Iron in PDB 4nbf: Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase

All present enzymatic activity of Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase:
1.14.12.22;

The structure of Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nbf was solved by Y.Ashikawa, Y.Usami, K.Inoue, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.23 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.250, 89.502, 105.114, 90.00, 104.08, 90.00
R / Rfree (%)	18.6 / 21.3

Pages:

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

Binding sites:

The binding sites of Iron atom in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (pdb code 4nbf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase, PDB code: 4nbf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.7 occ:1.00 OD1 A:ASP333 2.0 23.3 1.0 O A:HOH898 2.0 34.8 1.0 NE2 A:HIS183 2.0 23.6 1.0 NE2 A:HIS187 2.1 23.3 1.0 CG A:ASP333 2.6 22.5 1.0 OD2 A:ASP333 2.7 24.4 1.0 CD2 A:HIS183 2.8 22.4 1.0 O A:HOH710 2.9 45.7 1.0 CE1 A:HIS187 3.1 26.5 1.0 CD2 A:HIS187 3.1 25.7 1.0 CE1 A:HIS183 3.2 23.1 1.0 CG A:HIS183 4.0 22.7 1.0 CB A:ASP333 4.1 22.3 1.0 ND1 A:HIS183 4.2 22.2 1.0 ND2 A:ASN177 4.2 19.6 1.0 ND1 A:HIS187 4.2 26.5 1.0 CG A:HIS187 4.2 24.4 1.0 O A:HOH707 4.3 34.2 1.0 CE2 A:PHE329 4.4 27.7 1.0 CD1 A:ILE186 4.4 21.4 1.0 CA A:ASP333 4.8 21.7 1.0 CG1 A:ILE186 4.9 21.3 1.0 ND2 A:ASN330 4.9 23.1 1.0 CZ A:PHE329 5.0 27.1 1.0

Iron binding site 2 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:20.6 occ:1.00 FE1 A:FES502 0.0 20.6 1.0 S1 A:FES502 2.2 22.2 1.0 SG A:CYS90 2.2 23.4 1.0 S2 A:FES502 2.3 21.5 1.0 SG A:CYS69 2.3 16.1 1.0 FE2 A:FES502 2.8 22.9 1.0 CB A:CYS90 3.0 19.8 1.0 CB A:CYS69 3.1 16.7 1.0 CB A:TYR92 4.0 18.4 1.0 CB A:HIS71 4.1 20.2 1.0 CG2 A:VAL74 4.2 18.3 1.0 N A:HIS93 4.4 18.2 1.0 ND1 A:HIS93 4.5 16.1 1.0 CA A:CYS90 4.5 20.3 1.0 CA A:CYS69 4.6 18.7 1.0 ND1 A:HIS71 4.6 20.9 1.0 N A:TYR92 4.7 18.6 1.0 CB A:TRP95 4.8 18.9 1.0 CA A:TYR92 4.8 19.8 1.0 CG A:HIS71 4.9 21.6 1.0 N A:ARG72 4.9 20.2 1.0 CG A:TRP95 4.9 17.6 1.0 C A:CYS90 5.0 19.9 1.0

Iron binding site 3 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:22.9 occ:1.00 FE2 A:FES502 0.0 22.9 1.0 ND1 A:HIS93 2.1 16.1 1.0 ND1 A:HIS71 2.1 20.9 1.0 S1 A:FES502 2.2 22.2 1.0 S2 A:FES502 2.3 21.5 1.0 FE1 A:FES502 2.8 20.6 1.0 CE1 A:HIS93 3.0 19.4 1.0 CG A:HIS71 3.0 21.6 1.0 CG A:HIS93 3.1 19.7 1.0 CB A:HIS71 3.2 20.2 1.0 CE1 A:HIS71 3.2 22.8 1.0 CB A:HIS93 3.4 16.1 1.0 N A:HIS93 3.7 18.2 1.0 CB A:TYR92 3.9 18.4 1.0 NE2 A:HIS93 4.1 18.1 1.0 CA A:HIS93 4.1 18.1 1.0 CD2 A:HIS93 4.2 16.5 1.0 CD2 A:HIS71 4.2 19.0 1.0 NE2 A:HIS71 4.3 21.9 1.0 CG A:TYR92 4.3 20.6 1.0 N A:ARG72 4.3 20.2 1.0 SG A:CYS69 4.4 16.1 1.0 CG A:ARG72 4.4 20.4 1.0 CD2 A:TYR92 4.4 22.0 1.0 CD1 A:TRP95 4.5 17.8 1.0 C A:TYR92 4.5 19.0 1.0 NE1 A:TRP95 4.6 17.0 1.0 CA A:HIS71 4.6 21.5 1.0 SG A:CYS90 4.6 23.4 1.0 CB A:ARG72 4.7 19.1 1.0 CA A:TYR92 4.8 19.8 1.0 C A:HIS93 4.9 18.1 1.0 C A:HIS71 4.9 21.0 1.0 CG A:TRP95 4.9 17.6 1.0 CE2 A:TRP95 5.0 19.0 1.0

