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Iron in PDB 6ll1: Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase

Protein crystallography data

The structure of Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase, PDB code: 6ll1 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) 79.45 / 2.15
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 91.738, 91.738, 240.024, 90, 90, 120
R / Rfree (%) 15.3 / 20.9

Other elements in 6ll1:

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

Magnesium (Mg) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase (pdb code 6ll1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase, PDB code: 6ll1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6ll1

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

b:12.7
occ:1.00
 FE1 A:FES401 0.0 12.7 1.0
S2 A:FES401 2.2 12.4 1.0
S1 A:FES401 2.2 14.0 1.0
SG A:CYS90 2.3 13.3 1.0
SG A:CYS69 2.4 14.4 1.0
FE2 A:FES401 2.7 14.0 1.0
CB A:CYS90 3.1 13.7 1.0
CB A:CYS69 3.1 14.5 1.0
CG2 A:VAL74 4.2 12.1 1.0
CB A:HIS71 4.2 15.5 1.0
CB A:TYR92 4.2 13.7 1.0
N A:HIS93 4.4 13.2 1.0
ND1 A:HIS93 4.4 12.8 1.0
ND1 A:HIS71 4.5 13.5 1.0
CA A:CYS69 4.6 14.8 1.0
CA A:CYS90 4.6 13.1 1.0
CB A:TRP95 4.9 13.5 1.0
N A:ARG72 4.9 14.4 1.0
CG A:HIS71 4.9 13.5 1.0
N A:TYR92 4.9 12.1 1.0

Iron binding site 2 out of 9 in 6ll1

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

b:14.0
occ:1.00
 FE2 A:FES401 0.0 14.0 1.0
ND1 A:HIS93 2.1 12.8 1.0
ND1 A:HIS71 2.2 13.5 1.0
S1 A:FES401 2.2 14.0 1.0
S2 A:FES401 2.2 12.4 1.0
FE1 A:FES401 2.7 12.7 1.0
CE1 A:HIS93 2.9 11.9 1.0
CG A:HIS93 3.1 12.2 1.0
CE1 A:HIS71 3.2 15.4 1.0
CG A:HIS71 3.2 13.5 1.0
CB A:HIS71 3.5 15.5 1.0
CB A:HIS93 3.5 12.8 1.0
N A:HIS93 3.7 13.2 1.0
NE2 A:HIS93 4.1 12.0 1.0
CB A:TYR92 4.1 13.7 1.0
CA A:HIS93 4.1 12.1 1.0
CD2 A:HIS93 4.2 12.2 1.0
CG A:ARG72 4.3 17.8 1.0
NE2 A:HIS71 4.3 14.9 1.0
CD2 A:HIS71 4.3 14.1 1.0
SG A:CYS69 4.4 14.4 1.0
N A:ARG72 4.4 14.4 1.0
CD2 A:TYR92 4.4 15.5 1.0
CG A:TYR92 4.4 14.4 1.0
C A:TYR92 4.5 13.3 1.0
SG A:CYS90 4.6 13.3 1.0
CD1 A:TRP95 4.6 14.3 1.0
CB A:ARG72 4.7 16.6 1.0
NE1 A:TRP95 4.7 13.2 1.0
CA A:HIS71 4.8 15.1 1.0
C A:HIS93 4.9 12.5 1.0
CA A:TYR92 4.9 12.6 1.0

Iron binding site 3 out of 9 in 6ll1

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Iron binding site 3 out of 9 in the Oxygen-Exposed Reduced Terminal 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 Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:25.9
occ:1.00
 O A:HOH624 1.9 27.0 1.0
NE2 A:HIS183 2.0 24.2 1.0
OD1 A:ASP333 2.0 26.9 1.0
NE2 A:HIS187 2.2 28.2 1.0
CG A:ASP333 2.7 24.6 1.0
OD2 A:ASP333 2.7 27.3 1.0
CD2 A:HIS183 3.0 25.5 1.0
CE1 A:HIS183 3.0 23.6 1.0
CD2 A:HIS187 3.0 29.4 1.0
CE1 A:HIS187 3.3 30.1 1.0
ND1 A:HIS183 4.1 24.0 1.0
CG A:HIS183 4.1 23.3 1.0
CB A:ASP333 4.2 24.5 1.0
O A:HOH567 4.2 22.3 1.0
CG A:HIS187 4.2 30.0 1.0
CE2 A:PHE329 4.3 25.3 1.0
ND1 A:HIS187 4.3 30.1 1.0
ND2 A:ASN177 4.4 30.2 1.0
ND2 A:ASN330 4.6 22.7 1.0
CD1 A:ILE186 4.8 27.1 1.0
CA A:ASP333 4.9 24.9 1.0
O A:ASN177 4.9 25.5 1.0
CZ A:PHE329 5.0 26.8 1.0

