Atomistry » Iron » PDB 6ll1-6m54 » 6ll1
Atomistry »
  Iron »
    PDB 6ll1-6m54 »
      6ll1 »

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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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

Go back to Iron Binding Sites List in 6ll1
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 Aug 7 01:20:32 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy