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Iron in PDB 4nbh: Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase

Enzymatic activity of Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase

All present enzymatic activity of Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase:
1.14.12.22;

Protein crystallography data

The structure of Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nbh 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) 40.92 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.176, 89.950, 105.185, 90.00, 104.29, 90.00
R / Rfree (%) 18.3 / 21.1

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (pdb code 4nbh). 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nbh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in 4nbh

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Iron binding site 1 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:19.6
occ:1.00
 O A:HOH646 1.9 29.1 1.0
OD1 A:ASP333 2.0 16.2 1.0
NE2 A:HIS183 2.0 15.9 1.0
NE2 A:HIS187 2.1 19.2 1.0
O A:HOH880 2.6 35.8 1.0
CG A:ASP333 2.7 19.1 1.0
OD2 A:ASP333 2.7 21.7 1.0
CD2 A:HIS183 2.9 15.8 1.0
CE1 A:HIS187 3.0 20.5 1.0
CE1 A:HIS183 3.1 16.1 1.0
CD2 A:HIS187 3.1 20.3 1.0
CG A:HIS183 4.1 15.6 1.0
CB A:ASP333 4.1 16.7 1.0
ND1 A:HIS187 4.1 21.2 1.0
ND1 A:HIS183 4.1 16.2 1.0
CG A:HIS187 4.2 20.6 1.0
O A:HOH660 4.2 41.9 1.0
O A:HOH648 4.2 20.2 1.0
ND2 A:ASN177 4.3 15.9 1.0
CE2 A:PHE329 4.4 20.0 1.0
CD1 A:ILE186 4.6 14.2 1.0
ND2 A:ASN330 4.6 18.2 1.0
CA A:ASP333 4.9 17.6 1.0
CG1 A:ILE186 4.9 15.9 1.0

Iron binding site 2 out of 15 in 4nbh

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Iron binding site 2 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:16.0
occ:1.00
 FE1 A:FES502 0.0 16.0 1.0
S2 A:FES502 2.2 17.9 1.0
S1 A:FES502 2.3 17.8 1.0
SG A:CYS90 2.3 15.1 1.0
SG A:CYS69 2.4 17.3 1.0
FE2 A:FES502 2.8 20.0 1.0
CB A:CYS90 3.1 15.2 1.0
CB A:CYS69 3.2 17.3 1.0
CB A:TYR92 4.0 16.8 1.0
CB A:HIS71 4.1 14.2 1.0
CG2 A:VAL74 4.2 16.1 1.0
N A:HIS93 4.4 17.4 1.0
ND1 A:HIS71 4.5 10.8 1.0
ND1 A:HIS93 4.5 12.8 1.0
CA A:CYS90 4.5 16.7 1.0
CA A:CYS69 4.6 17.8 1.0
CB A:TRP95 4.7 16.0 1.0
N A:TYR92 4.8 16.3 1.0
CG A:HIS71 4.8 13.9 1.0
CA A:TYR92 4.8 17.0 1.0
N A:ARG72 4.9 16.1 1.0
CG A:TRP95 5.0 13.7 1.0
CG A:TYR92 5.0 18.9 1.0
C A:CYS90 5.0 16.3 1.0

Iron binding site 3 out of 15 in 4nbh

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Iron binding site 3 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:20.0
occ:1.00
 FE2 A:FES502 0.0 20.0 1.0
ND1 A:HIS93 2.1 12.8 1.0
ND1 A:HIS71 2.1 10.8 1.0
S1 A:FES502 2.2 17.8 1.0
S2 A:FES502 2.3 17.9 1.0
FE1 A:FES502 2.8 16.0 1.0
CG A:HIS93 3.0 15.0 1.0
CG A:HIS71 3.1 13.9 1.0
CE1 A:HIS93 3.1 15.2 1.0
CE1 A:HIS71 3.2 14.7 1.0
CB A:HIS93 3.3 14.7 1.0
CB A:HIS71 3.3 14.2 1.0
N A:HIS93 3.6 17.4 1.0
CB A:TYR92 3.9 16.8 1.0
CA A:HIS93 4.0 17.4 1.0
CD2 A:HIS93 4.1 17.1 1.0
NE2 A:HIS93 4.2 15.6 1.0
CD2 A:HIS71 4.2 11.5 1.0
NE2 A:HIS71 4.2 12.1 1.0
CG A:TYR92 4.3 18.9 1.0
N A:ARG72 4.3 16.1 1.0
CD2 A:TYR92 4.4 19.9 1.0
CG A:ARG72 4.4 17.4 1.0
SG A:CYS69 4.4 17.3 1.0
C A:TYR92 4.5 17.6 1.0
CD1 A:TRP95 4.6 12.8 1.0
NE1 A:TRP95 4.6 12.5 1.0
CA A:HIS71 4.7 14.9 1.0
SG A:CYS90 4.7 15.1 1.0
CB A:ARG72 4.8 16.8 1.0
CA A:TYR92 4.8 17.0 1.0
C A:HIS93 4.8 17.4 1.0
C A:HIS71 4.9 16.2 1.0
CG A:TRP95 4.9 13.7 1.0

