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Iron in PDB 3vmi: Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase

Enzymatic activity of Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase

All present enzymatic activity of Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase:
1.14.12.22;

Protein crystallography data

The structure of Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 3vmi was solved by Y.Ashikawa, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.68 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.012, 89.611, 104.820, 90.00, 104.18, 90.00
R / Rfree (%) 20.5 / 24

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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase (pdb code 3vmi). 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 3vmi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in 3vmi

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

b:33.3
occ:1.00
 O2 A:OXY601 1.9 43.2 1.0
OD1 A:ASP333 1.9 30.6 1.0
NE2 A:HIS183 2.1 30.5 1.0
NE2 A:HIS187 2.1 34.7 1.0
O1 A:OXY601 2.5 45.1 1.0
CG A:ASP333 2.6 32.1 1.0
OD2 A:ASP333 2.7 32.5 1.0
CD2 A:HIS183 2.9 28.8 1.0
CE1 A:HIS187 3.0 34.7 1.0
CD2 A:HIS187 3.1 33.3 1.0
CE1 A:HIS183 3.1 28.3 1.0
CB A:ASP333 4.1 30.0 1.0
CG A:HIS183 4.1 28.9 1.0
ND1 A:HIS187 4.1 34.4 1.0
ND1 A:HIS183 4.2 27.2 1.0
CG A:HIS187 4.2 33.9 1.0
ND2 A:ASN177 4.2 27.5 1.0
O A:HOH522 4.3 34.2 1.0
CE2 A:PHE329 4.4 33.7 1.0
ND2 A:ASN330 4.5 31.8 1.0
CD1 A:ILE186 4.5 31.2 1.0
CA A:ASP333 4.8 31.7 1.0
CG1 A:ILE186 4.9 30.7 1.0
O A:ASN177 5.0 28.9 1.0

Iron binding site 2 out of 15 in 3vmi

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Iron binding site 2 out of 15 in the Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:31.9
occ:1.00
 FE1 A:FES401 0.0 31.9 1.0
SG A:CYS90 2.3 29.9 1.0
S2 A:FES401 2.3 32.5 1.0
S1 A:FES401 2.3 30.0 1.0
SG A:CYS69 2.4 30.1 1.0
FE2 A:FES401 2.8 33.5 1.0
CB A:CYS90 3.1 30.6 1.0
CB A:CYS69 3.2 31.9 1.0
CB A:TYR92 4.0 32.9 1.0
CB A:HIS71 4.1 33.5 1.0
CG2 A:VAL74 4.2 31.7 1.0
N A:HIS93 4.4 33.5 1.0
ND1 A:HIS93 4.5 34.4 1.0
CA A:CYS90 4.5 31.6 1.0
ND1 A:HIS71 4.6 32.9 1.0
CA A:CYS69 4.7 31.7 1.0
CB A:TRP95 4.7 30.2 1.0
N A:TYR92 4.8 31.4 1.0
CG A:HIS71 4.8 34.5 1.0
CA A:TYR92 4.8 32.9 1.0
N A:ARG72 4.9 33.6 1.0
CG A:TRP95 5.0 30.0 1.0
CD2 A:LEU76 5.0 37.9 1.0
C A:CYS90 5.0 33.5 1.0

Iron binding site 3 out of 15 in 3vmi

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Iron binding site 3 out of 15 in the Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:33.5
occ:1.00
 FE2 A:FES401 0.0 33.5 1.0
ND1 A:HIS93 2.1 34.4 1.0
S1 A:FES401 2.1 30.0 1.0
ND1 A:HIS71 2.2 32.9 1.0
S2 A:FES401 2.3 32.5 1.0
FE1 A:FES401 2.8 31.9 1.0
CG A:HIS93 3.0 34.4 1.0
CG A:HIS71 3.1 34.5 1.0
CE1 A:HIS93 3.1 33.6 1.0
CE1 A:HIS71 3.2 33.8 1.0
CB A:HIS71 3.3 33.5 1.0
CB A:HIS93 3.3 32.9 1.0
N A:HIS93 3.6 33.5 1.0
CB A:TYR92 3.8 32.9 1.0
CA A:HIS93 4.1 33.3 1.0
CD2 A:HIS93 4.1 34.7 1.0
NE2 A:HIS93 4.1 35.9 1.0
CD2 A:HIS71 4.2 33.0 1.0
CG A:TYR92 4.3 35.3 1.0
NE2 A:HIS71 4.3 33.4 1.0
CG A:ARG72 4.3 35.5 1.0
CD2 A:TYR92 4.4 35.0 1.0
N A:ARG72 4.4 33.6 1.0
SG A:CYS69 4.4 30.1 1.0
C A:TYR92 4.5 33.2 1.0
CD1 A:TRP95 4.6 31.1 1.0
SG A:CYS90 4.6 29.9 1.0
CA A:HIS71 4.6 33.6 1.0
NE1 A:TRP95 4.7 29.4 1.0
CB A:ARG72 4.7 32.9 1.0
CA A:TYR92 4.8 32.9 1.0
C A:HIS93 4.8 32.3 1.0
C A:HIS71 4.9 33.3 1.0
CG A:TRP95 5.0 30.0 1.0

Iron binding site 4 out of 15 in 3vmi

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

b:44.5
occ:1.00
 O1 B:OXY602 1.8 57.6 1.0
O2 B:OXY602 1.8 58.0 1.0
OD1 B:ASP333 2.0 40.6 1.0
NE2 B:HIS183 2.0 36.7 1.0
NE2 B:HIS187 2.2 44.3 1.0
CG B:ASP333 2.5 40.5 1.0
OD2 B:ASP333 2.6 39.2 1.0
CD2 B:HIS183 2.9 34.4 1.0
CE1 B:HIS183 3.0 36.4 1.0
CD2 B:HIS187 3.2 43.9 1.0
CE1 B:HIS187 3.2 45.1 1.0
CB B:ASP333 4.0 40.6 1.0
CG B:HIS183 4.1 35.1 1.0
ND1 B:HIS183 4.1 34.7 1.0
O B:HOH431 4.1 36.6 1.0
ND2 B:ASN177 4.3 40.2 1.0
ND1 B:HIS187 4.3 45.0 1.0
CG B:HIS187 4.3 45.1 1.0
CD1 B:ILE186 4.3 45.1 1.0
ND2 B:ASN330 4.4 39.5 1.0
C9A B:9CA2001 4.5 49.0 1.0
N9 B:9CA2001 4.5 49.8 1.0
C1 B:9CA2001 4.6 47.7 1.0
CE2 B:PHE329 4.8 37.3 1.0
CG1 B:ILE186 4.8 42.3 1.0
CA B:ASP333 4.8 42.9 1.0
O B:ASN177 4.9 40.0 1.0
C4A B:9CA2001 4.9 48.8 1.0
CG B:ASN177 5.0 42.3 1.0

Iron binding site 5 out of 15 in 3vmi

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Iron binding site 5 out of 15 in the Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:29.1
occ:1.00
 FE1 B:FES401 0.0 29.1 1.0
S1 B:FES401 2.2 24.2 1.0
S2 B:FES401 2.2 29.9 1.0
SG B:CYS69 2.3 30.8 1.0
SG B:CYS90 2.3 31.6 1.0
FE2 B:FES401 2.7 30.7 1.0
CB B:CYS69 3.1 30.3 1.0
CB B:CYS90 3.1 30.0 1.0
CB B:TYR92 4.0 30.6 1.0
CB B:HIS71 4.1 26.6 1.0
CG2 B:VAL74 4.2 25.0 1.0
ND1 B:HIS93 4.4 27.5 1.0
N B:HIS93 4.4 28.7 1.0
CA B:CYS69 4.6 29.1 1.0
CA B:CYS90 4.6 28.8 1.0
ND1 B:HIS71 4.6 28.2 1.0
CB B:TRP95 4.7 27.2 1.0
N B:TYR92 4.8 28.1 1.0
CG B:HIS71 4.9 28.9 1.0
N B:ARG72 4.9 26.0 1.0
CA B:TYR92 4.9 29.3 1.0
CG B:TRP95 4.9 29.5 1.0

