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Iron in PDB 2de7: The Substrate-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase

Protein crystallography data

The structure of The Substrate-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 2de7 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) 41.91 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.862, 89.403, 104.665, 90.00, 104.18, 90.00
R / Rfree (%) 20.7 / 23.8

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the The Substrate-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase (pdb code 2de7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the The Substrate-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 2de7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in 2de7

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Iron binding site 1 out of 15 in the The Substrate-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 The Substrate-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:24.0
occ:1.00
O A:HOH528 1.9 33.7 1.0
OD1 A:ASP333 1.9 22.4 1.0
NE2 A:HIS183 2.0 23.1 1.0
NE2 A:HIS187 2.1 25.6 1.0
CG A:ASP333 2.6 23.2 1.0
OD2 A:ASP333 2.7 24.2 1.0
CD2 A:HIS183 2.9 22.2 1.0
CE1 A:HIS187 3.1 24.8 1.0
CE1 A:HIS183 3.1 21.8 1.0
CD2 A:HIS187 3.2 25.5 1.0
CB A:ASP333 4.1 21.8 1.0
CG A:HIS183 4.1 21.3 1.0
ND1 A:HIS183 4.2 20.5 1.0
ND1 A:HIS187 4.2 25.4 1.0
CG A:HIS187 4.3 24.9 1.0
O A:HOH579 4.3 25.1 1.0
ND2 A:ASN177 4.3 18.8 1.0
CE2 A:PHE329 4.4 26.4 1.0
ND2 A:ASN330 4.5 24.1 1.0
CD1 A:ILE186 4.5 23.2 1.0
CA A:ASP333 4.8 23.0 1.0
O A:ASN177 4.9 19.6 1.0
CG1 A:ILE186 5.0 21.1 1.0

Iron binding site 2 out of 15 in 2de7

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Iron binding site 2 out of 15 in the The Substrate-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 The Substrate-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:21.7
occ:1.00
FE1 A:FES401 0.0 21.7 1.0
SG A:CYS90 2.2 22.9 1.0
S2 A:FES401 2.3 25.0 1.0
S1 A:FES401 2.3 25.0 1.0
SG A:CYS69 2.4 22.7 1.0
FE2 A:FES401 2.7 26.2 1.0
CB A:CYS90 3.1 23.5 1.0
CB A:CYS69 3.1 23.0 1.0
CB A:TYR92 4.0 26.1 1.0
CB A:HIS71 4.0 21.9 1.0
CG2 A:VAL74 4.2 23.7 1.0
N A:HIS93 4.4 25.3 1.0
CA A:CYS90 4.5 23.9 1.0
ND1 A:HIS93 4.5 26.6 1.0
ND1 A:HIS71 4.6 20.5 1.0
CA A:CYS69 4.6 22.1 1.0
CB A:TRP95 4.8 22.7 1.0
N A:TYR92 4.8 23.9 1.0
CG A:HIS71 4.8 21.1 1.0
CA A:TYR92 4.9 25.5 1.0
N A:ARG72 4.9 23.3 1.0
CG A:TRP95 5.0 21.4 1.0
C A:CYS90 5.0 24.4 1.0

Iron binding site 3 out of 15 in 2de7

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Iron binding site 3 out of 15 in the The Substrate-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 The Substrate-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:26.2
occ:1.00
FE2 A:FES401 0.0 26.2 1.0
ND1 A:HIS93 2.1 26.6 1.0
ND1 A:HIS71 2.2 20.5 1.0
S1 A:FES401 2.2 25.0 1.0
S2 A:FES401 2.3 25.0 1.0
FE1 A:FES401 2.7 21.7 1.0
CG A:HIS71 3.0 21.1 1.0
CG A:HIS93 3.0 26.2 1.0
CE1 A:HIS93 3.1 26.8 1.0
CB A:HIS71 3.2 21.9 1.0
CE1 A:HIS71 3.3 22.7 1.0
CB A:HIS93 3.3 24.8 1.0
N A:HIS93 3.7 25.3 1.0
CB A:TYR92 3.9 26.1 1.0
CA A:HIS93 4.1 25.1 1.0
CD2 A:HIS93 4.2 27.0 1.0
NE2 A:HIS93 4.2 26.7 1.0
CD2 A:HIS71 4.2 20.1 1.0
CG A:TYR92 4.3 28.4 1.0
NE2 A:HIS71 4.3 21.8 1.0
N A:ARG72 4.3 23.3 1.0
CG A:ARG72 4.3 26.4 1.0
SG A:CYS69 4.3 22.7 1.0
CD2 A:TYR92 4.4 29.6 1.0
SG A:CYS90 4.6 22.9 1.0
C A:TYR92 4.6 25.1 1.0
CA A:HIS71 4.6 23.3 1.0
CD1 A:TRP95 4.6 21.0 1.0
NE1 A:TRP95 4.7 21.6 1.0
CB A:ARG72 4.8 23.6 1.0
CA A:TYR92 4.8 25.5 1.0
C A:HIS93 4.9 24.5 1.0
C A:HIS71 4.9 23.0 1.0
CG A:TRP95 5.0 21.4 1.0

