Iron in PDB 2de5: Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase

The structure of Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 2de5 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)	44.92 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.091, 89.835, 104.914, 90.00, 103.79, 90.00
R / Rfree (%)	19.9 / 23.3

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase (pdb code 2de5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase, PDB code: 2de5:
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 Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:43.4 occ:1.00 O A:HOH635 1.9 40.5 1.0 OD1 A:ASP333 2.0 31.6 1.0 NE2 A:HIS187 2.1 28.2 1.0 NE2 A:HIS183 2.2 28.0 1.0 CG A:ASP333 2.7 30.1 1.0 OD2 A:ASP333 2.7 32.2 1.0 CD2 A:HIS183 2.9 26.5 1.0 CE1 A:HIS187 3.1 30.0 1.0 CD2 A:HIS187 3.1 30.7 1.0 O A:HOH746 3.1 56.3 1.0 CE1 A:HIS183 3.3 26.8 1.0 CB A:ASP333 4.1 27.9 1.0 CG A:HIS183 4.1 25.3 1.0 ND1 A:HIS187 4.2 29.8 1.0 O A:HOH722 4.2 39.9 1.0 CG A:HIS187 4.2 28.9 1.0 ND1 A:HIS183 4.3 25.1 1.0 CE2 A:PHE329 4.3 29.6 1.0 ND2 A:ASN177 4.4 24.4 1.0 O A:HOH632 4.5 37.8 1.0 CD1 A:ILE186 4.6 25.7 1.0 ND2 A:ASN330 4.7 29.2 1.0 CA A:ASP333 4.9 27.4 1.0 CZ A:PHE329 5.0 31.4 1.0 CD2 A:PHE329 5.0 29.7 1.0 CG1 A:ILE186 5.0 25.6 1.0

Iron binding site 2 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:24.4 occ:1.00 FE1 A:FES401 0.0 24.4 1.0 SG A:CYS90 2.2 23.9 1.0 S1 A:FES401 2.3 25.3 1.0 SG A:CYS69 2.3 26.6 1.0 S2 A:FES401 2.4 25.5 1.0 FE2 A:FES401 2.8 26.0 1.0 CB A:CYS90 3.0 23.3 1.0 CB A:CYS69 3.1 25.1 1.0 CB A:TYR92 4.0 25.1 1.0 CB A:HIS71 4.0 21.4 1.0 CG2 A:VAL74 4.2 25.1 1.0 N A:HIS93 4.4 24.5 1.0 ND1 A:HIS71 4.5 18.3 1.0 CA A:CYS90 4.5 25.2 1.0 ND1 A:HIS93 4.5 22.9 1.0 CA A:CYS69 4.6 25.1 1.0 CB A:TRP95 4.7 22.4 1.0 CG A:HIS71 4.8 23.1 1.0 N A:TYR92 4.8 24.6 1.0 N A:ARG72 4.9 24.6 1.0 CA A:TYR92 4.9 24.9 1.0 CG A:TRP95 4.9 21.7 1.0 N A:HIS71 5.0 23.3 1.0

Iron binding site 3 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:26.0 occ:1.00 FE2 A:FES401 0.0 26.0 1.0 ND1 A:HIS71 2.1 18.3 1.0 ND1 A:HIS93 2.1 22.9 1.0 S1 A:FES401 2.2 25.3 1.0 S2 A:FES401 2.4 25.5 1.0 FE1 A:FES401 2.8 24.4 1.0 CG A:HIS71 3.0 23.1 1.0 CG A:HIS93 3.0 25.8 1.0 CE1 A:HIS93 3.0 25.7 1.0 CE1 A:HIS71 3.1 23.4 1.0 CB A:HIS71 3.2 21.4 1.0 CB A:HIS93 3.3 22.5 1.0 N A:HIS93 3.7 24.5 1.0 CB A:TYR92 3.9 25.1 1.0 CA A:HIS93 4.1 24.9 1.0 NE2 A:HIS93 4.1 24.4 1.0 CD2 A:HIS93 4.1 24.7 1.0 CD2 A:HIS71 4.2 18.0 1.0 NE2 A:HIS71 4.2 21.4 1.0 CG A:TYR92 4.3 26.4 1.0 CG A:ARG72 4.3 29.3 1.0 N A:ARG72 4.3 24.6 1.0 CD2 A:TYR92 4.4 27.1 1.0 SG A:CYS69 4.4 26.6 1.0 C A:TYR92 4.5 26.6 1.0 SG A:CYS90 4.6 23.9 1.0 CA A:HIS71 4.6 25.2 1.0 CD1 A:TRP95 4.6 24.1 1.0 NE1 A:TRP95 4.7 21.1 1.0 CB A:ARG72 4.7 26.9 1.0 CA A:TYR92 4.8 24.9 1.0 C A:HIS93 4.9 24.7 1.0 C A:HIS71 4.9 24.6 1.0 CG A:TRP95 5.0 21.7 1.0