Iron binding site 4 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:42.8 occ:1.00 OD1 B:ASP333 2.0 28.9 1.0 NE2 B:HIS183 2.0 26.7 1.0 O B:HOH869 2.2 48.0 1.0 NE2 B:HIS187 2.2 28.6 1.0 CG B:ASP333 2.8 26.4 1.0 CD2 B:HIS183 2.9 23.1 1.0 OD2 B:ASP333 2.9 28.3 1.0 CE1 B:HIS183 3.1 24.6 1.0 CE1 B:HIS187 3.2 30.5 1.0 CD2 B:HIS187 3.2 29.9 1.0 O B:HOH895 4.0 34.0 1.0 O B:HOH778 4.0 44.0 1.0 CG B:HIS183 4.1 24.7 1.0 ND1 B:HIS183 4.1 24.5 1.0 O B:HOH627 4.2 29.7 1.0 CB B:ASP333 4.2 26.4 1.0 ND2 B:ASN177 4.2 25.7 1.0 ND1 B:HIS187 4.3 28.7 1.0 CG B:HIS187 4.4 29.8 1.0 CE2 B:PHE329 4.5 28.5 1.0 CD1 B:ILE186 4.7 24.0 1.0 O B:ASN177 4.9 28.5 1.0 ND2 B:ASN330 4.9 27.6 1.0 CA B:ASP333 4.9 26.6 1.0

Iron binding site 5 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:25.3 occ:1.00 FE1 B:FES502 0.0 25.3 1.0 S1 B:FES502 2.1 17.8 1.0 SG B:CYS69 2.2 17.6 1.0 S2 B:FES502 2.2 18.7 1.0 SG B:CYS90 2.3 25.8 1.0 FE2 B:FES502 2.8 17.9 1.0 CB B:CYS90 3.1 19.5 1.0 CB B:CYS69 3.1 16.2 1.0 CB B:TYR92 4.1 18.9 1.0 CB B:HIS71 4.1 19.1 1.0 CG2 B:VAL74 4.2 16.6 1.0 N B:HIS93 4.4 20.6 1.0 ND1 B:HIS93 4.5 19.7 1.0 CA B:CYS90 4.5 20.7 1.0 CA B:CYS69 4.6 18.8 1.0 ND1 B:HIS71 4.7 20.3 1.0 CB B:TRP95 4.7 18.9 1.0 N B:TYR92 4.8 20.6 1.0 CG B:HIS71 4.9 20.5 1.0 CD2 B:LEU76 4.9 23.8 1.0 CA B:TYR92 4.9 20.8 1.0 N B:ARG72 4.9 18.5 1.0 CG B:TRP95 4.9 19.9 1.0 N B:HIS71 5.0 20.4 1.0

