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Iron in PDB 4nbb: Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase

Enzymatic activity of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase

All present enzymatic activity of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase:
1.14.12.22;

Protein crystallography data

The structure of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nbb was solved by Y.Ashikawa, Y.Usami, K.Inoue, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.61 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.424, 90.083, 105.324, 90.00, 104.26, 90.00
R / Rfree (%) 19.5 / 22.6

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iron atom in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (pdb code 4nbb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nbb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in 4nbb

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Iron binding site 1 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:32.2
occ:1.00
 O2 A:OXY503 1.9 45.0 1.0
OD1 A:ASP333 1.9 31.9 1.0
NE2 A:HIS183 2.0 29.8 1.0
NE2 A:HIS187 2.1 32.2 1.0
O1 A:OXY503 2.2 41.5 1.0
CG A:ASP333 2.6 30.7 1.0
OD2 A:ASP333 2.7 31.0 1.0
CD2 A:HIS183 2.9 25.2 1.0
CE1 A:HIS187 3.1 32.6 1.0
CD2 A:HIS187 3.1 32.7 1.0
CE1 A:HIS183 3.1 27.5 1.0
CB A:ASP333 4.1 28.7 1.0
CG A:HIS183 4.1 27.5 1.0
O A:HOH647 4.2 38.0 1.0
ND1 A:HIS183 4.2 27.3 1.0
ND1 A:HIS187 4.2 33.0 1.0
CG A:HIS187 4.2 32.3 1.0
ND2 A:ASN177 4.2 29.9 1.0
CE2 A:PHE329 4.5 31.6 1.0
CD1 A:ILE186 4.5 27.4 1.0
ND2 A:ASN330 4.6 29.2 1.0
CA A:ASP333 4.8 29.4 1.0
CG1 A:ILE186 4.9 27.6 1.0

Iron binding site 2 out of 15 in 4nbb

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Iron binding site 2 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:27.6
occ:1.00
 FE1 A:FES502 0.0 27.6 1.0
S2 A:FES502 2.3 27.2 1.0
SG A:CYS90 2.3 29.8 1.0
S1 A:FES502 2.3 29.3 1.0
SG A:CYS69 2.3 20.8 1.0
FE2 A:FES502 2.8 29.8 1.0
CB A:CYS90 3.1 29.6 1.0
CB A:CYS69 3.1 40.0 1.0
CB A:TYR92 4.1 31.7 1.0
CB A:HIS71 4.1 28.3 1.0
CG2 A:VAL74 4.1 29.3 1.0
N A:HIS93 4.4 32.6 1.0
CA A:CYS90 4.6 30.4 1.0
ND1 A:HIS71 4.6 26.1 1.0
ND1 A:HIS93 4.6 30.0 1.0
CA A:CYS69 4.6 33.9 1.0
CB A:TRP95 4.8 27.6 1.0
N A:TYR92 4.8 31.2 1.0
CG A:HIS71 4.9 29.0 1.0
N A:ARG72 4.9 30.2 1.0
CA A:TYR92 4.9 32.0 1.0
CG A:TRP95 5.0 26.5 1.0
CD2 A:LEU76 5.0 36.7 1.0

Iron binding site 3 out of 15 in 4nbb

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Iron binding site 3 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:29.8
occ:1.00
 FE2 A:FES502 0.0 29.8 1.0
ND1 A:HIS93 2.1 30.0 1.0
ND1 A:HIS71 2.2 26.1 1.0
S1 A:FES502 2.2 29.3 1.0
S2 A:FES502 2.4 27.2 1.0
FE1 A:FES502 2.8 27.6 1.0
CG A:HIS93 3.0 31.0 1.0
CG A:HIS71 3.1 29.0 1.0
CE1 A:HIS93 3.2 29.8 1.0
CE1 A:HIS71 3.2 28.6 1.0
CB A:HIS93 3.3 29.7 1.0
CB A:HIS71 3.3 28.3 1.0
N A:HIS93 3.6 32.6 1.0
CB A:TYR92 3.9 31.7 1.0
CA A:HIS93 4.0 31.8 1.0
CD2 A:HIS93 4.2 30.7 1.0
NE2 A:HIS93 4.2 31.2 1.0
CD2 A:HIS71 4.3 28.4 1.0
NE2 A:HIS71 4.3 28.6 1.0
CG A:TYR92 4.3 34.3 1.0
CG A:ARG72 4.3 34.1 1.0
N A:ARG72 4.4 30.2 1.0
SG A:CYS69 4.5 20.8 1.0
CD2 A:TYR92 4.5 35.1 1.0
C A:TYR92 4.5 32.1 1.0
CD1 A:TRP95 4.6 25.2 1.0
NE1 A:TRP95 4.6 25.9 1.0
SG A:CYS90 4.6 29.8 1.0
CA A:HIS71 4.7 29.8 1.0
CB A:ARG72 4.7 32.3 1.0
C A:HIS93 4.8 31.6 1.0
CA A:TYR92 4.8 32.0 1.0
C A:HIS71 4.9 30.2 1.0
CG A:TRP95 5.0 26.5 1.0

Iron binding site 4 out of 15 in 4nbb

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Iron binding site 4 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:48.6
occ:1.00
 O2 B:OXY503 1.9 60.9 1.0
OD1 B:ASP333 2.1 38.2 1.0
NE2 B:HIS183 2.1 34.4 1.0
O1 B:OXY503 2.1 59.7 1.0
NE2 B:HIS187 2.2 41.4 1.0
OD2 B:ASP333 2.4 37.1 1.0
CG B:ASP333 2.5 38.2 1.0
CD2 B:HIS183 2.9 33.7 1.0
CE1 B:HIS187 3.1 42.3 1.0
CE1 B:HIS183 3.1 35.4 1.0
CD2 B:HIS187 3.2 41.3 1.0
CB B:ASP333 4.0 37.3 1.0
CG B:HIS183 4.1 34.8 1.0
ND1 B:HIS183 4.2 34.3 1.0
ND1 B:HIS187 4.2 42.9 1.0
O B:HOH619 4.2 31.7 1.0
ND2 B:ASN177 4.3 38.7 1.0
CG B:HIS187 4.3 42.9 1.0
CD1 B:ILE186 4.4 40.3 1.0
ND2 B:ASN330 4.4 37.6 1.0
C9A B:9CA504 4.6 50.8 1.0
CE2 B:PHE329 4.7 37.0 1.0
C1 B:9CA504 4.7 49.0 1.0
CA B:ASP333 4.8 40.8 1.0
N9 B:9CA504 4.8 51.0 1.0
CG1 B:ILE186 4.9 39.0 1.0
O B:ASN177 4.9 39.0 1.0
C4A B:9CA504 4.9 50.2 1.0
CG B:ASN177 5.0 41.0 1.0

Iron binding site 5 out of 15 in 4nbb

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Iron binding site 5 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:25.6
occ:1.00
 FE1 B:FES502 0.0 25.6 1.0
S1 B:FES502 2.2 27.8 1.0
SG B:CYS90 2.3 20.1 1.0
SG B:CYS69 2.3 31.9 1.0
S2 B:FES502 2.3 29.4 1.0
FE2 B:FES502 2.8 32.2 1.0
CB B:CYS90 3.1 34.9 1.0
CB B:CYS69 3.1 22.5 1.0
CB B:TYR92 4.1 26.5 1.0
CB B:HIS71 4.1 27.3 1.0
CG2 B:VAL74 4.2 26.2 1.0
N B:HIS93 4.4 23.7 1.0
ND1 B:HIS93 4.5 25.5 1.0
CA B:CYS90 4.5 30.2 1.0
CA B:CYS69 4.6 25.6 1.0
ND1 B:HIS71 4.7 26.8 1.0
CB B:TRP95 4.8 23.7 1.0
N B:TYR92 4.8 23.7 1.0
CG B:HIS71 4.9 25.7 1.0
CA B:TYR92 4.9 25.6 1.0
N B:ARG72 4.9 23.0 1.0
CG B:TRP95 4.9 24.6 1.0
N B:TRP95 5.0 25.5 1.0

Iron binding site 6 out of 15 in 4nbb

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Iron binding site 6 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:32.2
occ:1.00
 FE2 B:FES502 0.0 32.2 1.0
ND1 B:HIS93 2.1 25.5 1.0
ND1 B:HIS71 2.2 26.8 1.0
S2 B:FES502 2.3 29.4 1.0
S1 B:FES502 2.3 27.8 1.0
FE1 B:FES502 2.8 25.6 1.0
CG B:HIS93 3.0 27.3 1.0
CE1 B:HIS93 3.0 26.9 1.0
CG B:HIS71 3.1 25.7 1.0
CB B:HIS71 3.2 27.3 1.0
CE1 B:HIS71 3.3 26.6 1.0
CB B:HIS93 3.3 24.6 1.0
N B:HIS93 3.6 23.7 1.0
CB B:TYR92 3.9 26.5 1.0
CA B:HIS93 4.0 24.9 1.0
NE2 B:HIS93 4.1 24.0 1.0
CD2 B:HIS93 4.1 25.1 1.0
CG B:ARG72 4.3 26.9 1.0
CD2 B:HIS71 4.3 24.9 1.0
CG B:TYR92 4.3 25.6 1.0
N B:ARG72 4.3 23.0 1.0
SG B:CYS69 4.4 31.9 1.0
NE2 B:HIS71 4.4 24.6 1.0
CD2 B:TYR92 4.4 26.4 1.0
C B:TYR92 4.5 24.4 1.0
CD1 B:TRP95 4.6 24.4 1.0
CA B:HIS71 4.6 25.9 1.0
SG B:CYS90 4.6 20.1 1.0
NE1 B:TRP95 4.7 24.3 1.0
CB B:ARG72 4.7 26.2 1.0
C B:HIS93 4.8 27.0 1.0
CA B:TYR92 4.8 25.6 1.0
C B:HIS71 4.9 25.5 1.0
CG B:TRP95 5.0 24.6 1.0

Iron binding site 7 out of 15 in 4nbb

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Iron binding site 7 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:39.6
occ:1.00
 OD1 C:ASP333 1.8 34.1 1.0
O1 C:OXY503 1.8 52.6 1.0
O2 C:OXY503 1.9 55.0 1.0
NE2 C:HIS187 2.1 34.4 1.0
NE2 C:HIS183 2.2 30.6 1.0
CG C:ASP333 2.5 34.6 1.0
OD2 C:ASP333 2.6 34.2 1.0
CD2 C:HIS183 2.8 27.9 1.0
CE1 C:HIS187 3.0 35.9 1.0
CD2 C:HIS187 3.1 34.4 1.0
CE1 C:HIS183 3.4 29.9 1.0
CB C:ASP333 4.0 32.8 1.0
CG C:HIS183 4.1 27.9 1.0
ND1 C:HIS187 4.1 34.8 1.0
CG C:HIS187 4.2 34.1 1.0
ND2 C:ASN177 4.2 39.6 1.0
O C:HOH626 4.3 32.6 1.0
ND1 C:HIS183 4.3 28.7 1.0
CD1 C:ILE186 4.3 35.5 1.0
ND2 C:ASN330 4.4 33.3 1.0
C1 C:9CA504 4.6 48.0 1.0
C9A C:9CA504 4.6 48.8 1.0
CE2 C:PHE329 4.7 34.4 1.0
CA C:ASP333 4.7 33.9 1.0
CG1 C:ILE186 4.8 34.1 1.0
O C:ASN177 4.9 37.5 1.0
N9 C:9CA504 4.9 49.3 1.0
C2 C:9CA504 4.9 48.0 1.0
OD1 C:ASN177 4.9 39.9 1.0
CG C:ASN177 4.9 39.4 1.0

Iron binding site 8 out of 15 in 4nbb

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Iron binding site 8 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:33.1
occ:1.00
 FE1 C:FES502 0.0 33.1 1.0
SG C:CYS69 2.2 31.5 1.0
S2 C:FES502 2.2 35.2 1.0
S1 C:FES502 2.3 35.8 1.0
SG C:CYS90 2.3 33.3 1.0
FE2 C:FES502 2.8 36.7 1.0
CB C:CYS69 3.0 31.2 1.0
CB C:CYS90 3.1 34.0 1.0
CB C:HIS71 4.0 32.4 1.0
CB C:TYR92 4.0 31.6 1.0
CG2 C:VAL74 4.3 27.5 1.0
N C:HIS93 4.4 34.1 1.0
CA C:CYS69 4.5 32.7 1.0
CA C:CYS90 4.6 33.0 1.0
ND1 C:HIS71 4.6 35.4 1.0
ND1 C:HIS93 4.6 35.5 1.0
CB C:TRP95 4.8 33.6 1.0
CG C:HIS71 4.8 33.7 1.0
N C:TYR92 4.8 32.0 1.0
N C:ARG72 4.8 31.9 1.0
CA C:TYR92 4.9 34.6 1.0
N C:HIS71 4.9 32.8 1.0
CD2 C:LEU76 5.0 37.6 1.0
CG C:TRP95 5.0 33.2 1.0

Iron binding site 9 out of 15 in 4nbb

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Iron binding site 9 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:36.7
occ:1.00
 FE2 C:FES502 0.0 36.7 1.0
ND1 C:HIS71 2.2 35.4 1.0
ND1 C:HIS93 2.2 35.5 1.0
S1 C:FES502 2.3 35.8 1.0
S2 C:FES502 2.4 35.2 1.0
FE1 C:FES502 2.8 33.1 1.0
CG C:HIS71 3.0 33.7 1.0
CG C:HIS93 3.1 35.6 1.0
CE1 C:HIS93 3.2 36.2 1.0
CB C:HIS71 3.2 32.4 1.0
CE1 C:HIS71 3.2 34.4 1.0
CB C:HIS93 3.3 35.0 1.0
N C:HIS93 3.7 34.1 1.0
CB C:TYR92 3.9 31.6 1.0
CA C:HIS93 4.1 36.1 1.0
CD2 C:HIS93 4.2 37.0 1.0
NE2 C:HIS93 4.2 36.8 1.0
CD2 C:HIS71 4.2 34.4 1.0
CG C:ARG72 4.3 36.1 1.0
SG C:CYS69 4.3 31.5 1.0
N C:ARG72 4.3 31.9 1.0
CG C:TYR92 4.3 35.3 1.0
NE2 C:HIS71 4.3 35.1 1.0
CD2 C:TYR92 4.3 35.1 1.0
C C:TYR92 4.5 33.7 1.0
CA C:HIS71 4.6 32.8 1.0
SG C:CYS90 4.7 33.3 1.0
CD1 C:TRP95 4.7 33.9 1.0
CB C:ARG72 4.7 33.5 1.0
NE1 C:TRP95 4.8 32.9 1.0
CA C:TYR92 4.8 34.6 1.0
C C:HIS71 4.9 32.6 1.0
C C:HIS93 4.9 36.4 1.0

Iron binding site 10 out of 15 in 4nbb

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Iron binding site 10 out of 15 in the Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Carbazole- and Oxygen-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:31.2
occ:1.00
 FE1 D:FES201 0.0 31.2 1.0
ND1 D:HIS48 2.1 31.1 1.0
S1 D:FES201 2.2 30.1 1.0
ND1 D:HIS68 2.2 28.5 1.0
S2 D:FES201 2.2 30.8 1.0
FE2 D:FES201 2.7 31.3 1.0
CE1 D:HIS48 3.0 27.2 1.0
CG D:HIS48 3.1 29.6 1.0
CE1 D:HIS68 3.1 30.3 1.0
CG D:HIS68 3.2 30.4 1.0
CB D:HIS48 3.5 31.1 1.0
CB D:HIS68 3.6 29.6 1.0
O D:HOH301 3.8 32.6 1.0
NE2 D:HIS48 4.1 27.9 1.0
N D:HIS68 4.1 31.4 1.0
CB D:PHE67 4.2 31.1 1.0
CD2 D:HIS48 4.2 28.9 1.0
C D:HIS48 4.2 33.9 1.0
O D:HIS48 4.2 36.3 1.0
NE2 D:HIS68 4.3 30.6 1.0
CD2 D:HIS68 4.4 29.7 1.0
SG D:CYS46 4.5 31.5 1.0
CA D:HIS68 4.5 31.2 1.0
CA D:HIS48 4.5 32.3 1.0
SG D:CYS65 4.5 32.2 1.0
CG D:PRO83 4.6 35.4 1.0
N D:GLY49 4.6 34.6 1.0
O A:VAL351 4.9 29.4 1.0
O A:GLU353 4.9 23.6 1.0
C D:PHE67 5.0 32.6 1.0
CA D:GLY49 5.0 34.3 1.0

Reference:

K.Inoue, Y.Usami, Y.Ashikawa, H.Noguchi, T.Umeda, A.Yamagami-Ashikawa, T.Horisaki, H.Uchimura, T.Terada, S.Nakamura, K.Shimizu, H.Habe, H.Yamane, Z.Fujimoto, H.Nojiri. Structural Basis of the Divergent Oxygenation Reactions Catalyzed By the Rieske Non-Heme Iron Oxygenase, Carbazole 1,9A-Dioxygenase Appl.Environ.Microbiol. 2014.
ISSN: ESSN 1098-5336
PubMed: 24584240
DOI: 10.1128/AEM.04000-13
Page generated: Sun Dec 13 15:42:32 2020

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