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Iron in PDB 3gcf: Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177

Protein crystallography data

The structure of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177, PDB code: 3gcf was solved by K.Inoue, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 280.002, 161.661, 194.665, 90.00, 118.65, 90.00
R / Rfree (%) 17.4 / 17.5

Other elements in 3gcf:

The structure of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 also contains other interesting chemical elements:

Chlorine (Cl) 34 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 45;

Binding sites:

The binding sites of Iron atom in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 (pdb code 3gcf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 45 binding sites of Iron where determined in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177, PDB code: 3gcf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 45 in 3gcf

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Iron binding site 1 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:8.5
occ:1.00
O A:HOH3146 2.0 11.5 1.0
OD1 A:ASP337 2.1 11.2 1.0
O A:HOH3147 2.1 9.6 1.0
NE2 A:HIS189 2.1 7.4 1.0
NE2 A:HIS193 2.1 8.3 1.0
OD2 A:ASP337 2.3 12.8 1.0
CG A:ASP337 2.5 11.6 1.0
CE1 A:HIS189 3.0 7.1 1.0
CE1 A:HIS193 3.0 9.4 1.0
CD2 A:HIS193 3.2 9.1 1.0
CD2 A:HIS189 3.2 7.2 1.0
CB A:ASP337 4.0 10.7 1.0
O A:HOH1578 4.1 13.4 1.0
ND1 A:HIS189 4.2 7.3 1.0
ND1 A:HIS193 4.2 7.5 1.0
CG A:HIS193 4.3 9.9 1.0
CG A:HIS189 4.3 8.9 1.0
ND2 A:ASN334 4.3 5.3 1.0
O A:HOH3293 4.4 28.0 1.0
ND2 A:ASN183 4.4 11.6 1.0
OD1 A:ASN183 4.4 14.9 1.0
O A:ASN183 4.4 12.6 1.0
O A:HOH642 4.6 23.6 1.0
O A:HOH3148 4.6 33.7 1.0
CE2 A:PHE333 4.7 11.2 1.0
CG A:ASN183 4.8 12.1 1.0
CA A:ASP337 4.8 11.0 1.0

Iron binding site 2 out of 45 in 3gcf

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Iron binding site 2 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:10.2
occ:1.00
FE1 A:FES401 0.0 10.2 1.0
S2 A:FES401 2.2 9.9 1.0
S1 A:FES401 2.2 12.4 1.0
SG A:CYS96 2.3 9.9 1.0
SG A:CYS75 2.3 12.1 1.0
FE2 A:FES401 2.7 10.5 1.0
CB A:CYS96 3.2 9.2 1.0
CB A:CYS75 3.2 12.3 1.0
CB A:HIS77 4.0 9.3 1.0
CG2 A:VAL80 4.1 9.4 1.0
CB A:TYR98 4.1 7.0 1.0
ND1 A:HIS77 4.5 11.5 1.0
N A:HIS99 4.5 8.3 1.0
ND1 A:HIS99 4.5 6.5 1.0
CA A:CYS96 4.6 9.5 1.0
CB A:TRP101 4.6 8.8 1.0
CA A:CYS75 4.7 11.8 1.0
CG A:HIS77 4.7 11.1 1.0
N A:TYR98 4.8 8.0 1.0
N A:ARG78 4.9 9.0 1.0
CG A:TRP101 4.9 8.4 1.0
CA A:TYR98 4.9 7.9 1.0

Iron binding site 3 out of 45 in 3gcf

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Iron binding site 3 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:10.5
occ:1.00
FE2 A:FES401 0.0 10.5 1.0
ND1 A:HIS99 2.1 6.5 1.0
ND1 A:HIS77 2.1 11.5 1.0
S1 A:FES401 2.2 12.4 1.0
S2 A:FES401 2.3 9.9 1.0
FE1 A:FES401 2.7 10.2 1.0
CE1 A:HIS99 3.0 8.6 1.0
CG A:HIS77 3.0 11.1 1.0
CG A:HIS99 3.1 7.0 1.0
CE1 A:HIS77 3.2 10.7 1.0
CB A:HIS77 3.3 9.3 1.0
CB A:HIS99 3.4 6.9 1.0
N A:HIS99 3.8 8.3 1.0
CB A:TYR98 4.0 7.0 1.0
NE2 A:HIS99 4.1 9.4 1.0
CD2 A:HIS99 4.1 6.6 1.0
CD2 A:TYR98 4.2 8.9 1.0
CA A:HIS99 4.2 7.1 1.0
CD2 A:HIS77 4.2 10.0 1.0
NE2 A:HIS77 4.2 10.2 1.0
SG A:CYS75 4.3 12.1 1.0
CG A:TYR98 4.4 8.9 1.0
N A:ARG78 4.5 9.0 1.0
SG A:CYS96 4.6 9.9 1.0
C A:TYR98 4.6 8.6 1.0
CG A:ARG78 4.6 9.0 1.0
CD1 A:TRP101 4.6 5.7 1.0
CA A:HIS77 4.7 8.9 1.0
NE1 A:TRP101 4.7 7.2 1.0
CG A:TRP101 4.9 8.4 1.0
CA A:TYR98 4.9 7.9 1.0
CB A:ARG78 4.9 8.5 1.0
C A:HIS77 5.0 9.5 1.0

Iron binding site 4 out of 45 in 3gcf

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Iron binding site 4 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:8.0
occ:1.00
O B:HOH3150 2.0 8.3 1.0
O B:HOH3149 2.0 7.5 1.0
OD1 B:ASP337 2.0 11.4 1.0
NE2 B:HIS193 2.1 7.7 1.0
NE2 B:HIS189 2.1 8.9 1.0
OD2 B:ASP337 2.3 12.0 1.0
CG B:ASP337 2.5 9.0 1.0
CE1 B:HIS193 3.0 8.5 1.0
CE1 B:HIS189 3.1 8.2 1.0
CD2 B:HIS193 3.1 7.1 1.0
CD2 B:HIS189 3.2 7.9 1.0
CB B:ASP337 4.0 10.6 1.0
O B:HOH1583 4.1 13.4 1.0
ND1 B:HIS193 4.1 7.9 1.0
ND1 B:HIS189 4.2 7.4 1.0
O B:HOH3151 4.2 34.8 1.0
CG B:HIS193 4.2 8.8 1.0
CG B:HIS189 4.3 9.6 1.0
ND2 B:ASN334 4.3 5.8 1.0
O B:ASN183 4.4 13.5 1.0
OD1 B:ASN183 4.4 13.6 1.0
ND2 B:ASN183 4.4 11.3 1.0
O B:HOH3297 4.4 27.7 1.0
O B:HOH906 4.7 22.0 1.0
CE2 B:PHE333 4.7 8.2 1.0
CG B:ASN183 4.8 12.6 1.0
CA B:ASP337 4.8 11.9 1.0

Iron binding site 5 out of 45 in 3gcf

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Iron binding site 5 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:11.1
occ:1.00
FE1 B:FES401 0.0 11.1 1.0
S2 B:FES401 2.2 10.2 1.0
S1 B:FES401 2.3 11.0 1.0
SG B:CYS75 2.3 11.3 1.0
SG B:CYS96 2.3 9.4 1.0
FE2 B:FES401 2.7 10.2 1.0
CB B:CYS96 3.2 8.9 1.0
CB B:CYS75 3.2 11.2 1.0
CB B:HIS77 4.0 10.4 1.0
CG2 B:VAL80 4.1 9.9 1.0
CB B:TYR98 4.1 7.3 1.0
ND1 B:HIS99 4.4 6.5 1.0
ND1 B:HIS77 4.5 12.7 1.0
N B:HIS99 4.5 8.7 1.0
CA B:CYS96 4.6 10.1 1.0
CA B:CYS75 4.6 11.3 1.0
CB B:TRP101 4.6 8.9 1.0
CG B:HIS77 4.7 11.4 1.0
N B:ARG78 4.8 10.6 1.0
N B:TYR98 4.8 7.4 1.0
CG B:TRP101 4.9 9.5 1.0
CA B:TYR98 4.9 8.1 1.0
N B:HIS77 5.0 9.7 1.0

Iron binding site 6 out of 45 in 3gcf

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Iron binding site 6 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:10.2
occ:1.00
FE2 B:FES401 0.0 10.2 1.0
ND1 B:HIS99 2.1 6.5 1.0
ND1 B:HIS77 2.1 12.7 1.0
S1 B:FES401 2.2 11.0 1.0
S2 B:FES401 2.3 10.2 1.0
FE1 B:FES401 2.7 11.1 1.0
CE1 B:HIS99 3.0 8.0 1.0
CG B:HIS77 3.0 11.4 1.0
CG B:HIS99 3.1 7.4 1.0
CE1 B:HIS77 3.2 11.2 1.0
CB B:HIS77 3.2 10.4 1.0
CB B:HIS99 3.4 7.6 1.0
N B:HIS99 3.8 8.7 1.0
CB B:TYR98 4.0 7.3 1.0
NE2 B:HIS99 4.1 7.6 1.0
CD2 B:HIS99 4.1 5.6 1.0
CD2 B:HIS77 4.2 10.3 1.0
CD2 B:TYR98 4.2 9.9 1.0
NE2 B:HIS77 4.2 10.9 1.0
CA B:HIS99 4.2 7.7 1.0
SG B:CYS75 4.3 11.3 1.0
N B:ARG78 4.4 10.6 1.0
CG B:TYR98 4.4 8.8 1.0
CG B:ARG78 4.6 10.1 1.0
SG B:CYS96 4.6 9.4 1.0
C B:TYR98 4.6 9.0 1.0
CA B:HIS77 4.6 9.9 1.0
CD1 B:TRP101 4.7 7.0 1.0
NE1 B:TRP101 4.8 9.0 1.0
CB B:ARG78 4.9 10.8 1.0
CG B:TRP101 4.9 9.5 1.0
CA B:TYR98 4.9 8.1 1.0
C B:HIS77 4.9 10.8 1.0

Iron binding site 7 out of 45 in 3gcf

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Iron binding site 7 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:7.1
occ:1.00
O C:HOH3152 2.0 7.0 1.0
O C:HOH3153 2.0 6.5 1.0
NE2 C:HIS193 2.1 9.4 1.0
OD1 C:ASP337 2.1 11.1 1.0
NE2 C:HIS189 2.1 7.5 1.0
OD2 C:ASP337 2.3 11.3 1.0
CG C:ASP337 2.5 10.4 1.0
CE1 C:HIS193 2.9 9.8 1.0
CE1 C:HIS189 3.0 7.8 1.0
CD2 C:HIS193 3.2 9.5 1.0
CD2 C:HIS189 3.2 6.7 1.0
CB C:ASP337 4.0 10.5 1.0
O C:HOH1601 4.0 12.2 1.0
ND1 C:HIS193 4.1 8.9 1.0
ND1 C:HIS189 4.2 7.4 1.0
CG C:HIS193 4.2 11.2 1.0
ND2 C:ASN334 4.3 7.2 1.0
CG C:HIS189 4.3 7.9 1.0
O C:HOH3154 4.3 30.2 1.0
O C:ASN183 4.4 12.9 1.0
ND2 C:ASN183 4.4 9.2 1.0
OD1 C:ASN183 4.4 11.1 1.0
O C:HOH3290 4.5 30.9 1.0
O C:HOH882 4.6 23.4 1.0
CE2 C:PHE333 4.7 11.2 1.0
CG C:ASN183 4.8 10.7 1.0
CA C:ASP337 4.8 11.3 1.0

Iron binding site 8 out of 45 in 3gcf

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Iron binding site 8 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:10.1
occ:1.00
FE1 C:FES401 0.0 10.1 1.0
S2 C:FES401 2.2 9.3 1.0
SG C:CYS96 2.2 11.4 1.0
S1 C:FES401 2.3 10.7 1.0
SG C:CYS75 2.3 11.4 1.0
FE2 C:FES401 2.7 11.1 1.0
CB C:CYS96 3.1 10.0 1.0
CB C:CYS75 3.1 11.8 1.0
CB C:HIS77 4.0 9.6 1.0
CG2 C:VAL80 4.1 9.1 1.0
CB C:TYR98 4.1 5.8 1.0
ND1 C:HIS77 4.4 11.7 1.0
ND1 C:HIS99 4.5 6.3 1.0
N C:HIS99 4.5 8.2 1.0
CA C:CYS96 4.6 9.3 1.0
CA C:CYS75 4.6 12.3 1.0
CB C:TRP101 4.7 8.9 1.0
CG C:HIS77 4.7 11.7 1.0
N C:ARG78 4.8 10.4 1.0
N C:TYR98 4.8 6.7 1.0
CG C:TRP101 4.9 8.6 1.0
CA C:TYR98 4.9 7.0 1.0
N C:HIS77 5.0 9.8 1.0

Iron binding site 9 out of 45 in 3gcf

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Iron binding site 9 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:11.1
occ:1.00
FE2 C:FES401 0.0 11.1 1.0
ND1 C:HIS99 2.1 6.3 1.0
ND1 C:HIS77 2.1 11.7 1.0
S1 C:FES401 2.2 10.7 1.0
S2 C:FES401 2.3 9.3 1.0
FE1 C:FES401 2.7 10.1 1.0
CE1 C:HIS99 3.0 9.5 1.0
CG C:HIS77 3.0 11.7 1.0
CG C:HIS99 3.0 7.2 1.0
CE1 C:HIS77 3.1 10.4 1.0
CB C:HIS77 3.2 9.6 1.0
CB C:HIS99 3.4 8.1 1.0
N C:HIS99 3.7 8.2 1.0
CB C:TYR98 4.0 5.8 1.0
NE2 C:HIS99 4.1 8.7 1.0
CD2 C:HIS99 4.1 6.2 1.0
CD2 C:HIS77 4.2 10.6 1.0
CA C:HIS99 4.2 7.6 1.0
NE2 C:HIS77 4.2 9.1 1.0
CD2 C:TYR98 4.2 8.6 1.0
SG C:CYS75 4.4 11.4 1.0
N C:ARG78 4.4 10.4 1.0
CG C:TYR98 4.5 7.6 1.0
SG C:CYS96 4.5 11.4 1.0
C C:TYR98 4.6 8.1 1.0
CG C:ARG78 4.6 10.9 1.0
CA C:HIS77 4.6 10.3 1.0
CD1 C:TRP101 4.6 6.3 1.0
NE1 C:TRP101 4.7 6.6 1.0
CB C:ARG78 4.8 10.5 1.0
CA C:TYR98 4.9 7.0 1.0
CG C:TRP101 4.9 8.6 1.0
C C:HIS77 4.9 10.3 1.0
C C:HIS99 5.0 10.0 1.0

Iron binding site 10 out of 45 in 3gcf

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Iron binding site 10 out of 45 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Nocardioides Aromaticivorans IC177 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:11.3
occ:1.00
O D:HOH3155 2.0 9.7 1.0
OD1 D:ASP337 2.0 14.2 1.0
NE2 D:HIS189 2.1 10.5 1.0
NE2 D:HIS193 2.1 14.0 1.0
OD2 D:ASP337 2.3 15.1 1.0
CG D:ASP337 2.4 13.4 1.0
CE1 D:HIS193 3.0 13.6 1.0
CE1 D:HIS189 3.0 9.3 1.0
CD2 D:HIS189 3.1 11.2 1.0
CD2 D:HIS193 3.1 13.4 1.0
CB D:ASP337 3.9 12.4 1.0
ND1 D:HIS193 4.1 12.8 1.0
ND1 D:HIS189 4.1 10.8 1.0
O D:HOH2238 4.1 18.5 1.0
CG D:HIS189 4.2 10.8 1.0
CG D:HIS193 4.2 14.7 1.0
ND2 D:ASN334 4.3 12.6 1.0
O D:HOH3156 4.3 15.4 1.0
OD1 D:ASN183 4.3 14.8 1.0
O D:HOH1603 4.4 29.9 1.0
O D:ASN183 4.4 16.5 1.0
ND2 D:ASN183 4.4 11.9 1.0
CG D:ASN183 4.7 13.8 1.0
CE2 D:PHE333 4.8 13.1 1.0
CA D:ASP337 4.8 13.6 1.0

Reference:

K.Inoue, Y.Ashikawa, T.Umeda, M.Abo, J.Katsuki, Y.Usami, H.Noguchi, Z.Fujimoto, T.Terada, H.Yamane, H.Nojiri. Specific Interactions Between the Ferredoxin and Terminal Oxygenase Components of A Class Iib Rieske Nonheme Iron Oxygenase, Carbazole 1,9A-Dioxygenase. J.Mol.Biol. V. 392 436 2009.
ISSN: ISSN 0022-2836
PubMed: 19616558
DOI: 10.1016/J.JMB.2009.07.029
Page generated: Sun Dec 13 15:06:26 2020

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