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Iron in PDB 4nbe: Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)

Enzymatic activity of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)

All present enzymatic activity of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2):
1.14.12.22;

Protein crystallography data

The structure of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2), PDB code: 4nbe 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) 33.75 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.455, 88.264, 108.621, 90.00, 106.72, 90.00
R / Rfree (%) 21.7 / 25.2

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) (pdb code 4nbe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2), PDB code: 4nbe:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 4nbe

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Iron binding site 1 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.4
occ:1.00
 O A:HOH823 1.8 53.7 1.0
OD1 A:ASP333 2.0 35.5 1.0
NE2 A:HIS183 2.1 37.1 1.0
NE2 A:HIS187 2.2 37.0 1.0
CG A:ASP333 2.6 34.1 1.0
OD2 A:ASP333 2.6 37.0 1.0
CD2 A:HIS183 3.0 36.6 1.0
CE1 A:HIS183 3.2 37.2 1.0
CE1 A:HIS187 3.2 35.6 1.0
CD2 A:HIS187 3.2 36.5 1.0
CB A:ASP333 4.0 32.9 1.0
C4 A:9FL503 4.1 52.3 1.0
CG A:HIS183 4.2 36.1 1.0
C3 A:9FL503 4.2 51.0 1.0
ND1 A:HIS183 4.2 36.7 1.0
ND2 A:ASN177 4.3 31.5 1.0
ND1 A:HIS187 4.3 36.8 1.0
CG A:HIS187 4.4 36.5 1.0
CE2 A:PHE329 4.4 37.8 1.0
O A:HOH648 4.4 32.4 1.0
C4A A:9FL503 4.5 53.5 1.0
C2 A:9FL503 4.6 51.7 1.0
CD1 A:ILE186 4.6 34.4 1.0
ND2 A:ASN330 4.6 37.1 1.0
CA A:ASP333 4.8 32.5 1.0
C9A A:9FL503 4.9 52.9 1.0
C1 A:9FL503 4.9 52.6 1.0

Iron binding site 2 out of 13 in 4nbe

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Iron binding site 2 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:32.3
occ:1.00
 FE1 A:FES502 0.0 32.3 1.0
S1 A:FES502 2.2 27.3 1.0
S2 A:FES502 2.2 27.9 1.0
SG A:CYS90 2.3 27.7 1.0
SG A:CYS69 2.4 31.8 1.0
FE2 A:FES502 2.8 31.2 1.0
CB A:CYS90 3.1 27.4 1.0
CB A:CYS69 3.2 29.5 1.0
CB A:HIS71 4.1 27.4 1.0
CB A:TYR92 4.1 33.1 1.0
CG2 A:VAL74 4.2 21.9 1.0
N A:HIS93 4.4 31.2 1.0
ND1 A:HIS93 4.5 27.9 1.0
ND1 A:HIS71 4.6 27.8 1.0
CA A:CYS90 4.6 28.9 1.0
CA A:CYS69 4.6 29.8 1.0
CB A:TRP95 4.8 28.6 1.0
CG A:HIS71 4.8 27.9 1.0
N A:ARG72 4.8 29.7 1.0
N A:TYR92 4.9 31.6 1.0
CA A:TYR92 4.9 31.1 1.0
CD2 A:LEU76 5.0 36.9 1.0
CG A:TRP95 5.0 29.3 1.0

