Iron in PDB 7bug: Reduced Oxygenase of Carbazole 1,9A-Dioxygenase

The structure of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase, PDB code: 7bug was solved by J.Matsuzawa, 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)	46.01 / 1.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	91.94, 91.94, 243.46, 90, 90, 120
R / Rfree (%)	15.4 / 18.8

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

Magnesium

(Mg)

5 atoms

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

Iron binding site 1 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:9.5 occ:1.00 FE1 A:FES401 0.0 9.5 1.0 S1 A:FES401 2.2 9.7 1.0 S2 A:FES401 2.2 9.4 1.0 SG A:CYS90 2.3 9.6 1.0 SG A:CYS69 2.4 9.6 1.0 FE2 A:FES401 2.7 9.3 1.0 CB A:CYS90 3.1 9.1 1.0 CB A:CYS69 3.2 8.8 1.0 CG2 A:VAL74 4.1 9.4 1.0 CB A:TYR92 4.2 9.7 1.0 CB A:HIS71 4.2 10.1 1.0 ND1 A:HIS71 4.4 9.5 1.0 N A:HIS93 4.5 8.7 1.0 ND1 A:HIS93 4.5 9.6 1.0 CA A:CYS90 4.5 9.5 1.0 CA A:CYS69 4.6 9.2 1.0 N A:TYR92 4.8 8.4 1.0 CB A:TRP95 4.8 10.3 1.0 CG A:HIS71 4.8 9.6 1.0 N A:ARG72 4.9 10.4 1.0 CA A:TYR92 4.9 8.8 1.0 CG A:TRP95 5.0 9.7 1.0

Iron binding site 2 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:9.3 occ:1.00 FE2 A:FES401 0.0 9.3 1.0 ND1 A:HIS93 2.1 9.6 1.0 ND1 A:HIS71 2.1 9.5 1.0 S1 A:FES401 2.2 9.7 1.0 S2 A:FES401 2.2 9.4 1.0 FE1 A:FES401 2.7 9.5 1.0 CE1 A:HIS93 3.0 9.0 1.0 CE1 A:HIS71 3.0 9.3 1.0 CG A:HIS93 3.1 8.9 1.0 CG A:HIS71 3.1 9.6 1.0 CB A:HIS71 3.4 10.1 1.0 CB A:HIS93 3.5 8.7 1.0 N A:HIS93 3.7 8.7 1.0 CB A:TYR92 4.0 9.7 1.0 CA A:HIS93 4.1 8.4 1.0 NE2 A:HIS93 4.2 10.2 1.0 CD2 A:HIS93 4.2 9.3 1.0 NE2 A:HIS71 4.2 8.6 1.0 CD2 A:HIS71 4.2 9.5 1.0 CG A:ARG72 4.3 11.1 1.0 SG A:CYS69 4.4 9.6 1.0 N A:ARG72 4.4 10.4 1.0 CD2 A:TYR92 4.4 10.2 1.0 CG A:TYR92 4.4 10.0 1.0 CD1 A:TRP95 4.5 9.8 1.0 C A:TYR92 4.5 8.8 1.0 SG A:CYS90 4.6 9.6 1.0 NE1 A:TRP95 4.7 10.1 1.0 CA A:HIS71 4.7 9.4 1.0 CB A:ARG72 4.7 10.9 1.0 CA A:TYR92 4.8 8.8 1.0 C A:HIS93 4.9 9.0 1.0 CG A:TRP95 5.0 9.7 1.0 C A:HIS71 5.0 10.4 1.0

Iron binding site 3 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:19.1 occ:1.00 O A:HOH705 1.8 23.6 1.0 NE2 A:HIS183 2.0 17.5 1.0 OD1 A:ASP333 2.0 16.3 1.0 NE2 A:HIS187 2.1 15.0 1.0 O A:HOH668 2.2 23.7 1.0 OD2 A:ASP333 2.5 17.7 1.0 CG A:ASP333 2.6 16.2 1.0 CD2 A:HIS183 3.0 15.7 1.0 CE1 A:HIS187 3.0 17.6 1.0 CE1 A:HIS183 3.0 20.5 1.0 CD2 A:HIS187 3.2 17.9 1.0 CB A:ASP333 4.0 14.6 1.0 ND1 A:HIS183 4.1 16.7 1.0 O A:HOH546 4.1 17.4 1.0 CG A:HIS183 4.1 16.4 1.0 ND1 A:HIS187 4.1 18.3 1.0 O A:HOH510 4.2 34.2 1.0 CG A:HIS187 4.3 16.0 1.0 ND2 A:ASN330 4.4 15.4 1.0 O4 A:PEG404 4.5 37.4 1.0 CE2 A:PHE329 4.5 18.8 1.0 OD1 A:ASN177 4.6 30.2 1.0 O A:ASN177 4.6 22.3 1.0 ND2 A:ASN177 4.7 25.9 1.0 CD1 A:ILE186 4.7 21.1 1.0 C4 A:PEG404 4.7 33.7 1.0 CA A:ASP333 4.8 16.2 1.0 O2 A:PEG404 4.8 40.9 1.0 CG A:ASN177 4.9 24.1 1.0