Iron binding site 6 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:17.9 occ:1.00 FE2 B:FES502 0.0 17.9 1.0 ND1 B:HIS93 2.1 19.7 1.0 S1 B:FES502 2.2 17.8 1.0 S2 B:FES502 2.2 18.7 1.0 ND1 B:HIS71 2.2 20.3 1.0 FE1 B:FES502 2.8 25.3 1.0 CG B:HIS93 3.0 20.5 1.0 CE1 B:HIS93 3.0 19.6 1.0 CG B:HIS71 3.1 20.5 1.0 CB B:HIS71 3.2 19.1 1.0 CE1 B:HIS71 3.3 21.3 1.0 CB B:HIS93 3.3 17.9 1.0 N B:HIS93 3.6 20.6 1.0 CB B:TYR92 3.9 18.9 1.0 CA B:HIS93 4.1 19.4 1.0 NE2 B:HIS93 4.1 19.5 1.0 CD2 B:HIS93 4.1 18.7 1.0 SG B:CYS69 4.3 17.6 1.0 CG B:TYR92 4.3 20.3 1.0 CG B:ARG72 4.3 18.1 1.0 CD2 B:HIS71 4.3 19.5 1.0 N B:ARG72 4.3 18.5 1.0 CD2 B:TYR92 4.4 19.5 1.0 NE2 B:HIS71 4.4 20.1 1.0 C B:TYR92 4.5 20.2 1.0 SG B:CYS90 4.6 25.8 1.0 CA B:HIS71 4.6 21.0 1.0 CD1 B:TRP95 4.6 20.9 1.0 NE1 B:TRP95 4.7 18.8 1.0 CB B:ARG72 4.7 18.7 1.0 CA B:TYR92 4.8 20.8 1.0 C B:HIS93 4.9 18.2 1.0 C B:HIS71 4.9 19.1 1.0 CG B:TRP95 5.0 19.9 1.0

Iron binding site 7 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:36.9 occ:1.00 OD1 C:ASP333 1.9 20.9 1.0 NE2 C:HIS183 2.1 25.2 1.0 O C:HOH744 2.2 37.9 1.0 NE2 C:HIS187 2.2 21.5 1.0 CG C:ASP333 2.7 21.6 1.0 O C:HOH907 2.7 41.5 1.0 OD2 C:ASP333 2.7 23.3 1.0 CD2 C:HIS183 2.8 23.5 1.0 CE1 C:HIS187 3.1 25.5 1.0 CD2 C:HIS187 3.2 23.7 1.0 CE1 C:HIS183 3.2 25.1 1.0 O C:HOH891 3.9 33.4 1.0 CG C:HIS183 4.0 23.0 1.0 ND2 C:ASN177 4.1 21.3 1.0 CB C:ASP333 4.1 20.4 1.0 O C:HOH806 4.2 26.4 1.0 ND1 C:HIS183 4.2 21.8 1.0 ND1 C:HIS187 4.3 23.5 1.0 CG C:HIS187 4.3 23.2 1.0 CE2 C:PHE329 4.5 24.9 1.0 CD1 C:ILE186 4.6 22.8 1.0 CA C:ASP333 4.8 20.6 1.0 ND2 C:ASN330 4.9 22.0 1.0 O C:ASN177 4.9 22.3 1.0 CG1 C:ILE186 5.0 21.3 1.0

Iron binding site 8 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:25.5 occ:1.00 FE1 C:FES502 0.0 25.5 1.0 SG C:CYS69 2.2 24.5 1.0 S2 C:FES502 2.2 23.9 1.0 S1 C:FES502 2.3 25.0 1.0 SG C:CYS90 2.3 24.8 1.0 FE2 C:FES502 2.8 28.5 1.0 CB C:CYS69 3.0 22.4 1.0 CB C:CYS90 3.1 23.6 1.0 CB C:HIS71 4.0 21.6 1.0 CB C:TYR92 4.0 21.5 1.0 CG2 C:VAL74 4.3 23.0 1.0 N C:HIS93 4.4 24.5 1.0 CA C:CYS69 4.5 23.4 1.0 ND1 C:HIS93 4.5 23.4 1.0 CA C:CYS90 4.5 24.1 1.0 ND1 C:HIS71 4.6 23.0 1.0 CB C:TRP95 4.8 23.7 1.0 CG C:HIS71 4.8 24.2 1.0 N C:TYR92 4.8 25.2 1.0 CA C:TYR92 4.9 25.5 1.0 N C:ARG72 4.9 22.1 1.0 CG C:TRP95 4.9 22.8 1.0