Iron binding site 4 out of 9 in 6ll1

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

b:14.8
occ:1.00
 FE1 B:FES401 0.0 14.8 1.0
S1 B:FES401 2.2 15.3 1.0
S2 B:FES401 2.2 16.9 1.0
SG B:CYS69 2.3 17.8 1.0
SG B:CYS90 2.3 15.5 1.0
FE2 B:FES401 2.7 16.5 1.0
CB B:CYS90 3.1 16.3 1.0
CB B:CYS69 3.1 16.1 1.0
CB B:HIS71 4.1 17.9 1.0
CG2 B:VAL74 4.2 17.0 1.0
CB B:TYR92 4.2 17.6 1.0
N B:HIS93 4.5 17.2 1.0
ND1 B:HIS93 4.5 14.6 1.0
ND1 B:HIS71 4.5 16.9 1.0
CA B:CYS90 4.6 15.3 1.0
CA B:CYS69 4.6 16.9 1.0
CB B:TRP95 4.8 17.5 1.0
CG B:HIS71 4.8 16.3 1.0
N B:ARG72 4.9 17.8 1.0
N B:TYR92 4.9 14.9 1.0
CG B:TRP95 4.9 17.2 1.0

Iron binding site 5 out of 9 in 6ll1

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

b:16.5
occ:1.00
 FE2 B:FES401 0.0 16.5 1.0
ND1 B:HIS93 2.1 14.6 1.0
S1 B:FES401 2.1 15.3 1.0
ND1 B:HIS71 2.2 16.9 1.0
S2 B:FES401 2.3 16.9 1.0
FE1 B:FES401 2.7 14.8 1.0
CE1 B:HIS93 3.1 15.2 1.0
CG B:HIS93 3.1 15.8 1.0
CG B:HIS71 3.2 16.3 1.0
CE1 B:HIS71 3.3 18.9 1.0
CB B:HIS71 3.3 17.9 1.0
CB B:HIS93 3.5 16.3 1.0
N B:HIS93 3.7 17.2 1.0
CB B:TYR92 4.1 17.6 1.0
CA B:HIS93 4.2 17.4 1.0
NE2 B:HIS93 4.2 14.2 1.0
CD2 B:HIS93 4.2 15.3 1.0
CG B:ARG72 4.3 16.2 1.0
SG B:CYS69 4.3 17.8 1.0
CD2 B:HIS71 4.3 16.4 1.0
N B:ARG72 4.3 17.8 1.0
NE2 B:HIS71 4.4 17.2 1.0
CG B:TYR92 4.4 18.7 1.0
CD2 B:TYR92 4.4 19.4 1.0
C B:TYR92 4.6 17.0 1.0
SG B:CYS90 4.6 15.5 1.0
CD1 B:TRP95 4.7 18.2 1.0
CA B:HIS71 4.7 17.3 1.0
CB B:ARG72 4.7 16.2 1.0
NE1 B:TRP95 4.8 17.8 1.0
C B:HIS93 4.8 17.4 1.0
CA B:TYR92 4.9 16.6 1.0
C B:HIS71 4.9 17.5 1.0
CG B:TRP95 5.0 17.2 1.0

Iron binding site 6 out of 9 in 6ll1

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Iron binding site 6 out of 9 in the Oxygen-Exposed Reduced Terminal 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 Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:16.0
occ:1.00
 O2 B:OXY404 1.6 30.8 1.0
O1 B:OXY404 1.9 37.9 1.0
OD1 B:ASP333 2.0 15.6 1.0
NE2 B:HIS183 2.0 13.3 1.0
NE2 B:HIS187 2.1 15.8 1.0
CG B:ASP333 2.6 14.4 1.0
OD2 B:ASP333 2.6 16.2 1.0
CD2 B:HIS183 2.9 13.6 1.0
CE1 B:HIS187 3.0 18.1 1.0
CE1 B:HIS183 3.1 14.5 1.0
CD2 B:HIS187 3.1 15.8 1.0
CB B:ASP333 4.1 13.4 1.0
CG B:HIS183 4.1 13.3 1.0
ND1 B:HIS183 4.1 14.4 1.0
ND1 B:HIS187 4.2 14.6 1.0
O B:HOH592 4.2 36.4 1.0
ND2 B:ASN177 4.2 15.4 1.0
CG B:HIS187 4.2 14.7 1.0
O B:HOH534 4.3 17.6 1.0
CE1 B:PHE329 4.3 16.6 1.0
ND2 B:ASN330 4.6 12.9 1.0
O2 B:PGE410 4.6 50.4 1.0
CD1 B:ILE186 4.6 15.4 1.0
O1 B:PGE410 4.7 41.6 1.0
CZ B:PHE329 4.9 17.4 1.0
CA B:ASP333 4.9 14.2 1.0
CG1 B:ILE186 5.0 15.1 1.0
O B:ASN177 5.0 19.1 1.0

Iron binding site 7 out of 9 in 6ll1

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

b:20.7
occ:1.00
 FE1 C:FES401 0.0 20.7 1.0
SG C:CYS69 2.2 23.2 1.0
S2 C:FES401 2.2 23.4 1.0
SG C:CYS90 2.2 22.8 1.0
S1 C:FES401 2.2 24.5 1.0
FE2 C:FES401 2.8 22.6 1.0
CB C:CYS90 3.1 23.2 1.0
CB C:CYS69 3.1 21.4 1.0
CG2 C:VAL74 4.2 21.0 1.0
CB C:HIS71 4.2 21.2 1.0
CB C:TYR92 4.2 25.9 1.0
ND1 C:HIS71 4.5 17.1 1.0
ND1 C:HIS93 4.5 25.5 1.0
CA C:CYS90 4.5 22.6 1.0
CA C:CYS69 4.6 22.2 1.0
N C:HIS93 4.6 24.4 1.0
CB C:TRP95 4.8 23.2 1.0
CG C:HIS71 4.9 19.8 1.0
N C:TYR92 4.9 20.6 1.0
N C:ARG72 4.9 20.1 1.0
CG C:TRP95 5.0 23.1 1.0
N C:HIS71 5.0 20.7 1.0

Iron binding site 8 out of 9 in 6ll1

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

b:22.6
occ:1.00
 FE2 C:FES401 0.0 22.6 1.0
ND1 C:HIS93 2.0 25.5 1.0
ND1 C:HIS71 2.1 17.1 1.0
S2 C:FES401 2.2 23.4 1.0
S1 C:FES401 2.3 24.5 1.0
FE1 C:FES401 2.8 20.7 1.0
CE1 C:HIS93 2.9 28.2 1.0
CG C:HIS93 3.0 28.2 1.0
CE1 C:HIS71 3.1 19.6 1.0
CG C:HIS71 3.1 19.8 1.0
CB C:HIS71 3.4 21.2 1.0
CB C:HIS93 3.5 24.6 1.0
N C:HIS93 3.8 24.4 1.0
CB C:TYR92 4.0 25.9 1.0
NE2 C:HIS93 4.0 27.9 1.0
CD2 C:HIS93 4.1 27.9 1.0
CA C:HIS93 4.2 26.5 1.0
NE2 C:HIS71 4.2 21.3 1.0
CG C:ARG72 4.2 24.9 1.0
SG C:CYS69 4.3 23.2 1.0
CD2 C:HIS71 4.3 20.5 1.0
N C:ARG72 4.3 20.1 1.0
CD2 C:TYR92 4.3 25.6 1.0
CG C:TYR92 4.3 27.2 1.0
SG C:CYS90 4.6 22.8 1.0
C C:TYR92 4.6 24.0 1.0
CD1 C:TRP95 4.6 22.6 1.0
CA C:HIS71 4.7 21.9 1.0
NE1 C:TRP95 4.7 22.2 1.0
CB C:ARG72 4.8 23.7 1.0
C C:HIS93 4.9 27.9 1.0
C C:HIS71 4.9 20.7 1.0
CA C:TYR92 4.9 25.0 1.0

Iron binding site 9 out of 9 in 6ll1

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Iron binding site 9 out of 9 in the Oxygen-Exposed Reduced Terminal 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 Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A- Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:19.3
occ:1.00
 O1 C:OXY404 1.8 28.4 1.0
NE2 C:HIS183 2.0 16.7 1.0
OD1 C:ASP333 2.1 17.9 1.0
NE2 C:HIS187 2.1 18.5 1.0
O2 C:OXY404 2.5 30.5 1.0
OD2 C:ASP333 2.6 20.7 1.0
CG C:ASP333 2.7 17.6 1.0
CD2 C:HIS183 2.9 16.3 1.0
CE1 C:HIS187 3.0 18.6 1.0
CE1 C:HIS183 3.1 18.1 1.0
CD2 C:HIS187 3.2 17.9 1.0
ND2 C:ASN177 4.1 20.3 1.0
CG C:HIS183 4.1 15.9 1.0
ND1 C:HIS183 4.1 17.6 1.0
CB C:ASP333 4.2 17.8 1.0
ND1 C:HIS187 4.2 17.3 1.0
O C:HOH562 4.2 19.9 1.0
CG C:HIS187 4.3 18.3 1.0
CE2 C:PHE329 4.3 24.5 1.0
ND2 C:ASN330 4.5 17.9 1.0
CD1 C:ILE186 4.6 17.5 1.0
CA C:ASP333 4.9 17.7 1.0
CD2 C:PHE329 4.9 24.9 1.0

Reference:

Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri. Oxygen-Exposed Reduced Terminal Oxygenase in Carbazole 1,9A-Dioxygenase To Be Published.
Page generated: Wed Mar 3 13:52:59 2021

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