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

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

All present enzymatic activity of Carbazole-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-Bound Oxygenase with ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nba 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) 32.79 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.287, 89.988, 105.258, 90.00, 104.11, 90.00
R / Rfree (%) 19 / 21.7

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 ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (pdb code 4nba). 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 ILE262 Replaced By Val and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nba:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in 4nba

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Iron binding site 1 out of 15 in the Carbazole-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-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:28.8
occ:1.00
 O A:HOH625 1.9 20.7 1.0
OD1 A:ASP333 2.0 17.8 1.0
NE2 A:HIS183 2.1 15.4 1.0
NE2 A:HIS187 2.1 20.6 1.0
CG A:ASP333 2.6 18.3 1.0
OD2 A:ASP333 2.7 20.1 1.0
CD2 A:HIS183 2.8 12.0 1.0
CE1 A:HIS187 3.1 21.7 1.0
CD2 A:HIS187 3.2 21.1 1.0
CE1 A:HIS183 3.2 13.6 1.0
CG A:HIS183 4.0 14.5 1.0
CB A:ASP333 4.1 16.2 1.0
O A:HOH658 4.1 31.6 1.0
ND2 A:ASN177 4.2 15.6 1.0
ND1 A:HIS183 4.2 14.4 1.0
ND1 A:HIS187 4.2 20.8 1.0
CG A:HIS187 4.3 21.0 1.0
O A:HOH652 4.3 41.4 1.0
O A:HOH648 4.4 17.7 1.0
CD1 A:ILE186 4.5 15.4 1.0
CE2 A:PHE329 4.5 18.5 1.0
ND2 A:ASN330 4.6 16.5 1.0
CA A:ASP333 4.8 16.9 1.0
CG1 A:ILE186 4.9 15.0 1.0
O A:ASN177 5.0 15.8 1.0

Iron binding site 2 out of 15 in 4nba

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Iron binding site 2 out of 15 in the Carbazole-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-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:18.5
occ:1.00
 FE1 A:FES502 0.0 18.5 1.0
S2 A:FES502 2.3 21.7 1.0
S1 A:FES502 2.3 20.4 1.0
SG A:CYS90 2.3 14.8 1.0
SG A:CYS69 2.3 18.0 1.0
FE2 A:FES502 2.7 14.9 1.0
CB A:CYS90 3.1 17.0 1.0
CB A:CYS69 3.2 16.2 1.0
CB A:TYR92 4.0 17.1 1.0
CB A:HIS71 4.0 16.2 1.0
CG2 A:VAL74 4.1 15.6 1.0
N A:HIS93 4.4 18.4 1.0
CA A:CYS90 4.5 16.9 1.0
ND1 A:HIS71 4.6 13.9 1.0
ND1 A:HIS93 4.6 17.5 1.0
CA A:CYS69 4.6 15.8 1.0
N A:TYR92 4.8 18.1 1.0
CB A:TRP95 4.8 16.8 1.0
CG A:HIS71 4.8 15.5 1.0
CA A:TYR92 4.8 18.2 1.0
N A:ARG72 4.9 16.5 1.0
CG A:TRP95 5.0 14.9 1.0
N A:HIS71 5.0 17.5 1.0
C A:CYS90 5.0 16.6 1.0

Iron binding site 3 out of 15 in 4nba

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Iron binding site 3 out of 15 in the Carbazole-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-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:14.9
occ:1.00
 FE2 A:FES502 0.0 14.9 1.0
ND1 A:HIS93 2.2 17.5 1.0
ND1 A:HIS71 2.2 13.9 1.0
S1 A:FES502 2.2 20.4 1.0
S2 A:FES502 2.3 21.7 1.0
FE1 A:FES502 2.7 18.5 1.0
CG A:HIS71 3.0 15.5 1.0
CG A:HIS93 3.1 18.4 1.0
CE1 A:HIS93 3.1 18.4 1.0
CE1 A:HIS71 3.2 16.6 1.0
CB A:HIS71 3.2 16.2 1.0
CB A:HIS93 3.4 16.9 1.0
N A:HIS93 3.6 18.4 1.0
CB A:TYR92 3.9 17.1 1.0
CA A:HIS93 4.1 18.7 1.0
NE2 A:HIS93 4.2 18.4 1.0
CD2 A:HIS93 4.2 19.0 1.0
CD2 A:HIS71 4.2 13.7 1.0
CG A:TYR92 4.3 18.1 1.0
NE2 A:HIS71 4.3 14.6 1.0
N A:ARG72 4.3 16.5 1.0
CG A:ARG72 4.3 18.3 1.0
CD2 A:TYR92 4.3 18.4 1.0
SG A:CYS69 4.4 18.0 1.0
C A:TYR92 4.5 18.4 1.0
CD1 A:TRP95 4.6 14.8 1.0
NE1 A:TRP95 4.6 16.1 1.0
CA A:HIS71 4.6 16.7 1.0
SG A:CYS90 4.6 14.8 1.0
CB A:ARG72 4.7 17.4 1.0
CA A:TYR92 4.8 18.2 1.0
C A:HIS93 4.9 18.5 1.0
C A:HIS71 4.9 16.6 1.0
CG A:TRP95 5.0 14.9 1.0