Iron binding site 4 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:54.9 occ:1.00 O B:HOH746 2.1 61.7 1.0 NE2 B:HIS183 2.1 32.3 1.0 OD1 B:ASP333 2.1 35.5 1.0 NE2 B:HIS187 2.2 39.6 1.0 CG B:ASP333 2.9 36.4 1.0 CD2 B:HIS183 3.0 30.9 1.0 OD2 B:ASP333 3.0 38.1 1.0 CE1 B:HIS183 3.1 31.4 1.0 CD2 B:HIS187 3.2 39.3 1.0 CE1 B:HIS187 3.2 40.8 1.0 O B:HOH763 3.7 42.9 1.0 CG B:HIS183 4.2 28.7 1.0 ND1 B:HIS183 4.2 32.6 1.0 CB B:ASP333 4.3 35.5 1.0 CG B:HIS187 4.3 39.1 1.0 ND1 B:HIS187 4.3 39.3 1.0 O B:HOH539 4.4 38.3 1.0 ND2 B:ASN177 4.4 37.5 1.0 CE2 B:PHE329 4.5 36.4 1.0 O B:HOH802 4.6 49.3 1.0 ND2 B:ASN330 4.7 38.6 1.0 CD1 B:ILE186 4.7 36.7 1.0 O B:HOH808 4.8 51.0 1.0 O B:ASN177 4.8 37.3 1.0

Iron binding site 5 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.5 occ:1.00 FE1 B:FES401 0.0 22.5 1.0 S1 B:FES401 2.2 20.1 1.0 SG B:CYS69 2.3 20.6 1.0 SG B:CYS90 2.3 22.1 1.0 S2 B:FES401 2.3 21.7 1.0 FE2 B:FES401 2.8 22.5 1.0 CB B:CYS69 3.1 22.6 1.0 CB B:CYS90 3.1 24.6 1.0 CB B:TYR92 4.1 23.3 1.0 CB B:HIS71 4.1 20.2 1.0 CG2 B:VAL74 4.2 19.1 1.0 N B:HIS93 4.4 23.5 1.0 ND1 B:HIS93 4.5 23.2 1.0 CA B:CYS69 4.5 22.2 1.0 CA B:CYS90 4.6 23.5 1.0 ND1 B:HIS71 4.6 18.6 1.0 CB B:TRP95 4.7 20.9 1.0 N B:TYR92 4.8 22.5 1.0 CG B:HIS71 4.9 18.6 1.0 CG B:TRP95 4.9 19.5 1.0 N B:ARG72 4.9 19.8 1.0 CA B:TYR92 4.9 23.5 1.0 N B:TRP95 5.0 24.0 1.0

Iron binding site 6 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.5 occ:1.00 FE2 B:FES401 0.0 22.5 1.0 ND1 B:HIS93 2.1 23.2 1.0 ND1 B:HIS71 2.2 18.6 1.0 S1 B:FES401 2.3 20.1 1.0 S2 B:FES401 2.3 21.7 1.0 FE1 B:FES401 2.8 22.5 1.0 CG B:HIS93 3.0 23.3 1.0 CE1 B:HIS93 3.1 18.2 1.0 CG B:HIS71 3.1 18.6 1.0 CB B:HIS71 3.3 20.2 1.0 CE1 B:HIS71 3.3 20.6 1.0 CB B:HIS93 3.3 22.6 1.0 N B:HIS93 3.7 23.5 1.0 CB B:TYR92 3.9 23.3 1.0 CA B:HIS93 4.1 22.0 1.0 CD2 B:HIS93 4.1 22.0 1.0 NE2 B:HIS93 4.1 20.6 1.0 CD2 B:HIS71 4.3 19.5 1.0 CG B:TYR92 4.3 23.5 1.0 SG B:CYS69 4.3 20.6 1.0 N B:ARG72 4.3 19.8 1.0 CG B:ARG72 4.3 24.6 1.0 NE2 B:HIS71 4.4 19.4 1.0 CD2 B:TYR92 4.4 22.0 1.0 C B:TYR92 4.6 21.9 1.0 CD1 B:TRP95 4.6 20.3 1.0 SG B:CYS90 4.6 22.1 1.0 CA B:HIS71 4.6 21.0 1.0 NE1 B:TRP95 4.7 21.2 1.0 CB B:ARG72 4.7 22.8 1.0 C B:HIS93 4.9 23.3 1.0 CA B:TYR92 4.9 23.5 1.0 C B:HIS71 4.9 21.5 1.0 CG B:TRP95 5.0 19.5 1.0

Iron binding site 7 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:43.7 occ:1.00 O C:HOH707 1.9 45.7 1.0 NE2 C:HIS183 2.1 32.9 1.0 OD1 C:ASP333 2.1 33.6 1.0 NE2 C:HIS187 2.2 27.8 1.0 CG C:ASP333 2.8 30.9 1.0 OD2 C:ASP333 2.8 32.9 1.0 CD2 C:HIS183 2.9 29.7 1.0 CE1 C:HIS187 3.1 28.0 1.0 CD2 C:HIS187 3.1 27.6 1.0 CE1 C:HIS183 3.2 30.9 1.0 O C:HOH746 4.1 51.0 1.0 CG C:HIS183 4.1 28.9 1.0 ND1 C:HIS183 4.2 30.9 1.0 CB C:ASP333 4.2 28.9 1.0 ND1 C:HIS187 4.2 26.5 1.0 ND2 C:ASN177 4.2 32.1 1.0 CG C:HIS187 4.3 26.9 1.0 CE2 C:PHE329 4.4 30.5 1.0 CD1 C:ILE186 4.5 26.6 1.0 O C:HOH543 4.5 34.1 1.0 ND2 C:ASN330 4.7 32.0 1.0 O C:ASN177 4.9 32.7 1.0 CG1 C:ILE186 4.9 26.2 1.0 CA C:ASP333 5.0 28.2 1.0

