Iron in PDB 6ll0: Carbazole-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase

Protein crystallography data

The structure of Carbazole-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase, PDB code: 6ll0 was solved by Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.44 / 2.20
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 92.087, 92.087, 243.504, 90, 90, 120
R / Rfree (%) 17.6 / 24.6

Other elements in 6ll0:

The structure of Carbazole-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Carbazole-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase (pdb code 6ll0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Carbazole-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase, PDB code: 6ll0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6ll0

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Iron binding site 1 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:20.1
occ:1.00
 FE1 A:FES401 0.0 20.1 1.0
S2 A:FES401 2.2 21.6 1.0
S1 A:FES401 2.2 23.2 1.0
SG A:CYS90 2.2 19.3 1.0
SG A:CYS69 2.3 21.6 1.0
FE2 A:FES401 2.8 20.0 1.0
CB A:CYS90 3.1 20.8 1.0
CB A:CYS69 3.1 20.8 1.0
CB A:TYR92 4.1 18.5 1.0
CG2 A:VAL74 4.1 21.2 1.0
CB A:HIS71 4.2 18.8 1.0
ND1 A:HIS93 4.4 20.9 1.0
N A:HIS93 4.4 16.8 1.0
ND1 A:HIS71 4.5 20.7 1.0
CA A:CYS90 4.5 20.0 1.0
CA A:CYS69 4.6 20.7 1.0
N A:TYR92 4.8 18.4 1.0
CG A:HIS71 4.9 18.6 1.0
CA A:TYR92 4.9 17.8 1.0
CB A:TRP95 4.9 18.0 1.0
C A:CYS90 5.0 19.4 1.0
N A:ARG72 5.0 18.5 1.0

Iron binding site 2 out of 9 in 6ll0

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Iron binding site 2 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:20.0
occ:1.00
 FE2 A:FES401 0.0 20.0 1.0
ND1 A:HIS93 1.9 20.9 1.0
ND1 A:HIS71 2.1 20.7 1.0
S1 A:FES401 2.2 23.2 1.0
S2 A:FES401 2.2 21.6 1.0
FE1 A:FES401 2.8 20.1 1.0
CE1 A:HIS93 2.8 20.9 1.0
CG A:HIS93 3.0 19.6 1.0
CE1 A:HIS71 3.1 22.8 1.0
CG A:HIS71 3.1 18.6 1.0
CB A:HIS71 3.4 18.8 1.0
CB A:HIS93 3.5 18.6 1.0
N A:HIS93 3.7 16.8 1.0
NE2 A:HIS93 3.9 21.9 1.0
CB A:TYR92 4.0 18.5 1.0
CD2 A:HIS93 4.0 20.5 1.0
CA A:HIS93 4.1 18.4 1.0
NE2 A:HIS71 4.2 20.6 1.0
CD2 A:HIS71 4.2 19.6 1.0
CG A:ARG72 4.2 20.9 1.0
SG A:CYS69 4.3 21.6 1.0
CD2 A:TYR92 4.4 18.9 1.0
CG A:TYR92 4.4 18.5 1.0
N A:ARG72 4.5 18.5 1.0
C A:TYR92 4.5 18.0 1.0
NE1 A:TRP95 4.6 16.4 1.0
SG A:CYS90 4.6 19.3 1.0
CD1 A:TRP95 4.6 17.2 1.0
CB A:ARG72 4.7 19.8 1.0
CA A:HIS71 4.7 19.1 1.0
CA A:TYR92 4.8 17.8 1.0
C A:HIS93 4.9 17.4 1.0
C A:HIS71 5.0 18.9 1.0

Iron binding site 3 out of 9 in 6ll0

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Iron binding site 3 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:50.1
occ:1.00
 OD1 A:ASP333 2.0 34.2 1.0
NE2 A:HIS183 2.0 32.0 1.0
NE2 A:HIS187 2.4 39.9 1.0
OD2 A:ASP333 2.5 38.9 1.0
CG A:ASP333 2.5 36.4 1.0
CE1 A:HIS183 2.8 31.0 1.0
CD2 A:HIS183 3.2 30.9 1.0
CD2 A:HIS187 3.3 39.4 1.0
CE1 A:HIS187 3.4 40.3 1.0
C9A A:9CA403 3.7 53.9 1.0
C1 A:9CA403 3.8 50.7 1.0
N9 A:9CA403 3.8 49.9 1.0
CB A:ASP333 4.0 37.2 1.0
ND1 A:HIS183 4.0 30.3 1.0
CG A:HIS183 4.2 31.0 1.0
C4A A:9CA403 4.2 53.8 1.0
ND2 A:ASN330 4.4 28.3 1.0
C8A A:9CA403 4.4 52.0 1.0
CG A:HIS187 4.4 42.2 1.0
C2 A:9CA403 4.5 46.0 1.0
ND1 A:HIS187 4.5 40.5 1.0
ND2 A:ASN177 4.5 58.1 1.0
CE2 A:PHE329 4.6 32.9 1.0
C4B A:9CA403 4.6 51.5 1.0
C4 A:9CA403 4.8 49.7 1.0
C3 A:9CA403 4.9 43.5 1.0
CA A:ASP333 4.9 41.3 1.0
O A:ASN177 5.0 41.1 1.0

Iron binding site 4 out of 9 in 6ll0

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Iron binding site 4 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.8
occ:1.00
 FE1 B:FES401 0.0 24.8 1.0
S1 B:FES401 2.2 27.1 1.0
S2 B:FES401 2.2 27.0 1.0
SG B:CYS90 2.2 26.6 1.0
SG B:CYS69 2.2 27.6 1.0
FE2 B:FES401 2.8 28.5 1.0
CB B:CYS69 3.0 27.4 1.0
CB B:CYS90 3.1 25.4 1.0
CG2 B:VAL74 4.1 31.7 1.0
CB B:HIS71 4.2 31.3 1.0
CB B:TYR92 4.3 31.0 1.0
ND1 B:HIS71 4.4 30.0 1.0
CA B:CYS69 4.5 26.2 1.0
CA B:CYS90 4.5 26.9 1.0
ND1 B:HIS93 4.5 24.7 1.0
N B:HIS93 4.5 27.9 1.0
CG B:HIS71 4.8 33.3 1.0
CB B:TRP95 4.8 28.9 1.0
N B:TYR92 4.9 28.3 1.0
N B:ARG72 5.0 25.6 1.0

Iron binding site 5 out of 9 in 6ll0

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Iron binding site 5 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:28.5
occ:1.00
 FE2 B:FES401 0.0 28.5 1.0
ND1 B:HIS71 2.1 30.0 1.0
ND1 B:HIS93 2.1 24.7 1.0
S1 B:FES401 2.2 27.1 1.0
S2 B:FES401 2.3 27.0 1.0
FE1 B:FES401 2.8 24.8 1.0
CE1 B:HIS71 3.0 33.6 1.0
CG B:HIS93 3.0 27.7 1.0
CE1 B:HIS93 3.1 26.6 1.0
CG B:HIS71 3.1 33.3 1.0
CB B:HIS93 3.3 26.3 1.0
CB B:HIS71 3.4 31.3 1.0
N B:HIS93 3.7 27.9 1.0
CB B:TYR92 4.0 31.0 1.0
CA B:HIS93 4.0 28.6 1.0
CD2 B:HIS93 4.1 28.2 1.0
NE2 B:HIS93 4.1 25.9 1.0
NE2 B:HIS71 4.2 31.5 1.0
CG B:ARG72 4.2 23.8 1.0
CD2 B:HIS71 4.2 34.9 1.0
SG B:CYS69 4.3 27.6 1.0
CD2 B:TYR92 4.4 35.2 1.0
CG B:TYR92 4.4 33.3 1.0
N B:ARG72 4.4 25.6 1.0
SG B:CYS90 4.5 26.6 1.0
C B:TYR92 4.6 29.0 1.0
CD1 B:TRP95 4.7 29.7 1.0
CA B:HIS71 4.7 28.1 1.0
NE1 B:TRP95 4.7 29.7 1.0
C B:HIS93 4.7 28.4 1.0
CA B:TYR92 4.9 29.4 1.0
CB B:ARG72 4.9 23.8 1.0
C B:HIS71 5.0 27.6 1.0

Iron binding site 6 out of 9 in 6ll0

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Iron binding site 6 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:23.4
occ:1.00
 O B:HOH621 2.0 27.1 1.0
OD1 B:ASP333 2.0 19.1 1.0
NE2 B:HIS183 2.1 23.9 1.0
NE2 B:HIS187 2.2 23.9 1.0
CG B:ASP333 2.6 19.9 1.0
OD2 B:ASP333 2.6 20.4 1.0
CD2 B:HIS183 3.0 21.3 1.0
CD2 B:HIS187 3.1 21.3 1.0
CE1 B:HIS183 3.1 22.7 1.0
CE1 B:HIS187 3.3 23.4 1.0
CB B:ASP333 4.1 20.5 1.0
CG B:HIS183 4.2 22.2 1.0
ND1 B:HIS183 4.2 22.1 1.0
O B:HOH543 4.2 26.1 1.0
ND2 B:ASN177 4.3 19.6 1.0
CG B:HIS187 4.3 21.3 1.0
O B:HOH522 4.3 20.7 1.0
ND1 B:HIS187 4.4 21.9 1.0
CE2 B:PHE329 4.4 22.8 1.0
ND2 B:ASN330 4.6 18.5 1.0
CD1 B:ILE186 4.7 17.6 1.0
CZ B:PHE329 4.8 22.4 1.0
CA B:ASP333 4.9 21.4 1.0
CG1 B:ILE186 5.0 17.0 1.0

