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

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

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

Protein crystallography data

The structure of Reduced Carbazole-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 3vmg 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) 40.62 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.156, 89.840, 105.207, 90.00, 104.40, 90.00
R / Rfree (%) 19.8 / 21.9

Iron Binding Sites:

Pages:

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

Binding sites:

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

Iron binding site 1 out of 15 in 3vmg

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Iron binding site 1 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:23.6
occ:1.00
 OD1 A:ASP333 1.9 21.9 1.0
O A:HOH887 1.9 35.3 1.0
NE2 A:HIS183 2.1 19.5 1.0
NE2 A:HIS187 2.1 22.2 1.0
CG A:ASP333 2.6 20.1 1.0
OD2 A:ASP333 2.7 20.0 1.0
CD2 A:HIS183 2.9 18.5 1.0
CE1 A:HIS187 3.1 21.8 1.0
CD2 A:HIS187 3.1 22.0 1.0
CE1 A:HIS183 3.1 18.4 1.0
CB A:ASP333 4.0 20.5 1.0
CG A:HIS183 4.1 18.4 1.0
O A:HOH451 4.2 34.3 1.0
ND1 A:HIS187 4.2 22.4 1.0
ND1 A:HIS183 4.2 18.8 1.0
ND2 A:ASN177 4.2 20.9 1.0
CG A:HIS187 4.2 22.4 1.0
O A:HOH524 4.3 22.6 1.0
ND2 A:ASN330 4.4 21.3 1.0
CE2 A:PHE329 4.4 21.9 1.0
CD1 A:ILE186 4.5 21.4 1.0
O A:HOH582 4.8 46.3 1.0
CA A:ASP333 4.8 21.2 1.0
O A:ASN177 4.8 19.8 1.0
CG1 A:ILE186 4.9 21.3 1.0
CG A:ASN177 5.0 20.6 1.0

Iron binding site 2 out of 15 in 3vmg

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Iron binding site 2 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:20.9
occ:1.00
 FE1 A:FES401 0.0 20.9 1.0
S1 A:FES401 2.2 21.0 1.0
S2 A:FES401 2.2 20.8 1.0
SG A:CYS90 2.3 21.4 1.0
SG A:CYS69 2.4 18.6 1.0
FE2 A:FES401 2.7 21.0 1.0
CB A:CYS90 3.1 20.4 1.0
CB A:CYS69 3.2 19.9 1.0
CB A:HIS71 4.0 18.5 1.0
CB A:TYR92 4.1 20.8 1.0
CG2 A:VAL74 4.2 18.1 1.0
N A:HIS93 4.5 19.8 1.0
ND1 A:HIS93 4.5 18.6 1.0
ND1 A:HIS71 4.5 18.2 1.0
CA A:CYS90 4.6 20.4 1.0
CA A:CYS69 4.6 19.5 1.0
CG A:HIS71 4.8 18.7 1.0
CB A:TRP95 4.8 18.0 1.0
N A:TYR92 4.8 19.8 1.0
N A:ARG72 4.8 19.6 1.0
CD2 A:LEU76 4.9 23.3 1.0
CA A:TYR92 4.9 20.1 1.0

Iron binding site 3 out of 15 in 3vmg

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Iron binding site 3 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:21.0
occ:1.00
 FE2 A:FES401 0.0 21.0 1.0
ND1 A:HIS93 2.1 18.6 1.0
ND1 A:HIS71 2.2 18.2 1.0
S1 A:FES401 2.2 21.0 1.0
S2 A:FES401 2.3 20.8 1.0
FE1 A:FES401 2.7 20.9 1.0
CG A:HIS71 3.0 18.7 1.0
CG A:HIS93 3.1 19.4 1.0
CE1 A:HIS93 3.1 18.9 1.0
CB A:HIS71 3.2 18.5 1.0
CE1 A:HIS71 3.2 18.7 1.0
CB A:HIS93 3.4 19.2 1.0
N A:HIS93 3.7 19.8 1.0
CB A:TYR92 3.9 20.8 1.0
CA A:HIS93 4.1 20.1 1.0
NE2 A:HIS93 4.2 18.9 1.0
CD2 A:HIS93 4.2 18.9 1.0
CD2 A:HIS71 4.2 18.2 1.0
N A:ARG72 4.3 19.6 1.0
CG A:ARG72 4.3 22.0 1.0
NE2 A:HIS71 4.3 19.1 1.0
CG A:TYR92 4.4 21.9 1.0
SG A:CYS69 4.4 18.6 1.0
CD2 A:TYR92 4.5 22.1 1.0
SG A:CYS90 4.6 21.4 1.0
CA A:HIS71 4.6 19.2 1.0
C A:TYR92 4.6 20.0 1.0
CD1 A:TRP95 4.6 18.0 1.0
CB A:ARG72 4.7 21.1 1.0
NE1 A:TRP95 4.7 18.1 1.0
CA A:TYR92 4.8 20.1 1.0
C A:HIS71 4.9 19.1 1.0
C A:HIS93 4.9 19.9 1.0