Iron binding site 4 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:13.4 occ:1.00 FE1 B:FES401 0.0 13.4 1.0 S2 B:FES401 2.2 14.0 1.0 S1 B:FES401 2.2 14.0 1.0 SG B:CYS90 2.3 13.9 1.0 SG B:CYS69 2.3 13.6 1.0 FE2 B:FES401 2.7 13.6 1.0 CB B:CYS90 3.1 12.8 1.0 CB B:CYS69 3.2 12.6 1.0 CB B:HIS71 4.2 15.6 1.0 CB B:TYR92 4.2 13.6 1.0 CG2 B:VAL74 4.2 13.4 1.0 ND1 B:HIS71 4.4 14.5 1.0 ND1 B:HIS93 4.5 11.9 1.0 N B:HIS93 4.5 12.8 1.0 CA B:CYS90 4.5 12.8 1.0 CA B:CYS69 4.6 14.2 1.0 CB B:TRP95 4.7 16.0 1.0 CG B:HIS71 4.8 14.1 1.0 N B:TYR92 4.8 11.8 1.0 N B:ARG72 4.9 13.2 1.0 CG B:TRP95 4.9 15.1 1.0 C B:CYS90 5.0 12.9 1.0 CA B:TYR92 5.0 12.5 1.0

Iron binding site 5 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:13.6 occ:1.00 FE2 B:FES401 0.0 13.6 1.0 ND1 B:HIS71 2.1 14.5 1.0 ND1 B:HIS93 2.1 11.9 1.0 S1 B:FES401 2.2 14.0 1.0 S2 B:FES401 2.2 14.0 1.0 FE1 B:FES401 2.7 13.4 1.0 CE1 B:HIS93 3.0 12.3 1.0 CG B:HIS71 3.1 14.1 1.0 CE1 B:HIS71 3.1 14.2 1.0 CG B:HIS93 3.2 12.7 1.0 CB B:HIS71 3.4 15.6 1.0 CB B:HIS93 3.5 12.9 1.0 N B:HIS93 3.7 12.8 1.0 CB B:TYR92 4.0 13.6 1.0 NE2 B:HIS93 4.1 12.3 1.0 CA B:HIS93 4.2 13.0 1.0 CD2 B:HIS93 4.2 12.9 1.0 CD2 B:HIS71 4.2 14.2 1.0 NE2 B:HIS71 4.3 14.0 1.0 CG B:ARG72 4.3 15.2 1.0 SG B:CYS69 4.3 13.6 1.0 N B:ARG72 4.4 13.2 1.0 CD2 B:TYR92 4.4 14.2 1.0 CG B:TYR92 4.5 13.7 1.0 CD1 B:TRP95 4.5 14.9 1.0 SG B:CYS90 4.6 13.9 1.0 C B:TYR92 4.6 13.6 1.0 NE1 B:TRP95 4.6 15.1 1.0 CA B:HIS71 4.6 15.6 1.0 CB B:ARG72 4.7 14.8 1.0 CA B:TYR92 4.8 12.5 1.0 C B:HIS93 4.9 14.7 1.0 CG B:TRP95 4.9 15.1 1.0 C B:HIS71 4.9 15.4 1.0

Iron binding site 6 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:13.8 occ:1.00 O B:HOH717 1.9 21.5 1.0 OD1 B:ASP333 2.0 13.5 1.0 NE2 B:HIS183 2.1 13.6 1.0 NE2 B:HIS187 2.1 11.4 1.0 O B:HOH660 2.3 20.2 1.0 OD2 B:ASP333 2.5 14.1 1.0 CG B:ASP333 2.5 12.4 1.0 CD2 B:HIS183 3.0 11.5 1.0 CE1 B:HIS187 3.0 12.1 1.0 CE1 B:HIS183 3.1 13.8 1.0 CD2 B:HIS187 3.1 11.0 1.0 CB B:ASP333 4.0 11.7 1.0 ND1 B:HIS183 4.2 11.9 1.0 CG B:HIS183 4.2 10.9 1.0 ND1 B:HIS187 4.2 11.1 1.0 ND2 B:ASN177 4.2 25.6 1.0 O B:HOH542 4.2 25.7 1.0 O B:HOH595 4.2 14.7 1.0 CG B:HIS187 4.2 10.9 1.0 C1 B:PG0412 4.3 19.4 1.0 CE1 B:PHE329 4.5 14.7 1.0 ND2 B:ASN330 4.5 11.4 1.0 CD1 B:ILE186 4.6 13.3 1.0 O B:ASN177 4.7 16.7 1.0 CA B:ASP333 4.8 11.9 1.0 C3 B:PG0412 4.9 26.4 1.0 OTT B:PG0412 4.9 25.5 1.0 CG1 B:ILE186 5.0 11.6 1.0