Iron binding site 6 out of 15 in 3vmi

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Iron binding site 6 out of 15 in the Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:30.7
occ:1.00
 FE2 B:FES401 0.0 30.7 1.0
ND1 B:HIS93 2.0 27.5 1.0
S2 B:FES401 2.3 29.9 1.0
ND1 B:HIS71 2.3 28.2 1.0
S1 B:FES401 2.3 24.2 1.0
FE1 B:FES401 2.7 29.1 1.0
CE1 B:HIS93 2.9 25.4 1.0
CG B:HIS93 3.0 27.9 1.0
CG B:HIS71 3.1 28.9 1.0
CB B:HIS71 3.3 26.6 1.0
CE1 B:HIS71 3.3 27.4 1.0
CB B:HIS93 3.4 27.1 1.0
N B:HIS93 3.6 28.7 1.0
CB B:TYR92 3.8 30.6 1.0
NE2 B:HIS93 4.0 25.8 1.0
CD2 B:HIS93 4.1 24.9 1.0
CA B:HIS93 4.1 27.5 1.0
CG B:TYR92 4.3 32.6 1.0
SG B:CYS69 4.3 30.8 1.0
CD2 B:HIS71 4.3 25.8 1.0
CG B:ARG72 4.3 28.1 1.0
CD2 B:TYR92 4.3 31.2 1.0
N B:ARG72 4.3 26.0 1.0
NE2 B:HIS71 4.4 25.6 1.0
C B:TYR92 4.5 28.8 1.0
SG B:CYS90 4.6 31.6 1.0
CD1 B:TRP95 4.6 28.3 1.0
CA B:HIS71 4.6 27.4 1.0
NE1 B:TRP95 4.7 29.1 1.0
CB B:ARG72 4.7 27.4 1.0
CA B:TYR92 4.8 29.3 1.0
C B:HIS93 4.9 27.1 1.0
C B:HIS71 4.9 27.7 1.0
CG B:TRP95 5.0 29.5 1.0

Iron binding site 7 out of 15 in 3vmi

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

b:35.3
occ:1.00
 O2 C:OXY603 1.8 51.8 1.0
O1 C:OXY603 1.8 49.6 1.0
OD1 C:ASP333 1.9 33.6 1.0
NE2 C:HIS187 2.1 39.4 1.0
NE2 C:HIS183 2.1 32.4 1.0
CG C:ASP333 2.5 34.9 1.0
OD2 C:ASP333 2.6 34.1 1.0
CD2 C:HIS183 2.9 28.6 1.0
CE1 C:HIS187 3.0 38.5 1.0
CD2 C:HIS187 3.1 36.7 1.0
CE1 C:HIS183 3.3 30.2 1.0
CB C:ASP333 4.0 34.5 1.0
ND1 C:HIS187 4.1 37.5 1.0
CG C:HIS183 4.1 29.9 1.0
CG C:HIS187 4.2 37.4 1.0
O C:HOH454 4.2 33.5 1.0
CD1 C:ILE186 4.3 37.0 1.0
ND1 C:HIS183 4.3 30.3 1.0
ND2 C:ASN330 4.4 33.5 1.0
ND2 C:ASN177 4.5 44.9 1.0
C9A C:9CA2002 4.5 47.9 1.0
C1 C:9CA2002 4.5 46.2 1.0
N9 C:9CA2002 4.7 47.4 1.0
OD1 C:ASN177 4.7 45.1 1.0
CE2 C:PHE329 4.7 33.1 1.0
CA C:ASP333 4.7 35.1 1.0
O C:ASN177 4.8 38.5 1.0
CG1 C:ILE186 4.8 35.2 1.0
CG C:ASN177 4.9 43.6 1.0

Iron binding site 8 out of 15 in 3vmi

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Iron binding site 8 out of 15 in the Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:35.8
occ:1.00
 FE1 C:FES401 0.0 35.8 1.0
SG C:CYS69 2.2 34.3 1.0
S2 C:FES401 2.3 35.9 1.0
S1 C:FES401 2.3 37.4 1.0
SG C:CYS90 2.3 34.2 1.0
FE2 C:FES401 2.8 36.3 1.0
CB C:CYS69 3.0 33.8 1.0
CB C:CYS90 3.1 34.5 1.0
CB C:TYR92 4.0 35.3 1.0
CB C:HIS71 4.1 36.0 1.0
CG2 C:VAL74 4.2 31.1 1.0
N C:HIS93 4.5 37.8 1.0
ND1 C:HIS93 4.5 36.7 1.0
CA C:CYS69 4.5 34.0 1.0
CA C:CYS90 4.6 35.8 1.0
ND1 C:HIS71 4.7 36.4 1.0
CB C:TRP95 4.8 36.6 1.0
N C:TYR92 4.8 37.2 1.0
N C:ARG72 4.9 34.6 1.0
CA C:TYR92 4.9 38.0 1.0
CG C:HIS71 4.9 36.1 1.0
CG C:TYR92 5.0 37.1 1.0