Iron binding site 4 out of 15 in 4nba

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Iron binding site 4 out of 15 in the Carbazole-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-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:44.0
occ:1.00
 O B:HOH821 1.8 41.1 1.0
OD1 B:ASP333 2.1 29.0 1.0
NE2 B:HIS183 2.2 20.4 1.0
NE2 B:HIS187 2.2 31.8 1.0
OD2 B:ASP333 2.5 27.4 1.0
CG B:ASP333 2.6 27.5 1.0
CD2 B:HIS183 2.9 17.4 1.0
CD2 B:HIS187 3.2 29.8 1.0
CE1 B:HIS187 3.3 30.9 1.0
CE1 B:HIS183 3.4 18.3 1.0
CB B:ASP333 4.1 25.3 1.0
CG B:HIS183 4.2 20.3 1.0
O B:HOH806 4.2 34.6 1.0
O B:HOH620 4.3 21.4 1.0
ND2 B:ASN177 4.3 26.6 1.0
C1 B:9CA503 4.3 38.2 1.0
CG B:HIS187 4.3 30.5 1.0
ND1 B:HIS187 4.3 32.0 1.0
ND1 B:HIS183 4.4 19.2 1.0
ND2 B:ASN330 4.4 24.7 1.0
C9A B:9CA503 4.4 38.8 1.0
CD1 B:ILE186 4.6 26.0 1.0
C2 B:9CA503 4.6 37.5 1.0
CE2 B:PHE329 4.7 24.4 1.0
O B:ASN177 4.7 26.9 1.0
C4A B:9CA503 4.8 37.9 1.0
N9 B:9CA503 4.8 39.2 1.0
CA B:ASP333 4.9 26.1 1.0
CG1 B:ILE186 5.0 25.0 1.0
C3 B:9CA503 5.0 38.9 1.0

Iron binding site 5 out of 15 in 4nba

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Iron binding site 5 out of 15 in the Carbazole-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-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:14.2
occ:1.00
 FE1 B:FES502 0.0 14.2 1.0
S1 B:FES502 2.2 18.7 1.0
S2 B:FES502 2.2 18.9 1.0
SG B:CYS69 2.2 15.5 1.0
SG B:CYS90 2.3 21.7 1.0
FE2 B:FES502 2.7 17.4 1.0
CB B:CYS69 3.1 15.0 1.0
CB B:CYS90 3.1 13.6 1.0
CB B:HIS71 4.0 13.6 1.0
CB B:TYR92 4.1 13.9 1.0
CG2 B:VAL74 4.2 10.5 1.0
N B:HIS93 4.4 16.4 1.0
ND1 B:HIS93 4.5 11.1 1.0
CA B:CYS69 4.5 14.4 1.0
ND1 B:HIS71 4.6 14.5 1.0
CA B:CYS90 4.6 15.3 1.0
CB B:TRP95 4.7 13.4 1.0
CG B:HIS71 4.8 13.1 1.0
CG B:TRP95 4.8 13.8 1.0
N B:ARG72 4.9 13.7 1.0
N B:TYR92 4.9 15.7 1.0
CA B:TYR92 4.9 16.0 1.0
CD2 B:LEU76 4.9 19.7 1.0
N B:HIS71 5.0 15.2 1.0
N B:TRP95 5.0 15.8 1.0