Iron binding site 4 out of 15 in 3vmg

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Iron binding site 4 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:29.8
occ:1.00
 O B:HOH889 1.9 50.2 1.0
OD1 B:ASP333 2.0 29.2 1.0
NE2 B:HIS183 2.1 23.7 1.0
NE2 B:HIS187 2.1 29.7 1.0
OD2 B:ASP333 2.2 28.9 1.0
O B:HOH943 2.3 40.5 1.0
CG B:ASP333 2.3 28.9 1.0
CD2 B:HIS183 3.0 23.7 1.0
CE1 B:HIS187 3.1 29.8 1.0
CD2 B:HIS187 3.2 29.6 1.0
CE1 B:HIS183 3.2 24.0 1.0
CB B:ASP333 3.8 28.8 1.0
O B:HOH492 4.1 27.3 1.0
CG B:HIS183 4.2 24.2 1.0
ND2 B:ASN330 4.2 26.8 1.0
ND1 B:HIS187 4.2 29.9 1.0
ND1 B:HIS183 4.3 23.4 1.0
CG B:HIS187 4.3 29.9 1.0
CD1 B:ILE186 4.3 29.3 1.0
ND2 B:ASN177 4.4 27.0 1.0
O B:ASN177 4.4 28.2 1.0
OD1 B:ASN177 4.6 30.0 1.0
C1 B:9CA2001 4.6 29.5 1.0
CA B:ASP333 4.7 28.9 1.0
C9A B:9CA2001 4.7 29.6 1.0
CE2 B:PHE329 4.8 26.5 1.0
CG B:ASN177 4.8 28.6 1.0
N9 B:9CA2001 4.8 29.7 1.0
CG1 B:ILE186 4.8 28.9 1.0

Iron binding site 5 out of 15 in 3vmg

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Iron binding site 5 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:18.9
occ:1.00
 FE1 B:FES401 0.0 18.9 1.0
S1 B:FES401 2.2 21.3 1.0
S2 B:FES401 2.2 21.5 1.0
SG B:CYS69 2.3 17.5 1.0
SG B:CYS90 2.3 22.8 1.0
FE2 B:FES401 2.8 19.2 1.0
CB B:CYS90 3.1 20.5 1.0
CB B:CYS69 3.1 18.0 1.0
CB B:HIS71 4.1 14.9 1.0
CB B:TYR92 4.1 19.5 1.0
CG2 B:VAL74 4.2 16.9 1.0
ND1 B:HIS93 4.5 16.0 1.0
N B:HIS93 4.5 18.0 1.0
CA B:CYS90 4.6 20.5 1.0
CA B:CYS69 4.6 17.8 1.0
ND1 B:HIS71 4.6 13.9 1.0
CB B:TRP95 4.7 15.8 1.0
N B:TYR92 4.8 19.0 1.0
CG B:HIS71 4.9 14.6 1.0
N B:ARG72 4.9 16.6 1.0
CG B:TRP95 4.9 16.1 1.0
CA B:TYR92 4.9 18.8 1.0
N B:TRP95 5.0 17.3 1.0
N B:HIS71 5.0 16.9 1.0

