
FE Q:HEC501 0.0 60.2 1.0
NC Q:HEC501 1.9 58.9 1.0
NB Q:HEC501 2.0 55.8 1.0
ND Q:HEC501 2.0 54.6 1.0
NE2 Q:HIS41 2.0 59.4 1.0
NA Q:HEC501 2.0 53.8 1.0
SD Q:MET160 2.2 62.2 1.0
C4C Q:HEC501 3.0 60.2 1.0
C1C Q:HEC501 3.0 59.5 1.0
CD2 Q:HIS41 3.0 61.0 1.0
C1D Q:HEC501 3.0 54.7 1.0
C4B Q:HEC501 3.0 56.3 1.0
CE1 Q:HIS41 3.0 60.7 1.0
C1B Q:HEC501 3.0 54.3 1.0
C4D Q:HEC501 3.0 53.1 1.0
C4A Q:HEC501 3.0 51.1 1.0
C1A Q:HEC501 3.1 51.7 1.0
CHD Q:HEC501 3.3 57.7 1.0
CHC Q:HEC501 3.3 57.2 1.0
CHB Q:HEC501 3.4 52.4 1.0
CHA Q:HEC501 3.4 52.9 1.0
CE Q:MET160 3.5 59.8 1.0
CG Q:MET160 3.6 62.5 1.0
ND1 Q:HIS41 4.1 61.3 1.0
CG Q:HIS41 4.1 62.2 1.0
C3C Q:HEC501 4.2 63.1 1.0
C2B Q:HEC501 4.2 55.1 1.0
C2D Q:HEC501 4.2 53.5 1.0
C2C Q:HEC501 4.2 61.5 1.0
C3B Q:HEC501 4.2 57.2 1.0
C3D Q:HEC501 4.3 53.9 1.0
C3A Q:HEC501 4.3 49.1 1.0
C2A Q:HEC501 4.3 49.6 1.0
CB Q:MET160 4.3 66.4 1.0

Iron binding site 9 out of 10 in 3l75

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Iron binding site 9 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.1
occ:0.88
FE1 R:FES501 0.0 0.1 0.9
S1 R:FES501 2.2 0.7 0.9
S2 R:FES501 2.2 0.7 0.9
SG R:CYS158 2.2 0.1 0.9
SG R:CYS139 2.3 0.1 0.9
FE2 R:FES501 2.7 0.9 0.9
CB R:CYS139 3.0 0.4 0.9
CB R:CYS158 3.1 0.9 0.9
CB R:HIS141 3.9 0.8 0.9
OG R:SER163 4.0 0.2 0.9
CB R:CYS144 4.1 96.8 0.9
CB R:SER163 4.2 0.3 0.9
CB R:CYS160 4.3 0.5 0.9
ND1 R:HIS141 4.4 0.7 0.9
CA R:CYS158 4.5 1.0 0.9
CA R:CYS139 4.5 0.0 0.9
N R:HIS161 4.5 0.6 0.9
ND1 R:HIS161 4.6 0.9 0.9
CG R:HIS141 4.6 0.9 0.9
N R:CYS144 4.7 97.3 0.9
SG R:CYS144 4.8 95.7 0.9
O R:CYS158 4.8 0.1 0.9
C R:CYS158 4.8 0.8 0.9
N R:LEU142 4.8 0.1 0.9
CA R:CYS144 4.9 97.2 0.9
N R:CYS160 4.9 0.6 0.9
N R:SER163 4.9 0.6 0.9

Iron binding site 10 out of 10 in 3l75

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Iron binding site 10 out of 10 in the Cytochrome BC1 Complex From Chicken with Fenamidone Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cytochrome BC1 Complex From Chicken with Fenamidone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.9
occ:0.88
FE2 R:FES501 0.0 0.9 0.9
ND1 R:HIS141 2.2 0.7 0.9
ND1 R:HIS161 2.2 0.9 0.9
S2 R:FES501 2.2 0.7 0.9
S1 R:FES501 2.2 0.7 0.9
FE1 R:FES501 2.7 0.1 0.9
CG R:HIS161 3.1 0.3 0.9
CG R:HIS141 3.1 0.9 0.9
CE1 R:HIS141 3.2 0.3 0.9
CE1 R:HIS161 3.2 0.5 0.9
CB R:HIS161 3.3 0.5 0.9
CB R:HIS141 3.3 0.8 0.9
N R:HIS161 3.7 0.6 0.9
CB R:CYS160 4.0 0.5 0.9
CA R:HIS161 4.1 0.8 0.9
N R:LEU142 4.1 0.1 0.9
CD2 R:HIS161 4.2 0.9 0.9
CD2 R:HIS141 4.3 1.0 0.9
NE2 R:HIS161 4.3 0.1 0.9
NE2 R:HIS141 4.3 0.1 0.9
SG R:CYS139 4.3 0.1 0.9
C R:CYS160 4.5 0.1 0.9
CB R:LEU142 4.5 96.8 0.9
SG R:CYS158 4.6 0.1 0.9
OG R:SER163 4.6 0.2 0.9
CG R:LEU142 4.7 95.5 0.9
CA R:HIS141 4.7 0.1 0.9
CD1 R:LEU142 4.8 95.5 0.9
C R:HIS161 4.8 0.9 0.9
CA R:CYS160 4.8 0.1 0.9
C R:HIS141 4.9 0.1 0.9
CA R:LEU142 4.9 98.3 0.9

Reference:

L.Huang, E.A.Berry. Famoxadone and Related Inhibitors Bind Like Methoxy Acrylate Inhibitors in the Qo Site of the BC1 Compl and Fix the Rieske Iron-Sulfur Protein in A Positio Close to But Distinct From That Seen with Stigmatellin and Other "Distal" Qo Inhibitors. To Be Published.
Page generated: Sun Aug 4 14:09:47 2024

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