Iron binding site 6 out of 15 in 4nba

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Iron binding site 6 out of 15 in the Carbazole-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-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:17.4
occ:1.00
 FE2 B:FES502 0.0 17.4 1.0
ND1 B:HIS93 2.1 11.1 1.0
ND1 B:HIS71 2.2 14.5 1.0
S2 B:FES502 2.2 18.9 1.0
S1 B:FES502 2.3 18.7 1.0
FE1 B:FES502 2.7 14.2 1.0
CG B:HIS93 3.0 16.4 1.0
CG B:HIS71 3.0 13.1 1.0
CE1 B:HIS93 3.1 14.3 1.0
CB B:HIS71 3.2 13.6 1.0
CE1 B:HIS71 3.2 16.4 1.0
CB B:HIS93 3.3 15.8 1.0
N B:HIS93 3.7 16.4 1.0
CB B:TYR92 3.9 13.9 1.0
CA B:HIS93 4.1 17.2 1.0
NE2 B:HIS93 4.1 14.3 1.0
CD2 B:HIS93 4.1 14.1 1.0
CD2 B:HIS71 4.2 13.1 1.0
CG B:ARG72 4.3 13.1 1.0
CG B:TYR92 4.3 14.4 1.0
SG B:CYS69 4.3 15.5 1.0
NE2 B:HIS71 4.3 13.2 1.0
CD2 B:TYR92 4.3 13.5 1.0
N B:ARG72 4.3 13.7 1.0
CD1 B:TRP95 4.5 14.8 1.0
C B:TYR92 4.6 16.3 1.0
NE1 B:TRP95 4.6 11.3 1.0
CA B:HIS71 4.6 14.8 1.0
SG B:CYS90 4.6 21.7 1.0
CB B:ARG72 4.7 13.6 1.0
CA B:TYR92 4.8 16.0 1.0
C B:HIS71 4.9 13.4 1.0
C B:HIS93 4.9 15.4 1.0
CG B:TRP95 4.9 13.8 1.0
CE2 B:TRP95 5.0 13.7 1.0

Iron binding site 7 out of 15 in 4nba

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Iron binding site 7 out of 15 in the Carbazole-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-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:35.9
occ:1.00
 O C:HOH647 1.9 33.6 1.0
OD1 C:ASP333 2.0 22.2 1.0
NE2 C:HIS187 2.1 19.1 1.0
NE2 C:HIS183 2.2 15.5 1.0
OD2 C:ASP333 2.5 24.0 1.0
CG C:ASP333 2.5 23.7 1.0
CD2 C:HIS183 2.9 14.4 1.0
CE1 C:HIS187 3.0 22.0 1.0
CD2 C:HIS187 3.1 19.9 1.0
CE1 C:HIS183 3.4 15.9 1.0
CB C:ASP333 4.0 21.3 1.0
CG C:HIS183 4.1 16.2 1.0
ND1 C:HIS187 4.2 19.7 1.0
ND2 C:ASN177 4.2 23.4 1.0
CG C:HIS187 4.3 21.0 1.0
O C:HOH626 4.3 19.4 1.0
ND1 C:HIS183 4.3 15.8 1.0
CD1 C:ILE186 4.4 21.0 1.0
ND2 C:ASN330 4.5 20.4 1.0
C1 C:9CA503 4.5 36.5 1.0
CE2 C:PHE329 4.5 21.8 1.0
C9A C:9CA503 4.6 37.4 1.0
C2 C:9CA503 4.8 34.4 1.0
CA C:ASP333 4.8 21.2 1.0
O C:ASN177 4.8 20.5 1.0
CG1 C:ILE186 4.9 19.2 1.0
C4A C:9CA503 4.9 36.8 1.0

Iron binding site 8 out of 15 in 4nba

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Iron binding site 8 out of 15 in the Carbazole-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-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:21.3
occ:1.00
 FE1 C:FES502 0.0 21.3 1.0
SG C:CYS69 2.1 21.4 1.0
S1 C:FES502 2.3 23.5 1.0
SG C:CYS90 2.3 22.9 1.0
S2 C:FES502 2.3 23.0 1.0
FE2 C:FES502 2.8 23.9 1.0
CB C:CYS69 3.0 20.8 1.0
CB C:CYS90 3.1 22.8 1.0
CB C:HIS71 4.0 21.8 1.0
CB C:TYR92 4.0 21.5 1.0
CG2 C:VAL74 4.3 17.3 1.0
CA C:CYS69 4.5 21.6 1.0
N C:HIS93 4.5 23.5 1.0
CA C:CYS90 4.5 22.6 1.0
ND1 C:HIS93 4.6 23.1 1.0
ND1 C:HIS71 4.7 22.7 1.0
CB C:TRP95 4.8 24.4 1.0
N C:TYR92 4.8 23.2 1.0
CD2 C:LEU76 4.9 26.8 1.0
CG C:HIS71 4.9 21.4 1.0
N C:ARG72 4.9 20.7 1.0
CA C:TYR92 4.9 23.1 1.0
N C:HIS71 5.0 22.6 1.0
CG C:TRP95 5.0 23.3 1.0