Iron binding site 4 out of 15 in 4nbh

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Iron binding site 4 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:37.1
occ:1.00
 OD1 B:ASP333 1.8 28.3 1.0
O B:HOH732 1.9 51.9 1.0
NE2 B:HIS187 2.2 31.8 1.0
NE2 B:HIS183 2.2 18.0 1.0
CG B:ASP333 2.5 28.6 1.0
OD2 B:ASP333 2.5 28.1 1.0
CD2 B:HIS183 3.0 18.6 1.0
CE1 B:HIS187 3.1 32.7 1.0
CD2 B:HIS187 3.2 31.9 1.0
CE1 B:HIS183 3.3 18.8 1.0
CB B:ASP333 3.9 27.5 1.0
O B:HOH619 4.0 24.7 1.0
CG B:HIS183 4.2 18.5 1.0
C8 B:9CA503 4.2 39.4 1.0
ND1 B:HIS187 4.2 32.8 1.0
ND1 B:HIS183 4.3 17.6 1.0
CG B:HIS187 4.3 32.5 1.0
CD1 B:ILE186 4.4 28.1 1.0
ND2 B:ASN177 4.4 30.9 1.0
C8A B:9CA503 4.4 40.1 1.0
C7 B:9CA503 4.6 40.1 1.0
CE2 B:PHE329 4.6 26.7 1.0
ND2 B:ASN330 4.6 32.4 1.0
CA B:ASP333 4.7 28.9 1.0
N9 B:9CA503 4.8 41.0 1.0
O B:ASN177 4.8 29.4 1.0
CG1 B:ILE186 4.9 27.6 1.0
C4B B:9CA503 5.0 40.6 1.0

Iron binding site 5 out of 15 in 4nbh

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Iron binding site 5 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:13.6
occ:1.00
 FE1 B:FES502 0.0 13.6 1.0
S1 B:FES502 2.1 19.9 1.0
S2 B:FES502 2.3 11.9 1.0
SG B:CYS69 2.3 13.9 1.0
SG B:CYS90 2.4 14.4 1.0
FE2 B:FES502 2.7 12.0 1.0
CB B:CYS69 3.1 11.1 1.0
CB B:CYS90 3.1 15.3 1.0
CB B:HIS71 4.0 13.1 1.0
CB B:TYR92 4.1 13.7 1.0
CG2 B:VAL74 4.2 9.9 1.0
N B:HIS93 4.4 15.5 1.0
ND1 B:HIS93 4.5 9.2 1.0
CA B:CYS69 4.5 14.4 1.0
ND1 B:HIS71 4.6 10.7 1.0
CA B:CYS90 4.6 16.2 1.0
CB B:TRP95 4.7 12.4 1.0
CG B:HIS71 4.8 12.4 1.0
N B:ARG72 4.8 13.2 1.0
N B:TYR92 4.9 14.9 1.0
CG B:TRP95 4.9 11.4 1.0
CA B:TYR92 4.9 14.9 1.0
N B:HIS71 5.0 14.6 1.0

