Atomistry » Iron » PDB 3vkt-3vti » 3vmi
Atomistry »
  Iron »
    PDB 3vkt-3vti »
      3vmi »

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

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

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

Protein crystallography data

The structure of Carbazole- and Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 3vmi 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) 32.68 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.012, 89.611, 104.820, 90.00, 104.18, 90.00
R / Rfree (%) 20.5 / 24

Iron Binding Sites:

Pages:

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

Binding sites:

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

Iron binding site 1 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 1 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:33.3
occ:1.00
O2 A:OXY601 1.9 43.2 1.0
OD1 A:ASP333 1.9 30.6 1.0
NE2 A:HIS183 2.1 30.5 1.0
NE2 A:HIS187 2.1 34.7 1.0
O1 A:OXY601 2.5 45.1 1.0
CG A:ASP333 2.6 32.1 1.0
OD2 A:ASP333 2.7 32.5 1.0
CD2 A:HIS183 2.9 28.8 1.0
CE1 A:HIS187 3.0 34.7 1.0
CD2 A:HIS187 3.1 33.3 1.0
CE1 A:HIS183 3.1 28.3 1.0
CB A:ASP333 4.1 30.0 1.0
CG A:HIS183 4.1 28.9 1.0
ND1 A:HIS187 4.1 34.4 1.0
ND1 A:HIS183 4.2 27.2 1.0
CG A:HIS187 4.2 33.9 1.0
ND2 A:ASN177 4.2 27.5 1.0
O A:HOH522 4.3 34.2 1.0
CE2 A:PHE329 4.4 33.7 1.0
ND2 A:ASN330 4.5 31.8 1.0
CD1 A:ILE186 4.5 31.2 1.0
CA A:ASP333 4.8 31.7 1.0
CG1 A:ILE186 4.9 30.7 1.0
O A:ASN177 5.0 28.9 1.0

Iron binding site 2 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 2 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:31.9
occ:1.00
FE1 A:FES401 0.0 31.9 1.0
SG A:CYS90 2.3 29.9 1.0
S2 A:FES401 2.3 32.5 1.0
S1 A:FES401 2.3 30.0 1.0
SG A:CYS69 2.4 30.1 1.0
FE2 A:FES401 2.8 33.5 1.0
CB A:CYS90 3.1 30.6 1.0
CB A:CYS69 3.2 31.9 1.0
CB A:TYR92 4.0 32.9 1.0
CB A:HIS71 4.1 33.5 1.0
CG2 A:VAL74 4.2 31.7 1.0
N A:HIS93 4.4 33.5 1.0
ND1 A:HIS93 4.5 34.4 1.0
CA A:CYS90 4.5 31.6 1.0
ND1 A:HIS71 4.6 32.9 1.0
CA A:CYS69 4.7 31.7 1.0
CB A:TRP95 4.7 30.2 1.0
N A:TYR92 4.8 31.4 1.0
CG A:HIS71 4.8 34.5 1.0
CA A:TYR92 4.8 32.9 1.0
N A:ARG72 4.9 33.6 1.0
CG A:TRP95 5.0 30.0 1.0
CD2 A:LEU76 5.0 37.9 1.0
C A:CYS90 5.0 33.5 1.0