Iron binding site 8 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:29.6 occ:1.00 FE1 C:FES401 0.0 29.6 1.0 SG C:CYS69 2.2 29.6 1.0 S1 C:FES401 2.3 29.6 1.0 S2 C:FES401 2.3 28.4 1.0 SG C:CYS90 2.4 27.4 1.0 FE2 C:FES401 2.8 29.6 1.0 CB C:CYS90 3.1 29.5 1.0 CB C:CYS69 3.1 27.2 1.0 CB C:TYR92 4.0 25.5 1.0 CB C:HIS71 4.1 25.4 1.0 CG2 C:VAL74 4.3 26.7 1.0 N C:HIS93 4.4 28.1 1.0 ND1 C:HIS93 4.5 28.4 1.0 CA C:CYS90 4.5 29.4 1.0 CA C:CYS69 4.5 27.5 1.0 ND1 C:HIS71 4.6 29.2 1.0 N C:TYR92 4.8 27.4 1.0 CB C:TRP95 4.8 29.2 1.0 CA C:TYR92 4.9 28.9 1.0 CG C:HIS71 4.9 25.9 1.0 N C:ARG72 4.9 25.8 1.0 C C:CYS90 5.0 30.2 1.0

Iron binding site 9 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:29.6 occ:1.00 FE2 C:FES401 0.0 29.6 1.0 ND1 C:HIS93 2.1 28.4 1.0 ND1 C:HIS71 2.3 29.2 1.0 S1 C:FES401 2.3 29.6 1.0 S2 C:FES401 2.3 28.4 1.0 FE1 C:FES401 2.8 29.6 1.0 CE1 C:HIS93 3.0 30.5 1.0 CG C:HIS93 3.0 30.6 1.0 CG C:HIS71 3.1 25.9 1.0 CB C:HIS71 3.3 25.4 1.0 CE1 C:HIS71 3.3 27.3 1.0 CB C:HIS93 3.4 29.9 1.0 N C:HIS93 3.7 28.1 1.0 CB C:TYR92 3.8 25.5 1.0 NE2 C:HIS93 4.1 29.2 1.0 CA C:HIS93 4.1 29.8 1.0 CD2 C:HIS93 4.1 30.8 1.0 CD2 C:TYR92 4.2 28.9 1.0 SG C:CYS69 4.2 29.6 1.0 CG C:TYR92 4.3 28.4 1.0 CG C:ARG72 4.3 29.7 1.0 CD2 C:HIS71 4.3 25.7 1.0 N C:ARG72 4.3 25.8 1.0 NE2 C:HIS71 4.4 27.2 1.0 C C:TYR92 4.6 27.7 1.0 CA C:HIS71 4.6 27.9 1.0 CD1 C:TRP95 4.7 29.9 1.0 SG C:CYS90 4.7 27.4 1.0 CB C:ARG72 4.7 26.9 1.0 NE1 C:TRP95 4.7 27.6 1.0 CA C:TYR92 4.8 28.9 1.0 C C:HIS71 4.9 26.2 1.0 C C:HIS93 4.9 30.3 1.0

Iron binding site 10 out of 15 in the Crystal Structure of the Electron Transfer 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 Crystal Structure of the Electron Transfer Complex Between Oxygenase and Ferredoxin in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:27.7 occ:1.00 FE1 D:FES201 0.0 27.7 1.0 S1 D:FES201 2.3 28.0 1.0 S2 D:FES201 2.3 27.2 1.0 SG D:CYS65 2.3 29.0 1.0 SG D:CYS46 2.4 28.5 1.0 FE2 D:FES201 2.7 27.3 1.0 CB D:CYS65 3.1 30.4 1.0 CB D:CYS46 3.1 27.1 1.0 CB D:HIS48 4.1 27.6 1.0 CB D:ALA51 4.2 29.1 1.0 CB D:PHE67 4.3 27.4 1.0 ND1 D:HIS48 4.3 26.1 1.0 ND1 D:HIS68 4.5 23.7 1.0 CA D:CYS65 4.6 29.1 1.0 SG D:CYS84 4.6 32.9 1.0 CA D:CYS46 4.6 30.6 1.0 N D:HIS68 4.6 24.9 1.0 CG D:HIS48 4.7 26.0 1.0 N D:GLY49 4.8 29.4 1.0 CA D:HIS48 4.9 28.2 1.0 N D:HIS48 4.9 29.2 1.0 C D:HIS48 4.9 29.2 1.0

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