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Iron in PDB 4nbc: Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)

Enzymatic activity of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)

All present enzymatic activity of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1):
1.14.12.22;

Protein crystallography data

The structure of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1), PDB code: 4nbc 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) 39.28 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.495, 90.083, 105.384, 90.00, 104.20, 90.00
R / Rfree (%) 18.8 / 21.5

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) (pdb code 4nbc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1), PDB code: 4nbc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in 4nbc

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Iron binding site 1 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:28.1
occ:1.00
 OD1 A:ASP333 1.9 18.3 1.0
O A:HOH622 2.0 31.0 1.0
NE2 A:HIS183 2.1 19.0 1.0
NE2 A:HIS187 2.2 20.9 1.0
CG A:ASP333 2.5 17.5 1.0
OD2 A:ASP333 2.6 18.5 1.0
CD2 A:HIS183 2.8 17.9 1.0
CE1 A:HIS187 3.1 22.7 1.0
CD2 A:HIS187 3.2 22.2 1.0
CE1 A:HIS183 3.3 18.3 1.0
CB A:ASP333 4.0 17.4 1.0
CG A:HIS183 4.1 15.9 1.0
ND2 A:ASN177 4.1 16.4 1.0
O A:HOH630 4.2 37.8 1.0
ND1 A:HIS187 4.2 21.5 1.0
ND1 A:HIS183 4.3 17.6 1.0
CG A:HIS187 4.3 21.4 1.0
O A:HOH653 4.4 20.9 1.0
CE2 A:PHE329 4.4 21.4 1.0
ND2 A:ASN330 4.5 18.1 1.0
CD1 A:ILE186 4.6 16.4 1.0
CA A:ASP333 4.7 18.0 1.0
O A:ASN177 5.0 16.4 1.0

Iron binding site 2 out of 15 in 4nbc

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Iron binding site 2 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.0
occ:1.00
 FE1 A:FES502 0.0 19.0 1.0
S1 A:FES502 2.2 17.2 1.0
S2 A:FES502 2.3 16.9 1.0
SG A:CYS90 2.3 18.7 1.0
SG A:CYS69 2.4 16.6 1.0
FE2 A:FES502 2.8 19.0 1.0
CB A:CYS90 3.1 13.7 1.0
CB A:CYS69 3.1 14.8 1.0
CB A:HIS71 4.1 14.8 1.0
CB A:TYR92 4.1 17.5 1.0
CG2 A:VAL74 4.2 15.8 1.0
N A:HIS93 4.5 14.7 1.0
ND1 A:HIS93 4.5 14.1 1.0
CA A:CYS90 4.6 15.6 1.0
ND1 A:HIS71 4.6 15.1 1.0
CA A:CYS69 4.6 15.5 1.0
CB A:TRP95 4.7 13.3 1.0
CG A:HIS71 4.8 16.0 1.0
N A:TYR92 4.8 16.8 1.0
N A:ARG72 4.8 14.3 1.0
CG A:TRP95 4.9 13.7 1.0
CA A:TYR92 4.9 16.6 1.0

Iron binding site 3 out of 15 in 4nbc

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Iron binding site 3 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.0
occ:1.00
 FE2 A:FES502 0.0 19.0 1.0
ND1 A:HIS93 2.1 14.1 1.0
ND1 A:HIS71 2.2 15.1 1.0
S1 A:FES502 2.2 17.2 1.0
S2 A:FES502 2.3 16.9 1.0
FE1 A:FES502 2.8 19.0 1.0
CE1 A:HIS93 3.0 15.9 1.0
CG A:HIS71 3.1 16.0 1.0
CG A:HIS93 3.1 16.0 1.0
CE1 A:HIS71 3.2 16.2 1.0
CB A:HIS71 3.3 14.8 1.0
CB A:HIS93 3.4 14.1 1.0
N A:HIS93 3.7 14.7 1.0
CB A:TYR92 3.9 17.5 1.0
NE2 A:HIS93 4.1 16.4 1.0
CA A:HIS93 4.1 15.7 1.0
CD2 A:HIS93 4.2 15.7 1.0
CD2 A:HIS71 4.2 13.8 1.0
NE2 A:HIS71 4.3 15.9 1.0
CG A:TYR92 4.3 18.5 1.0
CD2 A:TYR92 4.3 18.1 1.0
N A:ARG72 4.3 14.3 1.0
CG A:ARG72 4.4 16.2 1.0
SG A:CYS69 4.4 16.6 1.0
C A:TYR92 4.5 16.3 1.0
CD1 A:TRP95 4.6 14.1 1.0
NE1 A:TRP95 4.6 15.0 1.0
CA A:HIS71 4.6 15.1 1.0
SG A:CYS90 4.7 18.7 1.0
CB A:ARG72 4.7 15.7 1.0
CA A:TYR92 4.8 16.6 1.0
C A:HIS71 4.9 15.3 1.0
C A:HIS93 4.9 14.9 1.0
CG A:TRP95 4.9 13.7 1.0