Iron binding site 6 out of 15 in 3vmg

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Iron binding site 6 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:19.2
occ:1.00
 FE2 B:FES401 0.0 19.2 1.0
ND1 B:HIS93 2.0 16.0 1.0
ND1 B:HIS71 2.2 13.9 1.0
S1 B:FES401 2.3 21.3 1.0
S2 B:FES401 2.3 21.5 1.0
FE1 B:FES401 2.8 18.9 1.0
CG B:HIS93 3.0 16.6 1.0
CE1 B:HIS93 3.0 16.0 1.0
CG B:HIS71 3.1 14.6 1.0
CB B:HIS71 3.2 14.9 1.0
CE1 B:HIS71 3.3 14.7 1.0
CB B:HIS93 3.3 16.8 1.0
N B:HIS93 3.7 18.0 1.0
CB B:TYR92 3.9 19.5 1.0
NE2 B:HIS93 4.1 16.5 1.0
CD2 B:HIS93 4.1 15.9 1.0
CA B:HIS93 4.1 17.6 1.0
CD2 B:HIS71 4.3 13.7 1.0
N B:ARG72 4.3 16.6 1.0
CG B:ARG72 4.3 18.0 1.0
SG B:CYS69 4.3 17.5 1.0
NE2 B:HIS71 4.3 14.3 1.0
CG B:TYR92 4.4 20.0 1.0
CD2 B:TYR92 4.4 20.6 1.0
CD1 B:TRP95 4.5 15.7 1.0
C B:TYR92 4.6 18.5 1.0
NE1 B:TRP95 4.6 15.6 1.0
CA B:HIS71 4.6 16.1 1.0
SG B:CYS90 4.7 22.8 1.0
CB B:ARG72 4.7 17.2 1.0
C B:HIS93 4.9 17.7 1.0
CA B:TYR92 4.9 18.8 1.0
C B:HIS71 4.9 16.0 1.0
CG B:TRP95 4.9 16.1 1.0
CE2 B:TRP95 5.0 16.0 1.0

Iron binding site 7 out of 15 in 3vmg

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Iron binding site 7 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:25.4
occ:1.00
 O C:HOH888 1.9 30.6 1.0
OD1 C:ASP333 1.9 26.2 1.0
NE2 C:HIS187 2.1 23.6 1.0
NE2 C:HIS183 2.2 21.1 1.0
O C:HOH1060 2.2 38.5 1.0
OD2 C:ASP333 2.2 25.4 1.0
CG C:ASP333 2.4 25.4 1.0
CD2 C:HIS183 2.9 21.0 1.0
CE1 C:HIS187 3.0 24.2 1.0
CD2 C:HIS187 3.2 23.5 1.0
CE1 C:HIS183 3.3 21.0 1.0
CB C:ASP333 3.9 24.9 1.0
O C:HOH435 4.1 21.6 1.0
ND1 C:HIS187 4.2 23.9 1.0
CG C:HIS183 4.2 21.2 1.0
ND2 C:ASN330 4.2 22.9 1.0
CD1 C:ILE186 4.2 24.3 1.0
OD1 C:ASN177 4.3 26.4 1.0
CG C:HIS187 4.3 23.6 1.0
ND1 C:HIS183 4.3 21.1 1.0
ND2 C:ASN177 4.5 25.1 1.0
O C:ASN177 4.5 25.7 1.0
C1 C:9CA2002 4.6 28.0 1.0
CA C:ASP333 4.7 24.7 1.0
C9A C:9CA2002 4.7 28.1 1.0
CG C:ASN177 4.7 25.3 1.0
CG1 C:ILE186 4.8 23.6 1.0
CE2 C:PHE329 4.9 22.3 1.0
N9 C:9CA2002 4.9 28.1 1.0

Iron binding site 8 out of 15 in 3vmg

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Iron binding site 8 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:24.2
occ:1.00
 FE1 C:FES401 0.0 24.2 1.0
SG C:CYS69 2.1 26.5 1.0
S1 C:FES401 2.2 22.7 1.0
S2 C:FES401 2.3 21.7 1.0
SG C:CYS90 2.3 23.6 1.0
FE2 C:FES401 2.8 24.6 1.0
CB C:CYS69 3.1 24.8 1.0
CB C:CYS90 3.1 24.6 1.0
CB C:TYR92 4.0 24.9 1.0
CB C:HIS71 4.1 21.9 1.0
CG2 C:VAL74 4.2 21.2 1.0
N C:HIS93 4.4 25.8 1.0
ND1 C:HIS93 4.5 26.8 1.0
CA C:CYS69 4.6 24.1 1.0
ND1 C:HIS71 4.6 21.7 1.0
CA C:CYS90 4.6 24.8 1.0
N C:TYR92 4.8 25.1 1.0
CG C:HIS71 4.8 21.7 1.0
N C:ARG72 4.8 22.5 1.0
CB C:TRP95 4.8 24.2 1.0
CA C:TYR92 4.9 25.6 1.0
CD2 C:LEU76 4.9 25.7 1.0