Iron binding site 9 out of 15 in 3vmi

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Iron binding site 9 out of 15 in the Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in 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 Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:36.3
occ:1.00
 FE2 C:FES401 0.0 36.3 1.0
ND1 C:HIS93 2.1 36.7 1.0
S1 C:FES401 2.3 37.4 1.0
S2 C:FES401 2.3 35.9 1.0
ND1 C:HIS71 2.3 36.4 1.0
FE1 C:FES401 2.8 35.8 1.0
CG C:HIS93 3.0 37.7 1.0
CE1 C:HIS93 3.0 37.2 1.0
CG C:HIS71 3.2 36.1 1.0
CB C:HIS71 3.3 36.0 1.0
CB C:HIS93 3.3 38.7 1.0
CE1 C:HIS71 3.4 35.2 1.0
N C:HIS93 3.7 37.8 1.0
CB C:TYR92 3.9 35.3 1.0
CD2 C:HIS93 4.1 38.9 1.0
NE2 C:HIS93 4.1 38.3 1.0
CA C:HIS93 4.1 38.4 1.0
CD2 C:TYR92 4.2 36.8 1.0
CG C:TYR92 4.3 37.1 1.0
SG C:CYS69 4.3 34.3 1.0
CG C:ARG72 4.3 38.2 1.0
N C:ARG72 4.3 34.6 1.0
CD2 C:HIS71 4.4 36.0 1.0
NE2 C:HIS71 4.4 36.2 1.0
C C:TYR92 4.5 37.7 1.0
CD1 C:TRP95 4.6 37.6 1.0
CA C:HIS71 4.7 35.3 1.0
SG C:CYS90 4.7 34.2 1.0
CB C:ARG72 4.7 35.1 1.0
NE1 C:TRP95 4.8 36.1 1.0
CA C:TYR92 4.8 38.0 1.0
C C:HIS93 4.9 39.1 1.0
C C:HIS71 5.0 35.0 1.0

Iron binding site 10 out of 15 in 3vmi

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

b:33.1
occ:1.00
 FE1 D:FES201 0.0 33.1 1.0
ND1 D:HIS48 2.1 32.2 1.0
S1 D:FES201 2.1 33.5 1.0
ND1 D:HIS68 2.2 32.6 1.0
S2 D:FES201 2.3 33.2 1.0
FE2 D:FES201 2.7 33.1 1.0
CE1 D:HIS48 3.0 28.4 1.0
CE1 D:HIS68 3.0 34.2 1.0
CG D:HIS48 3.2 31.6 1.0
CG D:HIS68 3.2 33.2 1.0
CB D:HIS48 3.6 31.5 1.0
CB D:HIS68 3.6 32.9 1.0
O A:HOH419 3.8 31.7 1.0
NE2 D:HIS48 4.1 30.1 1.0
N D:HIS68 4.2 33.1 1.0
CB D:PHE67 4.2 34.9 1.0
NE2 D:HIS68 4.2 34.9 1.0
CD2 D:HIS48 4.2 31.6 1.0
C D:HIS48 4.3 35.0 1.0
O D:HIS48 4.3 36.9 1.0
CD2 D:HIS68 4.3 32.0 1.0
SG D:CYS46 4.4 34.0 1.0
SG D:CYS65 4.5 35.2 1.0
CA D:HIS68 4.5 33.7 1.0
CG D:PRO83 4.5 35.5 1.0
CA D:HIS48 4.5 34.0 1.0
N D:GLY49 4.6 35.0 1.0
O A:VAL351 4.8 32.0 1.0
O A:GLU353 4.9 28.5 1.0
C D:PHE67 5.0 34.1 1.0

Reference:

Y.Ashikawa, Z.Fujimoto, Y.Usami, K.Inoue, H.Noguchi, H.Yamane, H.Nojiri. Structural Insight Into the Substrate- and Dioxygenbinding Manner in the Catalytic Cycle of Rieske Nonheme Iron Oxygenase System, Carbazole 1,9ADIOXYGENASE Bmc Struct.Biol. V. 12 15 2012.
ISSN: ESSN 1472-6807
PubMed: 22727022
DOI: 10.1186/1472-6807-12-15
Page generated: Sun Aug 4 22:03:54 2024

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