Iron binding site 7 out of 9 in 6ll0

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Iron binding site 7 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:31.6
occ:1.00
 FE1 C:FES401 0.0 31.6 1.0
S1 C:FES401 2.2 37.0 1.0
S2 C:FES401 2.2 33.6 1.0
SG C:CYS69 2.2 33.2 1.0
SG C:CYS90 2.3 33.7 1.0
FE2 C:FES401 2.9 33.1 1.0
CB C:CYS90 3.0 33.8 1.0
CB C:CYS69 3.1 31.4 1.0
CB C:TYR92 4.1 43.9 1.0
CB C:HIS71 4.1 30.5 1.0
CG2 C:VAL74 4.2 31.4 1.0
ND1 C:HIS71 4.4 27.5 1.0
CA C:CYS90 4.4 33.1 1.0
N C:HIS93 4.5 36.2 1.0
CA C:CYS69 4.6 31.2 1.0
ND1 C:HIS93 4.6 45.2 1.0
CB C:TRP95 4.7 34.7 1.0
CG C:HIS71 4.7 28.3 1.0
N C:TYR92 4.8 39.8 1.0
CG C:TRP95 4.9 33.5 1.0
C C:CYS90 4.9 31.4 1.0
CA C:TYR92 4.9 41.0 1.0
CD1 C:LEU76 5.0 34.4 1.0

Iron binding site 8 out of 9 in 6ll0

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Iron binding site 8 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:33.1
occ:1.00
 FE2 C:FES401 0.0 33.1 1.0
ND1 C:HIS71 2.0 27.5 1.0
ND1 C:HIS93 2.1 45.2 1.0
S2 C:FES401 2.2 33.6 1.0
S1 C:FES401 2.2 37.0 1.0
FE1 C:FES401 2.9 31.6 1.0
CE1 C:HIS71 2.9 30.9 1.0
CG C:HIS71 3.0 28.3 1.0
CG C:HIS93 3.0 43.8 1.0
CE1 C:HIS93 3.0 44.9 1.0
CB C:HIS93 3.3 41.5 1.0
CB C:HIS71 3.3 30.5 1.0
N C:HIS93 3.7 36.2 1.0
CB C:TYR92 4.0 43.9 1.0
NE2 C:HIS71 4.0 28.4 1.0
CA C:HIS93 4.1 39.2 1.0
CD2 C:HIS71 4.1 27.6 1.0
NE2 C:HIS93 4.1 45.7 1.0
CD2 C:HIS93 4.1 45.2 1.0
CD2 C:TYR92 4.2 48.0 1.0
CG C:ARG72 4.3 34.5 1.0
CG C:TYR92 4.3 48.5 1.0
SG C:CYS69 4.3 33.2 1.0
N C:ARG72 4.4 31.6 1.0
C C:TYR92 4.6 39.6 1.0
CD1 C:TRP95 4.6 33.7 1.0
NE1 C:TRP95 4.7 36.9 1.0
SG C:CYS90 4.7 33.7 1.0
CA C:HIS71 4.7 30.9 1.0
CB C:ARG72 4.8 31.9 1.0
C C:HIS93 4.8 38.8 1.0
CA C:TYR92 4.9 41.0 1.0
C C:HIS71 5.0 30.9 1.0

Iron binding site 9 out of 9 in 6ll0

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Iron binding site 9 out of 9 in the Carbazole-Soaked Reduced Oxygenase 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-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:42.2
occ:1.00
 NE2 C:HIS183 1.9 26.5 1.0
NE2 C:HIS187 2.0 29.2 1.0
OD1 C:ASP333 2.0 28.6 1.0
CG C:ASP333 2.7 29.5 1.0
OD2 C:ASP333 2.7 29.9 1.0
CD2 C:HIS183 2.8 26.2 1.0
CD2 C:HIS187 3.0 32.1 1.0
CE1 C:HIS183 3.0 25.3 1.0
CE1 C:HIS187 3.0 30.4 1.0
CG C:HIS183 4.0 27.3 1.0
O C:HOH562 4.0 35.0 1.0
ND1 C:HIS183 4.1 28.1 1.0
ND1 C:HIS187 4.1 30.0 1.0
CG C:HIS187 4.1 31.1 1.0
CB C:ASP333 4.2 29.5 1.0
C8A C:9CA403 4.2 62.2 1.0
ND2 C:ASN177 4.3 39.9 1.0
N9 C:9CA403 4.3 59.6 1.0
CE2 C:PHE329 4.3 32.3 1.0
C8 C:9CA403 4.4 59.9 1.0
CD1 C:ILE186 4.6 32.3 1.0
C4B C:9CA403 4.6 58.2 1.0
ND2 C:ASN330 4.7 29.8 1.0
C9A C:9CA403 4.8 59.9 1.0
C7 C:9CA403 4.9 51.9 1.0
CD2 C:PHE329 5.0 32.8 1.0
C4A C:9CA403 5.0 57.0 1.0
CA C:ASP333 5.0 29.8 1.0
CZ C:PHE329 5.0 33.5 1.0
CG1 C:ILE186 5.0 28.8 1.0

Reference:

Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri. Carbazole-Soaked Reduced Oxygenase in Carbazole 1,9A-Dioxygenase To Be Published.
Page generated: Wed Aug 7 01:20:32 2024

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