Iron binding site 9 out of 15 in 3vmg

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Iron binding site 9 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:24.6
occ:1.00
 FE2 C:FES401 0.0 24.6 1.0
ND1 C:HIS93 2.1 26.8 1.0
ND1 C:HIS71 2.2 21.7 1.0
S1 C:FES401 2.3 22.7 1.0
S2 C:FES401 2.4 21.7 1.0
FE1 C:FES401 2.8 24.2 1.0
CG C:HIS93 3.0 26.7 1.0
CE1 C:HIS93 3.1 26.4 1.0
CG C:HIS71 3.1 21.7 1.0
CE1 C:HIS71 3.2 21.8 1.0
CB C:HIS71 3.3 21.9 1.0
CB C:HIS93 3.3 26.2 1.0
N C:HIS93 3.7 25.8 1.0
CB C:TYR92 3.9 24.9 1.0
CD2 C:HIS93 4.1 26.5 1.0
CA C:HIS93 4.1 26.0 1.0
NE2 C:HIS93 4.1 26.8 1.0
SG C:CYS69 4.2 26.5 1.0
CD2 C:TYR92 4.3 25.5 1.0
CG C:ARG72 4.3 24.8 1.0
CD2 C:HIS71 4.3 21.7 1.0
CG C:TYR92 4.3 25.6 1.0
N C:ARG72 4.3 22.5 1.0
NE2 C:HIS71 4.3 21.4 1.0
C C:TYR92 4.6 25.6 1.0
CA C:HIS71 4.6 22.4 1.0
CD1 C:TRP95 4.7 24.2 1.0
SG C:CYS90 4.7 23.6 1.0
CB C:ARG72 4.7 23.4 1.0
NE1 C:TRP95 4.7 23.9 1.0
CA C:TYR92 4.8 25.6 1.0
C C:HIS71 4.9 22.5 1.0
C C:HIS93 4.9 25.9 1.0

Iron binding site 10 out of 15 in 3vmg

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Iron binding site 10 out of 15 in the Reduced Carbazole-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 Reduced Carbazole-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:18.5
occ:1.00
 FE1 D:FES201 0.0 18.5 1.0
ND1 D:HIS48 2.1 18.7 1.0
ND1 D:HIS68 2.1 19.6 1.0
S1 D:FES201 2.2 20.9 1.0
S2 D:FES201 2.3 21.6 1.0
FE2 D:FES201 2.7 23.7 1.0
CE1 D:HIS48 3.0 17.5 1.0
CG D:HIS68 3.1 19.3 1.0
CE1 D:HIS68 3.1 19.3 1.0
CG D:HIS48 3.1 19.3 1.0
CB D:HIS68 3.4 20.0 1.0
CB D:HIS48 3.5 20.2 1.0
O A:HOH397 3.9 22.3 1.0
N D:HIS68 4.0 20.3 1.0
NE2 D:HIS48 4.1 18.4 1.0
O D:HIS48 4.2 23.0 1.0
CD2 D:HIS48 4.2 18.5 1.0
C D:HIS48 4.2 22.5 1.0
CD2 D:HIS68 4.2 19.2 1.0
NE2 D:HIS68 4.2 19.8 1.0
CA D:HIS68 4.3 20.5 1.0
O D:HOH187 4.3 23.9 1.0
CB D:PHE67 4.5 21.3 1.0
SG D:CYS46 4.5 22.3 1.0
SG D:CYS65 4.5 22.8 1.0
CA D:HIS48 4.5 22.0 1.0
CG D:PRO83 4.6 23.0 1.0
N D:GLY49 4.6 22.7 1.0
C D:PHE67 4.9 20.7 1.0
O A:VAL351 4.9 18.4 1.0
O A:GLU353 5.0 16.4 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 22:03:04 2024

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