Iron binding site 9 out of 15 in 4nba

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Iron binding site 9 out of 15 in the Carbazole-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-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:23.9
occ:1.00
 FE2 C:FES502 0.0 23.9 1.0
ND1 C:HIS93 2.1 23.1 1.0
ND1 C:HIS71 2.2 22.7 1.0
S1 C:FES502 2.3 23.5 1.0
S2 C:FES502 2.4 23.0 1.0
FE1 C:FES502 2.8 21.3 1.0
CG C:HIS93 3.0 24.5 1.0
CE1 C:HIS93 3.1 26.8 1.0
CG C:HIS71 3.1 21.4 1.0
CB C:HIS71 3.2 21.8 1.0
CE1 C:HIS71 3.3 20.4 1.0
CB C:HIS93 3.3 23.8 1.0
N C:HIS93 3.7 23.5 1.0
CB C:TYR92 3.8 21.5 1.0
CA C:HIS93 4.1 24.6 1.0
CD2 C:HIS93 4.1 26.7 1.0
NE2 C:HIS93 4.1 25.4 1.0
SG C:CYS69 4.2 21.4 1.0
CD2 C:HIS71 4.3 20.9 1.0
CG C:TYR92 4.3 23.6 1.0
CG C:ARG72 4.3 25.2 1.0
NE2 C:HIS71 4.3 21.0 1.0
CD2 C:TYR92 4.3 23.4 1.0
N C:ARG72 4.4 20.7 1.0
C C:TYR92 4.5 23.0 1.0
CD1 C:TRP95 4.5 24.3 1.0
NE1 C:TRP95 4.6 23.0 1.0
CA C:HIS71 4.6 22.1 1.0
SG C:CYS90 4.7 22.9 1.0
CB C:ARG72 4.8 23.3 1.0
CA C:TYR92 4.8 23.1 1.0
C C:HIS93 4.9 25.1 1.0
C C:HIS71 4.9 21.7 1.0
CG C:TRP95 5.0 23.3 1.0

Iron binding site 10 out of 15 in 4nba

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Iron binding site 10 out of 15 in the Carbazole-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-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:18.1
occ:1.00
 FE1 D:FES201 0.0 18.1 1.0
ND1 D:HIS48 2.1 18.4 1.0
ND1 D:HIS68 2.2 17.5 1.0
S1 D:FES201 2.2 20.9 1.0
S2 D:FES201 2.2 20.6 1.0
FE2 D:FES201 2.7 22.8 1.0
CE1 D:HIS48 3.0 18.7 1.0
CE1 D:HIS68 3.1 18.5 1.0
CG D:HIS48 3.1 19.5 1.0
CG D:HIS68 3.2 18.4 1.0
CB D:HIS48 3.5 20.4 1.0
CB D:HIS68 3.6 17.8 1.0
O D:HOH301 3.7 17.8 1.0
N D:HIS68 4.1 17.9 1.0
NE2 D:HIS48 4.1 17.7 1.0
CB D:PHE67 4.2 19.1 1.0
CD2 D:HIS48 4.2 18.9 1.0
NE2 D:HIS68 4.2 19.2 1.0
C D:HIS48 4.3 22.4 1.0
O D:HIS48 4.3 24.7 1.0
CD2 D:HIS68 4.3 17.6 1.0
SG D:CYS46 4.5 22.9 1.0
CA D:HIS68 4.5 18.1 1.0
CA D:HIS48 4.5 21.3 1.0
SG D:CYS65 4.5 21.2 1.0
CG D:PRO83 4.6 23.2 1.0
N D:GLY49 4.6 22.5 1.0
O A:VAL351 4.8 17.2 1.0
O A:GLU353 4.9 14.5 1.0
C D:PHE67 4.9 19.1 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 07:19:26 2024

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