Iron binding site 6 out of 15 in 4nbh

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Iron binding site 6 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:12.0
occ:1.00
 FE2 B:FES502 0.0 12.0 1.0
ND1 B:HIS93 2.1 9.2 1.0
ND1 B:HIS71 2.2 10.7 1.0
S1 B:FES502 2.2 19.9 1.0
S2 B:FES502 2.3 11.9 1.0
FE1 B:FES502 2.7 13.6 1.0
CG B:HIS93 3.0 14.3 1.0
CG B:HIS71 3.0 12.4 1.0
CE1 B:HIS93 3.1 12.5 1.0
CB B:HIS71 3.2 13.1 1.0
CE1 B:HIS71 3.3 14.9 1.0
CB B:HIS93 3.3 13.9 1.0
N B:HIS93 3.7 15.5 1.0
CB B:TYR92 3.9 13.7 1.0
CA B:HIS93 4.1 14.7 1.0
NE2 B:HIS93 4.1 9.2 1.0
CD2 B:HIS93 4.1 10.8 1.0
CD2 B:HIS71 4.2 10.9 1.0
CG B:ARG72 4.3 13.8 1.0
CG B:TYR92 4.3 15.2 1.0
NE2 B:HIS71 4.3 12.2 1.0
N B:ARG72 4.3 13.2 1.0
CD2 B:TYR92 4.3 14.6 1.0
SG B:CYS69 4.3 13.9 1.0
C B:TYR92 4.5 14.6 1.0
CA B:HIS71 4.6 14.4 1.0
CD1 B:TRP95 4.6 11.5 1.0
SG B:CYS90 4.6 14.4 1.0
NE1 B:TRP95 4.7 10.1 1.0
CB B:ARG72 4.7 12.9 1.0
CA B:TYR92 4.8 14.9 1.0
C B:HIS93 4.9 14.4 1.0
C B:HIS71 4.9 13.3 1.0
CG B:TRP95 5.0 11.4 1.0

Iron binding site 7 out of 15 in 4nbh

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Iron binding site 7 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:28.0
occ:1.00
 O C:HOH652 1.8 27.7 1.0
OD1 C:ASP333 1.8 22.7 1.0
NE2 C:HIS187 2.1 20.3 1.0
NE2 C:HIS183 2.1 17.4 1.0
CG C:ASP333 2.5 22.8 1.0
OD2 C:ASP333 2.6 22.9 1.0
CD2 C:HIS183 2.9 14.6 1.0
CE1 C:HIS187 3.1 20.4 1.0
CD2 C:HIS187 3.1 18.6 1.0
CE1 C:HIS183 3.3 15.7 1.0
CB C:ASP333 4.0 21.3 1.0
O C:HOH628 4.1 19.0 1.0
CG C:HIS183 4.1 17.0 1.0
ND2 C:ASN177 4.2 27.9 1.0
ND1 C:HIS187 4.2 19.5 1.0
CG C:HIS187 4.3 19.5 1.0
ND1 C:HIS183 4.3 17.0 1.0
CD1 C:ILE186 4.3 18.6 1.0
C1 C:9CA503 4.4 37.8 1.0
C2 C:9CA503 4.5 36.2 1.0
ND2 C:ASN330 4.6 24.0 1.0
CE2 C:PHE329 4.6 20.2 1.0
CA C:ASP333 4.7 22.1 1.0
C9A C:9CA503 4.7 38.7 1.0
CG1 C:ILE186 4.8 17.4 1.0
C3 C:9CA503 4.8 37.1 1.0
O C:ASN177 4.9 23.3 1.0
CG C:ASN177 4.9 26.4 1.0
OD1 C:ASN177 4.9 26.4 1.0

Iron binding site 8 out of 15 in 4nbh

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Iron binding site 8 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:24.7
occ:1.00
 FE1 C:FES502 0.0 24.7 1.0
SG C:CYS69 2.1 21.9 1.0
S1 C:FES502 2.3 27.2 1.0
SG C:CYS90 2.3 21.5 1.0
S2 C:FES502 2.3 20.8 1.0
FE2 C:FES502 2.9 26.9 1.0
CB C:CYS69 3.0 20.8 1.0
CB C:CYS90 3.1 24.4 1.0
CB C:HIS71 4.0 21.6 1.0
CB C:TYR92 4.0 23.2 1.0
CG2 C:VAL74 4.3 21.1 1.0
CA C:CYS69 4.4 22.3 1.0
N C:HIS93 4.4 23.8 1.0
CA C:CYS90 4.5 24.0 1.0
ND1 C:HIS93 4.6 26.0 1.0
ND1 C:HIS71 4.7 21.8 1.0
CB C:TRP95 4.7 23.9 1.0
N C:TYR92 4.8 23.4 1.0
CG C:HIS71 4.9 21.5 1.0
CA C:TYR92 4.9 24.4 1.0
N C:ARG72 4.9 21.1 1.0
N C:HIS71 4.9 22.4 1.0
CG C:TRP95 4.9 23.7 1.0