Iron binding site 4 out of 15 in 4nbc

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Iron binding site 4 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:36.0
occ:1.00
 OD1 B:ASP333 1.9 24.8 1.0
O B:HOH638 2.0 40.8 1.0
NE2 B:HIS183 2.0 22.9 1.0
NE2 B:HIS187 2.3 25.7 1.0
OD2 B:ASP333 2.4 23.9 1.0
CG B:ASP333 2.5 23.4 1.0
CD2 B:HIS183 2.9 20.4 1.0
CE1 B:HIS183 3.1 22.0 1.0
CD2 B:HIS187 3.2 26.1 1.0
CE1 B:HIS187 3.3 27.2 1.0
CB B:ASP333 4.0 23.0 1.0
ND2 B:ASN177 4.1 23.8 1.0
CG B:HIS183 4.1 20.6 1.0
O B:HOH636 4.2 41.1 1.0
ND1 B:HIS183 4.2 21.2 1.0
O B:HOH684 4.2 20.9 1.0
ND1 B:HIS187 4.4 26.1 1.0
CG B:HIS187 4.4 26.4 1.0
CE2 B:PHE329 4.5 24.9 1.0
O B:HOH821 4.5 37.8 1.0
CD1 B:ILE186 4.6 23.4 1.0
ND2 B:ASN330 4.6 23.8 1.0
CA B:ASP333 4.8 24.0 1.0
O B:ASN177 4.8 24.8 1.0
CG B:ASN177 5.0 24.1 1.0

Iron binding site 5 out of 15 in 4nbc

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Iron binding site 5 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:18.9
occ:1.00
 FE1 B:FES502 0.0 18.9 1.0
S2 B:FES502 2.2 14.4 1.0
S1 B:FES502 2.2 17.1 1.0
SG B:CYS69 2.3 17.0 1.0
SG B:CYS90 2.3 17.7 1.0
FE2 B:FES502 2.7 18.9 1.0
CB B:CYS69 3.1 13.7 1.0
CB B:CYS90 3.1 13.5 1.0
CB B:HIS71 4.1 12.5 1.0
CB B:TYR92 4.1 15.5 1.0
CG2 B:VAL74 4.2 13.8 1.0
N B:HIS93 4.4 13.8 1.0
ND1 B:HIS93 4.5 13.1 1.0
CA B:CYS69 4.6 13.8 1.0
ND1 B:HIS71 4.6 13.0 1.0
CA B:CYS90 4.6 14.9 1.0
CB B:TRP95 4.7 13.0 1.0
CG B:HIS71 4.8 11.9 1.0
N B:ARG72 4.8 14.2 1.0
N B:TYR92 4.8 14.0 1.0
CG B:TRP95 4.9 15.2 1.0
CA B:TYR92 4.9 15.4 1.0
N B:HIS71 5.0 14.1 1.0