Iron binding site 9 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:28.5 occ:1.00 FE2 C:FES502 0.0 28.5 1.0 ND1 C:HIS71 2.1 23.0 1.0 ND1 C:HIS93 2.1 23.4 1.0 S1 C:FES502 2.2 25.0 1.0 S2 C:FES502 2.3 23.9 1.0 FE1 C:FES502 2.8 25.5 1.0 CG C:HIS71 3.0 24.2 1.0 CG C:HIS93 3.0 25.5 1.0 CE1 C:HIS93 3.1 25.1 1.0 CE1 C:HIS71 3.2 23.5 1.0 CB C:HIS71 3.2 21.6 1.0 CB C:HIS93 3.4 25.1 1.0 N C:HIS93 3.7 24.5 1.0 CB C:TYR92 3.9 21.5 1.0 CA C:HIS93 4.1 25.5 1.0 NE2 C:HIS93 4.1 24.7 1.0 CD2 C:HIS93 4.1 24.9 1.0 CD2 C:HIS71 4.2 22.2 1.0 NE2 C:HIS71 4.2 22.5 1.0 SG C:CYS69 4.3 24.5 1.0 CG C:TYR92 4.3 23.6 1.0 N C:ARG72 4.3 22.1 1.0 CG C:ARG72 4.4 21.9 1.0 CD2 C:TYR92 4.4 21.7 1.0 C C:TYR92 4.5 23.7 1.0 CA C:HIS71 4.6 23.9 1.0 CD1 C:TRP95 4.6 23.7 1.0 SG C:CYS90 4.6 24.8 1.0 NE1 C:TRP95 4.7 22.3 1.0 CB C:ARG72 4.7 21.4 1.0 CA C:TYR92 4.8 25.5 1.0 C C:HIS71 4.9 23.5 1.0 C C:HIS93 4.9 26.2 1.0 CG C:TRP95 5.0 22.8 1.0

Iron binding site 10 out of 15 in the Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex 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 10 of Oxygenase with GLN282 Replaced By Asn and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:22.7 occ:1.00 FE1 D:FES201 0.0 22.7 1.0 ND1 D:HIS48 2.0 25.7 1.0 S1 D:FES201 2.2 23.9 1.0 ND1 D:HIS68 2.2 23.8 1.0 S2 D:FES201 2.2 24.2 1.0 FE2 D:FES201 2.7 26.8 1.0 CE1 D:HIS48 2.9 24.1 1.0 CE1 D:HIS68 3.1 24.0 1.0 CG D:HIS48 3.1 22.8 1.0 CG D:HIS68 3.2 21.8 1.0 CB D:HIS48 3.5 24.5 1.0 CB D:HIS68 3.6 21.4 1.0 O A:HOH606 3.8 22.0 1.0 NE2 D:HIS48 4.1 24.5 1.0 N D:HIS68 4.1 23.0 1.0 CD2 D:HIS48 4.2 25.4 1.0 CB D:PHE67 4.2 26.0 1.0 C D:HIS48 4.2 24.8 1.0 O D:HIS48 4.2 25.2 1.0 NE2 D:HIS68 4.2 23.5 1.0 CD2 D:HIS68 4.3 21.6 1.0 SG D:CYS65 4.4 25.1 1.0 SG D:CYS46 4.4 25.0 1.0 CG D:PRO83 4.5 25.9 1.0 CA D:HIS48 4.5 24.6 1.0 CA D:HIS68 4.5 22.5 1.0 N D:GLY49 4.6 24.9 1.0 O A:VAL351 4.9 20.8 1.0 C D:PHE67 5.0 25.3 1.0 O A:GLU353 5.0 18.4 1.0

K.Inoue, Y.Usami, Y.Ashikawa, H.Noguchi, T.Umeda, A.Yamagami-Ashikawa, T.Horisaki, H.Uchimura, T.Terada, S.Nakamura, K.Shimizu, H.Habe, H.Yamane, Z.Fujimoto, H.Nojiri. Structural Basis of the Divergent Oxygenation Reactions Catalyzed By the Rieske Non-Heme Iron Oxygenase, Carbazole 1,9A-Dioxygenase Appl.Environ.Microbiol. 2014.
ISSN: ESSN 1098-5336
PubMed: 24584240
DOI: 10.1128/AEM.04000-13