Iron binding site 4 out of 15 in 2de7

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Iron binding site 4 out of 15 in the The Substrate-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 The Substrate-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:41.6
occ:1.00
O B:HOH2114 1.7 48.7 1.0
OD1 B:ASP333 2.0 30.7 1.0
NE2 B:HIS183 2.0 28.6 1.0
NE2 B:HIS187 2.3 34.9 1.0
CG B:ASP333 2.6 30.0 1.0
OD2 B:ASP333 2.7 29.8 1.0
CD2 B:HIS183 3.0 27.4 1.0
CE1 B:HIS183 3.0 28.7 1.0
CD2 B:HIS187 3.2 33.2 1.0
CE1 B:HIS187 3.4 35.1 1.0
CB B:ASP333 4.1 30.5 1.0
ND1 B:HIS183 4.1 27.5 1.0
CG B:HIS183 4.1 27.5 1.0
ND2 B:ASN177 4.2 35.4 1.0
C9A B:9CA2001 4.2 34.5 1.0
O B:HOH2028 4.2 25.4 1.0
C1 B:9CA2001 4.3 34.0 1.0
CG B:HIS187 4.4 34.2 1.0
N9 B:9CA2001 4.4 35.8 1.0
ND1 B:HIS187 4.4 34.2 1.0
ND2 B:ASN330 4.5 28.1 1.0
CD1 B:ILE186 4.6 33.9 1.0
O B:ASN177 4.7 32.9 1.0
C4A B:9CA2001 4.8 35.0 1.0
CE2 B:PHE329 4.8 29.9 1.0
C2 B:9CA2001 4.8 34.7 1.0
CA B:ASP333 4.9 31.4 1.0
C8A B:9CA2001 4.9 35.9 1.0
CG B:ASN177 4.9 35.9 1.0

Iron binding site 5 out of 15 in 2de7

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Iron binding site 5 out of 15 in the The Substrate-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 The Substrate-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:22.9
occ:1.00
FE1 B:FES401 0.0 22.9 1.0
S1 B:FES401 2.1 21.4 1.0
SG B:CYS69 2.2 20.4 1.0
S2 B:FES401 2.3 19.9 1.0
SG B:CYS90 2.3 19.1 1.0
FE2 B:FES401 2.8 18.5 1.0
CB B:CYS90 3.1 20.0 1.0
CB B:CYS69 3.1 19.0 1.0
CB B:TYR92 4.0 19.6 1.0
CB B:HIS71 4.1 18.3 1.0
CG2 B:VAL74 4.3 16.3 1.0
N B:HIS93 4.4 20.1 1.0
ND1 B:HIS93 4.4 18.0 1.0
CA B:CYS69 4.6 19.6 1.0
CA B:CYS90 4.6 19.5 1.0
ND1 B:HIS71 4.6 18.4 1.0
CB B:TRP95 4.7 19.4 1.0
N B:TYR92 4.8 19.4 1.0
CG B:TRP95 4.9 19.6 1.0
CG B:HIS71 4.9 19.6 1.0
CA B:TYR92 4.9 20.3 1.0
N B:ARG72 4.9 18.5 1.0
N B:TRP95 5.0 20.8 1.0