Iron binding site 3 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 3 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:33.5
occ:1.00
FE2 A:FES401 0.0 33.5 1.0
ND1 A:HIS93 2.1 34.4 1.0
S1 A:FES401 2.1 30.0 1.0
ND1 A:HIS71 2.2 32.9 1.0
S2 A:FES401 2.3 32.5 1.0
FE1 A:FES401 2.8 31.9 1.0
CG A:HIS93 3.0 34.4 1.0
CG A:HIS71 3.1 34.5 1.0
CE1 A:HIS93 3.1 33.6 1.0
CE1 A:HIS71 3.2 33.8 1.0
CB A:HIS71 3.3 33.5 1.0
CB A:HIS93 3.3 32.9 1.0
N A:HIS93 3.6 33.5 1.0
CB A:TYR92 3.8 32.9 1.0
CA A:HIS93 4.1 33.3 1.0
CD2 A:HIS93 4.1 34.7 1.0
NE2 A:HIS93 4.1 35.9 1.0
CD2 A:HIS71 4.2 33.0 1.0
CG A:TYR92 4.3 35.3 1.0
NE2 A:HIS71 4.3 33.4 1.0
CG A:ARG72 4.3 35.5 1.0
CD2 A:TYR92 4.4 35.0 1.0
N A:ARG72 4.4 33.6 1.0
SG A:CYS69 4.4 30.1 1.0
C A:TYR92 4.5 33.2 1.0
CD1 A:TRP95 4.6 31.1 1.0
SG A:CYS90 4.6 29.9 1.0
CA A:HIS71 4.6 33.6 1.0
NE1 A:TRP95 4.7 29.4 1.0
CB A:ARG72 4.7 32.9 1.0
CA A:TYR92 4.8 32.9 1.0
C A:HIS93 4.8 32.3 1.0
C A:HIS71 4.9 33.3 1.0
CG A:TRP95 5.0 30.0 1.0

Iron binding site 4 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 4 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:44.5
occ:1.00
O1 B:OXY602 1.8 57.6 1.0
O2 B:OXY602 1.8 58.0 1.0
OD1 B:ASP333 2.0 40.6 1.0
NE2 B:HIS183 2.0 36.7 1.0
NE2 B:HIS187 2.2 44.3 1.0
CG B:ASP333 2.5 40.5 1.0
OD2 B:ASP333 2.6 39.2 1.0
CD2 B:HIS183 2.9 34.4 1.0
CE1 B:HIS183 3.0 36.4 1.0
CD2 B:HIS187 3.2 43.9 1.0
CE1 B:HIS187 3.2 45.1 1.0
CB B:ASP333 4.0 40.6 1.0
CG B:HIS183 4.1 35.1 1.0
ND1 B:HIS183 4.1 34.7 1.0
O B:HOH431 4.1 36.6 1.0
ND2 B:ASN177 4.3 40.2 1.0
ND1 B:HIS187 4.3 45.0 1.0
CG B:HIS187 4.3 45.1 1.0
CD1 B:ILE186 4.3 45.1 1.0
ND2 B:ASN330 4.4 39.5 1.0
C9A B:9CA2001 4.5 49.0 1.0
N9 B:9CA2001 4.5 49.8 1.0
C1 B:9CA2001 4.6 47.7 1.0
CE2 B:PHE329 4.8 37.3 1.0
CG1 B:ILE186 4.8 42.3 1.0
CA B:ASP333 4.8 42.9 1.0
O B:ASN177 4.9 40.0 1.0
C4A B:9CA2001 4.9 48.8 1.0
CG B:ASN177 5.0 42.3 1.0

Iron binding site 5 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 5 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:29.1
occ:1.00
FE1 B:FES401 0.0 29.1 1.0
S1 B:FES401 2.2 24.2 1.0
S2 B:FES401 2.2 29.9 1.0
SG B:CYS69 2.3 30.8 1.0
SG B:CYS90 2.3 31.6 1.0
FE2 B:FES401 2.7 30.7 1.0
CB B:CYS69 3.1 30.3 1.0
CB B:CYS90 3.1 30.0 1.0
CB B:TYR92 4.0 30.6 1.0
CB B:HIS71 4.1 26.6 1.0
CG2 B:VAL74 4.2 25.0 1.0
ND1 B:HIS93 4.4 27.5 1.0
N B:HIS93 4.4 28.7 1.0
CA B:CYS69 4.6 29.1 1.0
CA B:CYS90 4.6 28.8 1.0
ND1 B:HIS71 4.6 28.2 1.0
CB B:TRP95 4.7 27.2 1.0
N B:TYR92 4.8 28.1 1.0
CG B:HIS71 4.9 28.9 1.0
N B:ARG72 4.9 26.0 1.0
CA B:TYR92 4.9 29.3 1.0
CG B:TRP95 4.9 29.5 1.0