Iron binding site 6 out of 15 in 4nbc

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Iron binding site 6 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:18.9
occ:1.00
 FE2 B:FES502 0.0 18.9 1.0
ND1 B:HIS93 2.1 13.1 1.0
ND1 B:HIS71 2.2 13.0 1.0
S1 B:FES502 2.3 17.1 1.0
S2 B:FES502 2.3 14.4 1.0
FE1 B:FES502 2.7 18.9 1.0
CG B:HIS93 3.0 13.8 1.0
CE1 B:HIS93 3.1 13.6 1.0
CG B:HIS71 3.1 11.9 1.0
CB B:HIS71 3.2 12.5 1.0
CE1 B:HIS71 3.3 13.6 1.0
CB B:HIS93 3.3 13.3 1.0
N B:HIS93 3.7 13.8 1.0
CB B:TYR92 3.9 15.5 1.0
CA B:HIS93 4.1 14.6 1.0
CD2 B:HIS93 4.1 12.2 1.0
NE2 B:HIS93 4.1 13.7 1.0
CG B:ARG72 4.3 15.6 1.0
CD2 B:HIS71 4.3 12.3 1.0
N B:ARG72 4.3 14.2 1.0
CD2 B:TYR92 4.3 14.8 1.0
CG B:TYR92 4.3 15.5 1.0
SG B:CYS69 4.3 17.0 1.0
NE2 B:HIS71 4.4 12.8 1.0
C B:TYR92 4.6 14.5 1.0
CD1 B:TRP95 4.6 14.4 1.0
CA B:HIS71 4.6 13.2 1.0
NE1 B:TRP95 4.6 15.3 1.0
SG B:CYS90 4.6 17.7 1.0
CB B:ARG72 4.7 15.5 1.0
CA B:TYR92 4.8 15.4 1.0
C B:HIS71 4.9 14.1 1.0
C B:HIS93 4.9 14.7 1.0
CG B:TRP95 5.0 15.2 1.0

Iron binding site 7 out of 15 in 4nbc

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Iron binding site 7 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:32.2
occ:1.00
 OD1 C:ASP333 1.9 21.0 1.0
O C:HOH653 2.0 33.2 1.0
NE2 C:HIS183 2.1 20.8 1.0
NE2 C:HIS187 2.2 17.9 1.0
CG C:ASP333 2.5 18.6 1.0
OD2 C:ASP333 2.6 19.4 1.0
CD2 C:HIS183 2.8 18.2 1.0
CD2 C:HIS187 3.2 19.3 1.0
CE1 C:HIS187 3.2 19.3 1.0
CE1 C:HIS183 3.3 20.3 1.0
CB C:ASP333 4.0 19.0 1.0
O C:HOH625 4.1 34.3 1.0
CG C:HIS183 4.1 16.7 1.0
ND2 C:ASN177 4.1 19.5 1.0
ND1 C:HIS183 4.2 17.2 1.0
ND1 C:HIS187 4.3 18.4 1.0
CG C:HIS187 4.3 18.2 1.0
O C:HOH604 4.3 19.9 1.0
CE2 C:PHE329 4.4 21.1 1.0
CD1 C:ILE186 4.5 21.5 1.0
ND2 C:ASN330 4.6 19.9 1.0
CA C:ASP333 4.8 18.1 1.0
O C:HOH819 4.8 35.8 1.0
O C:ASN177 4.9 19.0 1.0
CG1 C:ILE186 5.0 20.3 1.0

Iron binding site 8 out of 15 in 4nbc

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Iron binding site 8 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:22.0
occ:1.00
 FE1 C:FES502 0.0 22.0 1.0
S2 C:FES502 2.3 19.6 1.0
SG C:CYS69 2.3 20.9 1.0
S1 C:FES502 2.3 20.3 1.0
SG C:CYS90 2.3 19.9 1.0
FE2 C:FES502 2.7 21.5 1.0
CB C:CYS90 3.1 21.1 1.0
CB C:CYS69 3.1 19.6 1.0
CB C:TYR92 4.0 19.2 1.0
CB C:HIS71 4.1 17.3 1.0
CG2 C:VAL74 4.3 16.0 1.0
N C:HIS93 4.4 21.2 1.0
ND1 C:HIS93 4.5 23.3 1.0
CA C:CYS90 4.6 20.3 1.0
CA C:CYS69 4.6 19.6 1.0
ND1 C:HIS71 4.6 17.3 1.0
CB C:TRP95 4.8 20.2 1.0
N C:TYR92 4.8 18.9 1.0
CA C:TYR92 4.8 20.9 1.0
CG C:HIS71 4.9 17.6 1.0
N C:ARG72 4.9 18.7 1.0
CG C:TRP95 5.0 19.6 1.0
C C:CYS90 5.0 20.9 1.0