Iron binding site 7 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:15.5 occ:1.00 FE1 C:FES401 0.0 15.5 1.0 S1 C:FES401 2.2 15.6 1.0 S2 C:FES401 2.2 13.8 1.0 SG C:CYS90 2.4 16.1 1.0 SG C:CYS69 2.4 16.4 1.0 FE2 C:FES401 2.7 15.2 1.0 CB C:CYS90 3.2 13.5 1.0 CB C:CYS69 3.2 14.1 1.0 CB C:TYR92 4.1 14.7 1.0 CG2 C:VAL74 4.2 15.1 1.0 CB C:HIS71 4.2 15.4 1.0 ND1 C:HIS71 4.4 14.3 1.0 N C:HIS93 4.4 15.1 1.0 ND1 C:HIS93 4.4 16.7 1.0 CA C:CYS90 4.6 15.4 1.0 CA C:CYS69 4.6 14.8 1.0 CB C:TRP95 4.7 18.2 1.0 N C:TYR92 4.8 15.2 1.0 CG C:HIS71 4.8 13.8 1.0 N C:ARG72 4.9 14.9 1.0 CA C:TYR92 4.9 15.4 1.0 CG C:TRP95 4.9 16.8 1.0

Iron binding site 8 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:15.2 occ:1.00 FE2 C:FES401 0.0 15.2 1.0 ND1 C:HIS93 2.1 16.7 1.0 ND1 C:HIS71 2.1 14.3 1.0 S1 C:FES401 2.2 15.6 1.0 S2 C:FES401 2.2 13.8 1.0 FE1 C:FES401 2.7 15.5 1.0 CE1 C:HIS93 3.0 18.6 1.0 CE1 C:HIS71 3.0 15.6 1.0 CG C:HIS71 3.1 13.8 1.0 CG C:HIS93 3.1 14.2 1.0 CB C:HIS71 3.4 15.4 1.0 CB C:HIS93 3.5 14.4 1.0 N C:HIS93 3.7 15.1 1.0 CB C:TYR92 3.9 14.7 1.0 CA C:HIS93 4.1 15.4 1.0 NE2 C:HIS93 4.1 16.4 1.0 NE2 C:HIS71 4.2 13.3 1.0 CD2 C:HIS93 4.2 16.8 1.0 CD2 C:HIS71 4.2 15.6 1.0 N C:ARG72 4.3 14.9 1.0 CG C:ARG72 4.3 16.1 1.0 SG C:CYS69 4.4 16.4 1.0 CD2 C:TYR92 4.4 17.3 1.0 CG C:TYR92 4.4 15.4 1.0 C C:TYR92 4.5 15.4 1.0 CD1 C:TRP95 4.5 17.1 1.0 NE1 C:TRP95 4.6 16.9 1.0 SG C:CYS90 4.6 16.1 1.0 CA C:HIS71 4.7 15.6 1.0 CB C:ARG72 4.7 16.1 1.0 CA C:TYR92 4.8 15.4 1.0 C C:HIS93 4.9 17.2 1.0 C C:HIS71 4.9 15.6 1.0 CG C:TRP95 4.9 16.8 1.0

Iron binding site 9 out of 9 in the Reduced Oxygenase of 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 Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:17.0 occ:1.00 O C:HOH656 2.0 19.8 1.0 NE2 C:HIS187 2.1 14.2 1.0 NE2 C:HIS183 2.1 14.6 1.0 OD1 C:ASP333 2.1 14.9 1.0 O C:HOH692 2.3 22.6 1.0 OD2 C:ASP333 2.4 16.7 1.0 CG C:ASP333 2.6 14.6 1.0 CD2 C:HIS183 3.0 13.6 1.0 CE1 C:HIS187 3.1 15.1 1.0 CD2 C:HIS187 3.1 13.3 1.0 CE1 C:HIS183 3.2 15.9 1.0 CB C:ASP333 4.1 12.9 1.0 O C:HOH594 4.2 18.8 1.0 ND1 C:HIS187 4.2 13.1 1.0 O C:HOH602 4.2 29.8 1.0 CG C:HIS183 4.2 14.6 1.0 ND1 C:HIS183 4.2 15.4 1.0 CG C:HIS187 4.2 14.1 1.0 O2 C:PG0411 4.3 26.0 1.0 CE2 C:PHE329 4.5 16.1 1.0 ND2 C:ASN330 4.5 16.5 1.0 O C:ASN177 4.6 21.9 1.0 OD1 C:ASN177 4.6 26.2 1.0 ND2 C:ASN177 4.7 24.0 1.0 CD1 C:ILE186 4.7 15.0 1.0 C5 C:PG0411 4.8 25.2 1.0 CA C:ASP333 4.9 14.1 1.0 CG C:ASN177 4.9 21.1 1.0

J.Matsuzawa, Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri. Reduced Oxygenase of Carbazole 1,9A-Dioxygenase To Be Published.