Iron binding site 3 out of 13 in 4nbe

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Iron binding site 3 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:31.2
occ:1.00
 FE2 A:FES502 0.0 31.2 1.0
ND1 A:HIS71 2.1 27.8 1.0
ND1 A:HIS93 2.2 27.9 1.0
S2 A:FES502 2.2 27.9 1.0
S1 A:FES502 2.3 27.3 1.0
FE1 A:FES502 2.8 32.3 1.0
CG A:HIS93 3.0 28.8 1.0
CG A:HIS71 3.0 27.9 1.0
CE1 A:HIS93 3.2 29.8 1.0
CE1 A:HIS71 3.2 29.1 1.0
CB A:HIS71 3.2 27.4 1.0
CB A:HIS93 3.3 29.5 1.0
N A:HIS93 3.7 31.2 1.0
CB A:TYR92 4.0 33.1 1.0
CA A:HIS93 4.1 29.2 1.0
CD2 A:HIS93 4.1 29.1 1.0
NE2 A:HIS93 4.2 26.4 1.0
CD2 A:HIS71 4.2 27.6 1.0
CG A:ARG72 4.2 32.4 1.0
NE2 A:HIS71 4.3 28.8 1.0
N A:ARG72 4.3 29.7 1.0
CG A:TYR92 4.4 35.8 1.0
SG A:CYS69 4.4 31.8 1.0
CD2 A:TYR92 4.5 35.7 1.0
CA A:HIS71 4.6 27.9 1.0
C A:TYR92 4.6 32.1 1.0
SG A:CYS90 4.7 27.7 1.0
CD1 A:TRP95 4.7 30.6 1.0
CB A:ARG72 4.7 31.0 1.0
NE1 A:TRP95 4.8 28.4 1.0
C A:HIS71 4.8 29.5 1.0
C A:HIS93 4.9 28.6 1.0
CA A:TYR92 4.9 31.1 1.0

Iron binding site 4 out of 13 in 4nbe

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Iron binding site 4 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:61.5
occ:1.00
 O B:HOH610 1.9 65.8 1.0
OD1 B:ASP333 2.1 51.4 1.0
NE2 B:HIS183 2.2 43.1 1.0
NE2 B:HIS187 2.3 44.5 1.0
OD2 B:ASP333 2.8 50.4 1.0
CG B:ASP333 2.8 48.8 1.0
CD2 B:HIS183 3.0 42.3 1.0
CD2 B:HIS187 3.2 44.8 1.0
CE1 B:HIS183 3.4 41.6 1.0
CE1 B:HIS187 3.4 45.6 1.0
O B:HOH735 4.1 66.9 1.0
CG B:HIS183 4.2 42.4 1.0
CB B:ASP333 4.2 46.5 1.0
ND1 B:HIS183 4.4 42.4 1.0
CG B:HIS187 4.4 45.2 1.0
ND1 B:HIS187 4.5 45.5 1.0
ND2 B:ASN330 4.5 50.1 1.0
CE2 B:PHE329 4.5 45.8 1.0
O B:HOH726 4.6 69.1 1.0
O B:HOH685 4.6 44.8 1.0
CD1 B:ILE186 4.6 43.8 1.0
ND2 B:ASN177 4.7 51.3 1.0
O B:HOH727 4.7 74.4 1.0

Iron binding site 5 out of 13 in 4nbe

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Iron binding site 5 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:33.0
occ:1.00
 FE1 B:FES502 0.0 33.0 1.0
S1 B:FES502 2.2 43.3 1.0
SG B:CYS90 2.2 33.1 1.0
S2 B:FES502 2.3 37.8 1.0
SG B:CYS69 2.3 33.7 1.0
FE2 B:FES502 2.9 30.3 1.0
CB B:CYS90 3.1 34.5 1.0
CB B:CYS69 3.1 31.5 1.0
CB B:TYR92 4.0 30.4 1.0
CG2 B:VAL74 4.1 29.6 1.0
CB B:HIS71 4.2 29.1 1.0
N B:HIS93 4.5 32.2 1.0
CA B:CYS90 4.6 33.1 1.0
CA B:CYS69 4.6 30.6 1.0
ND1 B:HIS93 4.6 36.5 1.0
CB B:TRP95 4.6 36.0 1.0
ND1 B:HIS71 4.7 29.6 1.0
N B:TYR92 4.8 31.2 1.0
CG B:TRP95 4.9 36.5 1.0
CA B:TYR92 4.9 31.7 1.0
CG B:HIS71 4.9 31.4 1.0
N B:ARG72 4.9 31.6 1.0
CD2 B:LEU76 4.9 38.6 1.0
N B:TRP95 5.0 35.7 1.0