Iron binding site 9 out of 15 in 4nbc

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Iron binding site 9 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:21.5
occ:1.00
 FE2 C:FES502 0.0 21.5 1.0
ND1 C:HIS93 2.2 23.3 1.0
ND1 C:HIS71 2.2 17.3 1.0
S1 C:FES502 2.3 20.3 1.0
S2 C:FES502 2.3 19.6 1.0
FE1 C:FES502 2.7 22.0 1.0
CG C:HIS71 3.1 17.6 1.0
CG C:HIS93 3.1 23.5 1.0
CE1 C:HIS93 3.1 22.8 1.0
CB C:HIS71 3.2 17.3 1.0
CE1 C:HIS71 3.3 17.2 1.0
CB C:HIS93 3.4 22.0 1.0
N C:HIS93 3.7 21.2 1.0
CB C:TYR92 3.9 19.2 1.0
CA C:HIS93 4.1 22.9 1.0
CD2 C:HIS93 4.2 23.2 1.0
NE2 C:HIS93 4.2 22.9 1.0
CD2 C:HIS71 4.3 17.5 1.0
N C:ARG72 4.3 18.7 1.0
SG C:CYS69 4.3 20.9 1.0
CG C:ARG72 4.3 19.2 1.0
CG C:TYR92 4.3 19.9 1.0
NE2 C:HIS71 4.3 18.5 1.0
CD2 C:TYR92 4.4 19.1 1.0
CD1 C:TRP95 4.6 20.1 1.0
C C:TYR92 4.6 20.3 1.0
CA C:HIS71 4.6 18.6 1.0
NE1 C:TRP95 4.6 20.0 1.0
SG C:CYS90 4.7 19.9 1.0
CB C:ARG72 4.7 17.9 1.0
CA C:TYR92 4.8 20.9 1.0
C C:HIS71 4.9 18.3 1.0
C C:HIS93 4.9 23.2 1.0
CG C:TRP95 4.9 19.6 1.0

Iron binding site 10 out of 15 in 4nbc

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Iron binding site 10 out of 15 in the Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:20.6
occ:1.00
 FE1 D:FES201 0.0 20.6 1.0
ND1 D:HIS48 2.1 18.2 1.0
ND1 D:HIS68 2.2 16.1 1.0
S1 D:FES201 2.2 19.9 1.0
S2 D:FES201 2.3 20.7 1.0
FE2 D:FES201 2.7 21.5 1.0
CE1 D:HIS48 3.0 16.3 1.0
CE1 D:HIS68 3.1 16.0 1.0
CG D:HIS48 3.2 17.1 1.0
CG D:HIS68 3.2 15.2 1.0
CB D:HIS48 3.5 18.9 1.0
CB D:HIS68 3.6 16.6 1.0
O A:HOH662 3.9 17.5 1.0
NE2 D:HIS48 4.1 17.5 1.0
N D:HIS68 4.2 18.7 1.0
NE2 D:HIS68 4.2 17.4 1.0
O D:HIS48 4.2 21.2 1.0
CD2 D:HIS48 4.2 19.0 1.0
C D:HIS48 4.2 20.3 1.0
CB D:PHE67 4.2 19.6 1.0
CD2 D:HIS68 4.3 15.6 1.0
SG D:CYS46 4.5 20.6 1.0
CA D:HIS68 4.5 17.5 1.0
CA D:HIS48 4.5 18.9 1.0
CG D:PRO83 4.5 20.4 1.0
SG D:CYS65 4.5 20.2 1.0
N D:GLY49 4.6 20.5 1.0
O A:VAL351 4.9 18.2 1.0
O A:GLU353 4.9 14.7 1.0
C D:PHE67 5.0 19.8 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 07:20:40 2024

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