Iron binding site 6 out of 15 in 2de7

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Iron binding site 6 out of 15 in the The Substrate-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 The Substrate-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:18.5
occ:1.00
FE2 B:FES401 0.0 18.5 1.0
ND1 B:HIS93 2.0 18.0 1.0
ND1 B:HIS71 2.2 18.4 1.0
S2 B:FES401 2.2 19.9 1.0
S1 B:FES401 2.3 21.4 1.0
FE1 B:FES401 2.8 22.9 1.0
CG B:HIS93 3.0 20.0 1.0
CE1 B:HIS93 3.0 18.5 1.0
CG B:HIS71 3.1 19.6 1.0
CB B:HIS71 3.2 18.3 1.0
CE1 B:HIS71 3.3 20.5 1.0
CB B:HIS93 3.3 19.0 1.0
N B:HIS93 3.7 20.1 1.0
CB B:TYR92 3.9 19.6 1.0
NE2 B:HIS93 4.1 17.6 1.0
CD2 B:HIS93 4.1 19.2 1.0
CA B:HIS93 4.1 19.5 1.0
CD2 B:HIS71 4.3 15.9 1.0
SG B:CYS69 4.3 20.4 1.0
CG B:TYR92 4.3 21.5 1.0
NE2 B:HIS71 4.3 17.1 1.0
CD2 B:TYR92 4.3 21.2 1.0
N B:ARG72 4.4 18.5 1.0
CG B:ARG72 4.4 19.7 1.0
CD1 B:TRP95 4.6 20.5 1.0
C B:TYR92 4.6 19.9 1.0
NE1 B:TRP95 4.6 18.4 1.0
SG B:CYS90 4.6 19.1 1.0
CA B:HIS71 4.6 19.8 1.0
CB B:ARG72 4.7 20.1 1.0
CA B:TYR92 4.9 20.3 1.0
C B:HIS93 4.9 18.1 1.0
CG B:TRP95 4.9 19.6 1.0
C B:HIS71 4.9 18.4 1.0
CE2 B:TRP95 5.0 22.2 1.0

Iron binding site 7 out of 15 in 2de7

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Iron binding site 7 out of 15 in the The Substrate-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 The Substrate-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:35.8
occ:1.00
O C:HOH2052 1.6 35.0 1.0
OD1 C:ASP333 2.0 26.8 1.0
NE2 C:HIS183 2.2 23.9 1.0
NE2 C:HIS187 2.2 30.6 1.0
CG C:ASP333 2.6 25.1 1.0
OD2 C:ASP333 2.6 23.8 1.0
CD2 C:HIS183 3.0 20.7 1.0
CE1 C:HIS187 3.2 31.7 1.0
CD2 C:HIS187 3.2 28.5 1.0
CE1 C:HIS183 3.3 23.4 1.0
CB C:ASP333 4.1 24.8 1.0
CG C:HIS183 4.2 22.7 1.0
C1 C:9CA2002 4.2 34.1 1.0
C9A C:9CA2002 4.3 35.1 1.0
O C:HOH2048 4.3 24.9 1.0
ND1 C:HIS183 4.3 20.3 1.0
ND1 C:HIS187 4.3 30.5 1.0
ND2 C:ASN177 4.3 36.3 1.0
CG C:HIS187 4.4 29.4 1.0
ND2 C:ASN330 4.4 25.6 1.0
N9 C:9CA2002 4.4 35.1 1.0
CD1 C:ILE186 4.5 30.4 1.0
CE2 C:PHE329 4.6 25.9 1.0
O C:ASN177 4.7 31.5 1.0
C2 C:9CA2002 4.8 33.6 1.0
C4A C:9CA2002 4.8 35.3 1.0
CA C:ASP333 4.8 25.1 1.0
CG1 C:ILE186 5.0 26.6 1.0

Iron binding site 8 out of 15 in 2de7

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Iron binding site 8 out of 15 in the The Substrate-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 The Substrate-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:27.3
occ:1.00
FE1 C:FES401 0.0 27.3 1.0
SG C:CYS69 2.1 25.5 1.0
S1 C:FES401 2.2 30.4 1.0
S2 C:FES401 2.3 26.9 1.0
SG C:CYS90 2.4 26.0 1.0
FE2 C:FES401 2.8 27.3 1.0
CB C:CYS69 3.0 24.8 1.0
CB C:CYS90 3.1 25.3 1.0
CB C:TYR92 3.9 25.2 1.0
CB C:HIS71 4.1 24.3 1.0
CG2 C:VAL74 4.2 22.3 1.0
N C:HIS93 4.4 27.8 1.0
ND1 C:HIS93 4.4 26.9 1.0
CA C:CYS69 4.5 23.8 1.0
CA C:CYS90 4.6 26.3 1.0
ND1 C:HIS71 4.7 24.5 1.0
CB C:TRP95 4.8 27.8 1.0
N C:TYR92 4.8 27.5 1.0
CA C:TYR92 4.8 27.5 1.0
CG C:HIS71 4.9 24.6 1.0
N C:ARG72 4.9 23.0 1.0
CD2 C:LEU76 5.0 28.2 1.0
CG C:TYR92 5.0 26.6 1.0

Iron binding site 9 out of 15 in 2de7

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Iron binding site 9 out of 15 in the The Substrate-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 The Substrate-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:27.3
occ:1.00
FE2 C:FES401 0.0 27.3 1.0
ND1 C:HIS93 2.0 26.9 1.0
ND1 C:HIS71 2.3 24.5 1.0
S1 C:FES401 2.3 30.4 1.0
S2 C:FES401 2.3 26.9 1.0
FE1 C:FES401 2.8 27.3 1.0
CG C:HIS93 2.9 29.1 1.0
CE1 C:HIS93 3.0 28.8 1.0
CG C:HIS71 3.1 24.6 1.0
CB C:HIS93 3.3 27.6 1.0
CB C:HIS71 3.3 24.3 1.0
CE1 C:HIS71 3.3 25.0 1.0
N C:HIS93 3.7 27.8 1.0
CB C:TYR92 3.8 25.2 1.0
NE2 C:HIS93 4.0 29.3 1.0
CD2 C:HIS93 4.0 28.3 1.0
CA C:HIS93 4.1 28.9 1.0
CD2 C:TYR92 4.2 26.0 1.0
CG C:TYR92 4.2 26.6 1.0
SG C:CYS69 4.2 25.5 1.0
CG C:ARG72 4.3 28.8 1.0
CD2 C:HIS71 4.3 24.4 1.0
N C:ARG72 4.3 23.0 1.0
NE2 C:HIS71 4.4 25.1 1.0
C C:TYR92 4.5 27.7 1.0
CD1 C:TRP95 4.7 30.1 1.0
CA C:HIS71 4.7 24.2 1.0
CB C:ARG72 4.7 23.9 1.0
SG C:CYS90 4.7 26.0 1.0
NE1 C:TRP95 4.8 30.1 1.0
CA C:TYR92 4.8 27.5 1.0
C C:HIS93 4.9 28.9 1.0
C C:HIS71 5.0 23.7 1.0

Iron binding site 10 out of 15 in 2de7

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Iron binding site 10 out of 15 in the The Substrate-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 The Substrate-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:26.0
occ:1.00
FE1 D:FES201 0.0 26.0 1.0
S2 D:FES201 2.2 30.3 1.0
S1 D:FES201 2.2 28.6 1.0
SG D:CYS46 2.2 27.4 1.0
SG D:CYS65 2.3 29.5 1.0
FE2 D:FES201 2.7 26.0 1.0
CB D:CYS46 3.1 28.2 1.0
CB D:CYS65 3.1 31.6 1.0
CB D:HIS48 4.1 26.0 1.0
ND1 D:HIS48 4.2 24.5 1.0
CB D:ALA51 4.3 31.3 1.0
CB D:PHE67 4.3 29.5 1.0
ND1 D:HIS68 4.4 28.1 1.0
CA D:CYS46 4.5 29.7 1.0
CA D:CYS65 4.6 30.4 1.0
CG D:HIS48 4.6 24.9 1.0
SG D:CYS84 4.7 31.8 1.0
N D:HIS68 4.7 27.7 1.0
N D:GLY49 4.8 28.8 1.0
CA D:HIS48 4.9 27.9 1.0
N D:HIS48 4.9 29.4 1.0
C D:HIS48 4.9 29.0 1.0

Reference:

Y.Ashikawa, Z.Fujimoto, H.Noguchi, H.Habe, T.Omori, H.Yamane, H.Nojiri. Electron Transfer Complex Formation Between Oxygenase and Ferredoxin Components in Rieske Nonheme Iron Oxygenase System Structure V. 14 1779 2006.
ISSN: ISSN 0969-2126
PubMed: 17161368
DOI: 10.1016/J.STR.2006.10.004
Page generated: Sun Dec 13 14:42:41 2020

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