Iron binding site 6 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 6 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:30.7
occ:1.00
FE2 B:FES401 0.0 30.7 1.0
ND1 B:HIS93 2.0 27.5 1.0
S2 B:FES401 2.3 29.9 1.0
ND1 B:HIS71 2.3 28.2 1.0
S1 B:FES401 2.3 24.2 1.0
FE1 B:FES401 2.7 29.1 1.0
CE1 B:HIS93 2.9 25.4 1.0
CG B:HIS93 3.0 27.9 1.0
CG B:HIS71 3.1 28.9 1.0
CB B:HIS71 3.3 26.6 1.0
CE1 B:HIS71 3.3 27.4 1.0
CB B:HIS93 3.4 27.1 1.0
N B:HIS93 3.6 28.7 1.0
CB B:TYR92 3.8 30.6 1.0
NE2 B:HIS93 4.0 25.8 1.0
CD2 B:HIS93 4.1 24.9 1.0
CA B:HIS93 4.1 27.5 1.0
CG B:TYR92 4.3 32.6 1.0
SG B:CYS69 4.3 30.8 1.0
CD2 B:HIS71 4.3 25.8 1.0
CG B:ARG72 4.3 28.1 1.0
CD2 B:TYR92 4.3 31.2 1.0
N B:ARG72 4.3 26.0 1.0
NE2 B:HIS71 4.4 25.6 1.0
C B:TYR92 4.5 28.8 1.0
SG B:CYS90 4.6 31.6 1.0
CD1 B:TRP95 4.6 28.3 1.0
CA B:HIS71 4.6 27.4 1.0
NE1 B:TRP95 4.7 29.1 1.0
CB B:ARG72 4.7 27.4 1.0
CA B:TYR92 4.8 29.3 1.0
C B:HIS93 4.9 27.1 1.0
C B:HIS71 4.9 27.7 1.0
CG B:TRP95 5.0 29.5 1.0

Iron binding site 7 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 7 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:35.3
occ:1.00
O2 C:OXY603 1.8 51.8 1.0
O1 C:OXY603 1.8 49.6 1.0
OD1 C:ASP333 1.9 33.6 1.0
NE2 C:HIS187 2.1 39.4 1.0
NE2 C:HIS183 2.1 32.4 1.0
CG C:ASP333 2.5 34.9 1.0
OD2 C:ASP333 2.6 34.1 1.0
CD2 C:HIS183 2.9 28.6 1.0
CE1 C:HIS187 3.0 38.5 1.0
CD2 C:HIS187 3.1 36.7 1.0
CE1 C:HIS183 3.3 30.2 1.0
CB C:ASP333 4.0 34.5 1.0
ND1 C:HIS187 4.1 37.5 1.0
CG C:HIS183 4.1 29.9 1.0
CG C:HIS187 4.2 37.4 1.0
O C:HOH454 4.2 33.5 1.0
CD1 C:ILE186 4.3 37.0 1.0
ND1 C:HIS183 4.3 30.3 1.0
ND2 C:ASN330 4.4 33.5 1.0
ND2 C:ASN177 4.5 44.9 1.0
C9A C:9CA2002 4.5 47.9 1.0
C1 C:9CA2002 4.5 46.2 1.0
N9 C:9CA2002 4.7 47.4 1.0
OD1 C:ASN177 4.7 45.1 1.0
CE2 C:PHE329 4.7 33.1 1.0
CA C:ASP333 4.7 35.1 1.0
O C:ASN177 4.8 38.5 1.0
CG1 C:ILE186 4.8 35.2 1.0
CG C:ASN177 4.9 43.6 1.0

Iron binding site 8 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 8 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:35.8
occ:1.00
FE1 C:FES401 0.0 35.8 1.0
SG C:CYS69 2.2 34.3 1.0
S2 C:FES401 2.3 35.9 1.0
S1 C:FES401 2.3 37.4 1.0
SG C:CYS90 2.3 34.2 1.0
FE2 C:FES401 2.8 36.3 1.0
CB C:CYS69 3.0 33.8 1.0
CB C:CYS90 3.1 34.5 1.0
CB C:TYR92 4.0 35.3 1.0
CB C:HIS71 4.1 36.0 1.0
CG2 C:VAL74 4.2 31.1 1.0
N C:HIS93 4.5 37.8 1.0
ND1 C:HIS93 4.5 36.7 1.0
CA C:CYS69 4.5 34.0 1.0
CA C:CYS90 4.6 35.8 1.0
ND1 C:HIS71 4.7 36.4 1.0
CB C:TRP95 4.8 36.6 1.0
N C:TYR92 4.8 37.2 1.0
N C:ARG72 4.9 34.6 1.0
CA C:TYR92 4.9 38.0 1.0
CG C:HIS71 4.9 36.1 1.0
CG C:TYR92 5.0 37.1 1.0