Iron binding site 9 out of 15 in 4nbh

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Iron binding site 9 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:26.9
occ:1.00
 FE2 C:FES502 0.0 26.9 1.0
ND1 C:HIS93 2.2 26.0 1.0
ND1 C:HIS71 2.2 21.8 1.0
S1 C:FES502 2.3 27.2 1.0
S2 C:FES502 2.4 20.8 1.0
FE1 C:FES502 2.9 24.7 1.0
CG C:HIS71 3.0 21.5 1.0
CG C:HIS93 3.0 26.6 1.0
CE1 C:HIS93 3.1 28.0 1.0
CB C:HIS71 3.2 21.6 1.0
CE1 C:HIS71 3.3 22.4 1.0
CB C:HIS93 3.3 24.7 1.0
N C:HIS93 3.7 23.8 1.0
CB C:TYR92 3.9 23.2 1.0
CA C:HIS93 4.1 25.2 1.0
CD2 C:HIS93 4.1 28.0 1.0
NE2 C:HIS93 4.2 26.5 1.0
CD2 C:HIS71 4.2 21.4 1.0
SG C:CYS69 4.2 21.9 1.0
CG C:ARG72 4.3 23.2 1.0
NE2 C:HIS71 4.3 19.9 1.0
CG C:TYR92 4.3 26.2 1.0
N C:ARG72 4.3 21.1 1.0
CD2 C:TYR92 4.3 26.2 1.0
CA C:HIS71 4.6 21.5 1.0
C C:TYR92 4.6 24.3 1.0
CD1 C:TRP95 4.6 24.6 1.0
NE1 C:TRP95 4.7 23.8 1.0
SG C:CYS90 4.7 21.5 1.0
CB C:ARG72 4.7 20.8 1.0
CA C:TYR92 4.8 24.4 1.0
C C:HIS93 4.9 25.2 1.0
C C:HIS71 4.9 21.2 1.0
CG C:TRP95 5.0 23.7 1.0

Iron binding site 10 out of 15 in 4nbh

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Iron binding site 10 out of 15 in the Carbazole-Bound Oxygenase with GLN282 Replaced By Tyr 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-Bound Oxygenase with GLN282 Replaced By Tyr and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:20.5
occ:1.00
 FE1 D:FES201 0.0 20.5 1.0
ND1 D:HIS48 2.1 16.5 1.0
ND1 D:HIS68 2.2 15.4 1.0
S1 D:FES201 2.2 19.7 1.0
S2 D:FES201 2.2 16.9 1.0
FE2 D:FES201 2.7 19.6 1.0
CE1 D:HIS48 3.0 13.9 1.0
CE1 D:HIS68 3.0 16.4 1.0
CG D:HIS48 3.2 16.1 1.0
CG D:HIS68 3.3 16.1 1.0
CB D:HIS48 3.6 16.6 1.0
CB D:HIS68 3.7 17.2 1.0
O D:HOH301 3.7 18.6 1.0
NE2 D:HIS48 4.1 13.9 1.0
N D:HIS68 4.1 18.6 1.0
O D:HIS48 4.2 21.9 1.0
NE2 D:HIS68 4.2 16.7 1.0
C D:HIS48 4.2 19.7 1.0
CB D:PHE67 4.2 21.1 1.0
CD2 D:HIS48 4.2 15.0 1.0
CD2 D:HIS68 4.3 17.0 1.0
SG D:CYS46 4.5 22.9 1.0
CA D:HIS48 4.5 19.0 1.0
CA D:HIS68 4.5 18.3 1.0
CG D:PRO83 4.5 18.8 1.0
SG D:CYS65 4.5 19.4 1.0
N D:GLY49 4.6 20.6 1.0
O A:VAL351 4.9 16.7 1.0
O A:GLU353 4.9 14.2 1.0
C D:PHE67 5.0 20.2 1.0
CA D:GLY49 5.0 20.9 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 07:36:35 2024

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