Iron binding site 6 out of 13 in 4nbe

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Iron binding site 6 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:30.3
occ:1.00
 FE2 B:FES502 0.0 30.3 1.0
ND1 B:HIS93 2.1 36.5 1.0
ND1 B:HIS71 2.2 29.6 1.0
S2 B:FES502 2.2 37.8 1.0
S1 B:FES502 2.3 43.3 1.0
FE1 B:FES502 2.9 33.0 1.0
CE1 B:HIS93 3.0 32.5 1.0
CG B:HIS93 3.0 34.3 1.0
CG B:HIS71 3.1 31.4 1.0
CE1 B:HIS71 3.2 29.0 1.0
CB B:HIS71 3.3 29.1 1.0
CB B:HIS93 3.4 31.9 1.0
N B:HIS93 3.7 32.2 1.0
CB B:TYR92 3.8 30.4 1.0
NE2 B:HIS93 4.1 34.9 1.0
CG B:ARG72 4.1 34.4 1.0
CA B:HIS93 4.1 32.4 1.0
CD2 B:HIS93 4.1 34.2 1.0
CG B:TYR92 4.2 30.4 1.0
CD2 B:HIS71 4.2 28.2 1.0
NE2 B:HIS71 4.3 29.6 1.0
N B:ARG72 4.3 31.6 1.0
CD2 B:TYR92 4.3 29.5 1.0
SG B:CYS69 4.4 33.7 1.0
C B:TYR92 4.6 32.0 1.0
SG B:CYS90 4.6 33.1 1.0
CD1 B:TRP95 4.6 35.5 1.0
CA B:HIS71 4.6 31.0 1.0
CB B:ARG72 4.6 33.2 1.0
NE1 B:TRP95 4.8 35.2 1.0
CA B:TYR92 4.8 31.7 1.0
C B:HIS71 4.9 31.3 1.0
C B:HIS93 4.9 32.8 1.0
CG B:TRP95 5.0 36.5 1.0

Iron binding site 7 out of 13 in 4nbe

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Iron binding site 7 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:42.3
occ:1.00
 OD1 C:ASP333 1.8 32.3 1.0
O C:HOH748 1.9 35.0 1.0
NE2 C:HIS187 2.3 32.4 1.0
OD2 C:ASP333 2.3 33.5 1.0
NE2 C:HIS183 2.3 31.3 1.0
CG C:ASP333 2.3 32.5 1.0
CD2 C:HIS183 3.0 26.8 1.0
CD2 C:HIS187 3.2 27.8 1.0
CE1 C:HIS187 3.2 31.4 1.0
CE1 C:HIS183 3.5 30.0 1.0
CB C:ASP333 3.8 29.9 1.0
ND2 C:ASN177 4.0 33.8 1.0
CG C:HIS183 4.2 30.2 1.0
O C:HOH654 4.3 32.7 1.0
ND2 C:ASN330 4.3 36.6 1.0
ND1 C:HIS187 4.3 30.8 1.0
CG C:HIS187 4.4 30.9 1.0
CD1 C:ILE186 4.4 36.4 1.0
ND1 C:HIS183 4.4 29.8 1.0
C4 C:9FL503 4.5 42.6 1.0
CA C:ASP333 4.6 33.1 1.0
C3 C:9FL503 4.7 42.3 1.0
CE2 C:PHE329 4.7 34.3 1.0
CG C:ASN177 4.8 35.4 1.0
OD1 C:ASN177 4.8 32.8 1.0
C4A C:9FL503 4.9 44.2 1.0
O C:ASN177 4.9 37.7 1.0
N C:ASP333 5.0 32.1 1.0
CG1 C:ILE186 5.0 36.5 1.0

Iron binding site 8 out of 13 in 4nbe

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Iron binding site 8 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:36.0
occ:1.00
 FE1 C:FES502 0.0 36.0 1.0
S2 C:FES502 2.2 35.6 1.0
SG C:CYS90 2.2 35.5 1.0
SG C:CYS69 2.3 38.6 1.0
S1 C:FES502 2.3 42.0 1.0
FE2 C:FES502 2.8 37.3 1.0
CB C:CYS90 3.1 37.0 1.0
CB C:CYS69 3.1 35.2 1.0
CB C:HIS71 4.0 31.7 1.0
CB C:TYR92 4.1 36.7 1.0
CG2 C:VAL74 4.2 38.7 1.0
ND1 C:HIS71 4.4 29.2 1.0
N C:HIS93 4.5 41.0 1.0
CA C:CYS90 4.5 38.3 1.0
CA C:CYS69 4.6 34.2 1.0
ND1 C:HIS93 4.7 45.0 1.0
CG C:HIS71 4.7 31.9 1.0
N C:TYR92 4.8 37.7 1.0
CB C:TRP95 4.8 37.0 1.0
CD2 C:LEU76 4.9 42.3 1.0
N C:ARG72 4.9 36.0 1.0
CA C:TYR92 5.0 38.3 1.0

Iron binding site 9 out of 13 in 4nbe

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Iron binding site 9 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:37.3
occ:1.00
 FE2 C:FES502 0.0 37.3 1.0
ND1 C:HIS71 2.0 29.2 1.0
S1 C:FES502 2.1 42.0 1.0
S2 C:FES502 2.3 35.6 1.0
ND1 C:HIS93 2.4 45.0 1.0
FE1 C:FES502 2.8 36.0 1.0
CG C:HIS71 2.9 31.9 1.0
CE1 C:HIS71 3.0 32.8 1.0
CG C:HIS93 3.1 43.5 1.0
CB C:HIS71 3.2 31.7 1.0
CB C:HIS93 3.3 41.9 1.0
CE1 C:HIS93 3.4 44.3 1.0
N C:HIS93 3.7 41.0 1.0
CB C:TYR92 4.0 36.7 1.0
CD2 C:HIS71 4.1 30.7 1.0
CA C:HIS93 4.1 41.0 1.0
NE2 C:HIS71 4.1 29.5 1.0
CD2 C:HIS93 4.2 44.8 1.0
SG C:CYS69 4.3 38.6 1.0
CG C:ARG72 4.3 41.0 1.0
NE2 C:HIS93 4.3 44.1 1.0
N C:ARG72 4.3 36.0 1.0
CG C:TYR92 4.4 37.1 1.0
CD2 C:TYR92 4.4 36.7 1.0
CD1 C:TRP95 4.6 35.4 1.0
SG C:CYS90 4.6 35.5 1.0
CA C:HIS71 4.6 34.4 1.0
C C:TYR92 4.6 39.4 1.0
NE1 C:TRP95 4.6 33.4 1.0
CB C:ARG72 4.8 38.1 1.0
C C:HIS93 4.9 41.1 1.0
C C:HIS71 4.9 35.0 1.0
CA C:TYR92 4.9 38.3 1.0
CG C:TRP95 5.0 34.2 1.0

Iron binding site 10 out of 13 in 4nbe

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Iron binding site 10 out of 13 in the Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Fluorene-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:40.8
occ:1.00
 FE1 D:FES201 0.0 40.8 1.0
ND1 D:HIS48 2.1 40.0 1.0
S1 D:FES201 2.2 34.4 1.0
S2 D:FES201 2.3 38.8 1.0
ND1 D:HIS68 2.3 37.0 1.0
FE2 D:FES201 2.7 37.8 1.0
CE1 D:HIS48 3.1 40.6 1.0
CG D:HIS48 3.1 41.9 1.0
CE1 D:HIS68 3.2 36.1 1.0
CG D:HIS68 3.3 36.1 1.0
CB D:HIS48 3.5 41.2 1.0
CB D:HIS68 3.6 38.1 1.0
O A:HOH605 3.8 30.8 1.0
N D:HIS68 4.2 39.5 1.0
C D:HIS48 4.2 42.2 1.0
NE2 D:HIS48 4.2 41.0 1.0
CD2 D:HIS48 4.2 41.4 1.0
O D:HIS48 4.3 44.2 1.0
NE2 D:HIS68 4.4 36.0 1.0
CB D:PHE67 4.4 39.5 1.0
CD2 D:HIS68 4.4 36.1 1.0
N D:GLY49 4.4 42.2 1.0
CA D:HIS48 4.4 41.8 1.0
SG D:CYS65 4.5 37.3 1.0
CA D:HIS68 4.5 39.6 1.0
CG D:PRO83 4.5 41.6 1.0
SG D:CYS46 4.5 39.8 1.0
O A:VAL351 4.8 36.5 1.0
CA D:GLY49 4.9 41.0 1.0
O A:GLU353 4.9 33.7 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: Mon Aug 5 07:23:40 2024

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