Iron binding site 9 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 9 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:36.3
occ:1.00
FE2 C:FES401 0.0 36.3 1.0
ND1 C:HIS93 2.1 36.7 1.0
S1 C:FES401 2.3 37.4 1.0
S2 C:FES401 2.3 35.9 1.0
ND1 C:HIS71 2.3 36.4 1.0
FE1 C:FES401 2.8 35.8 1.0
CG C:HIS93 3.0 37.7 1.0
CE1 C:HIS93 3.0 37.2 1.0
CG C:HIS71 3.2 36.1 1.0
CB C:HIS71 3.3 36.0 1.0
CB C:HIS93 3.3 38.7 1.0
CE1 C:HIS71 3.4 35.2 1.0
N C:HIS93 3.7 37.8 1.0
CB C:TYR92 3.9 35.3 1.0
CD2 C:HIS93 4.1 38.9 1.0
NE2 C:HIS93 4.1 38.3 1.0
CA C:HIS93 4.1 38.4 1.0
CD2 C:TYR92 4.2 36.8 1.0
CG C:TYR92 4.3 37.1 1.0
SG C:CYS69 4.3 34.3 1.0
CG C:ARG72 4.3 38.2 1.0
N C:ARG72 4.3 34.6 1.0
CD2 C:HIS71 4.4 36.0 1.0
NE2 C:HIS71 4.4 36.2 1.0
C C:TYR92 4.5 37.7 1.0
CD1 C:TRP95 4.6 37.6 1.0
CA C:HIS71 4.7 35.3 1.0
SG C:CYS90 4.7 34.2 1.0
CB C:ARG72 4.7 35.1 1.0
NE1 C:TRP95 4.8 36.1 1.0
CA C:TYR92 4.8 38.0 1.0
C C:HIS93 4.9 39.1 1.0
C C:HIS71 5.0 35.0 1.0

Iron binding site 10 out of 15 in 3vmi

Go back to Iron Binding Sites List in 3vmi
Iron binding site 10 out of 15 in the Carbazole- and Oxygen-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 Carbazole- and Oxygen-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:33.1
occ:1.00
FE1 D:FES201 0.0 33.1 1.0
ND1 D:HIS48 2.1 32.2 1.0
S1 D:FES201 2.1 33.5 1.0
ND1 D:HIS68 2.2 32.6 1.0
S2 D:FES201 2.3 33.2 1.0
FE2 D:FES201 2.7 33.1 1.0
CE1 D:HIS48 3.0 28.4 1.0
CE1 D:HIS68 3.0 34.2 1.0
CG D:HIS48 3.2 31.6 1.0
CG D:HIS68 3.2 33.2 1.0
CB D:HIS48 3.6 31.5 1.0
CB D:HIS68 3.6 32.9 1.0
O A:HOH419 3.8 31.7 1.0
NE2 D:HIS48 4.1 30.1 1.0
N D:HIS68 4.2 33.1 1.0
CB D:PHE67 4.2 34.9 1.0
NE2 D:HIS68 4.2 34.9 1.0
CD2 D:HIS48 4.2 31.6 1.0
C D:HIS48 4.3 35.0 1.0
O D:HIS48 4.3 36.9 1.0
CD2 D:HIS68 4.3 32.0 1.0
SG D:CYS46 4.4 34.0 1.0
SG D:CYS65 4.5 35.2 1.0
CA D:HIS68 4.5 33.7 1.0
CG D:PRO83 4.5 35.5 1.0
CA D:HIS48 4.5 34.0 1.0
N D:GLY49 4.6 35.0 1.0
O A:VAL351 4.8 32.0 1.0
O A:GLU353 4.9 28.5 1.0
C D:PHE67 5.0 34.1 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 Dec 13 15:24:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy