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

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

The structure of Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1, 9A-Dioxygenase, PDB code: 3vmh 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)	47.61 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.169, 89.365, 104.995, 90.00, 104.10, 90.00
R / Rfree (%)	19.6 / 22.5

Pages:

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

Binding sites:

The binding sites of Iron atom in the Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1, 9A-Dioxygenase (pdb code 3vmh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Oxygen-Bound Complex Between Oxygenase and Ferredoxin in Carbazole 1, 9A-Dioxygenase, PDB code: 3vmh:
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 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 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:28.4 occ:1.00 O2 A:OXY601 1.9 31.7 1.0 OD1 A:ASP333 2.0 23.6 1.0 NE2 A:HIS183 2.1 22.4 1.0 NE2 A:HIS187 2.1 25.7 1.0 CG A:ASP333 2.6 23.7 1.0 O1 A:OXY601 2.6 34.5 1.0 OD2 A:ASP333 2.6 23.9 1.0 CD2 A:HIS183 3.0 22.4 1.0 CE1 A:HIS187 3.1 25.7 1.0 CD2 A:HIS187 3.1 26.1 1.0 CE1 A:HIS183 3.2 22.4 1.0 CB A:ASP333 4.1 23.4 1.0 CG A:HIS183 4.2 21.9 1.0 ND2 A:ASN177 4.2 20.1 1.0 ND1 A:HIS187 4.2 26.3 1.0 ND1 A:HIS183 4.2 22.0 1.0 CG A:HIS187 4.3 25.9 1.0 O A:HOH528 4.3 28.0 1.0 CE2 A:PHE329 4.4 25.9 1.0 CD1 A:ILE186 4.4 23.5 1.0 ND2 A:ASN330 4.6 24.7 1.0 CA A:ASP333 4.8 23.2 1.0 CG1 A:ILE186 4.9 23.1 1.0 O A:ASN177 5.0 20.8 1.0

Iron binding site 2 out of 15 in the 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 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:22.3 occ:1.00 FE1 A:FES401 0.0 22.3 1.0 SG A:CYS90 2.2 22.2 1.0 S1 A:FES401 2.3 22.8 1.0 S2 A:FES401 2.3 21.2 1.0 SG A:CYS69 2.3 20.5 1.0 FE2 A:FES401 2.8 24.1 1.0 CB A:CYS90 3.1 22.7 1.0 CB A:CYS69 3.1 23.1 1.0 CB A:TYR92 4.0 23.3 1.0 CB A:HIS71 4.1 21.0 1.0 CG2 A:VAL74 4.2 22.7 1.0 N A:HIS93 4.4 23.0 1.0 CA A:CYS90 4.5 23.0 1.0 ND1 A:HIS93 4.6 22.3 1.0 ND1 A:HIS71 4.6 20.3 1.0 CA A:CYS69 4.6 22.7 1.0 CB A:TRP95 4.7 21.7 1.0 N A:TYR92 4.7 22.8 1.0 CA A:TYR92 4.8 23.2 1.0 CG A:HIS71 4.8 21.0 1.0 CG A:TRP95 4.9 21.4 1.0 N A:ARG72 4.9 22.1 1.0 C A:CYS90 5.0 23.0 1.0 CD2 A:LEU76 5.0 27.7 1.0

Iron binding site 3 out of 15 in the 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 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:24.1 occ:1.00 FE2 A:FES401 0.0 24.1 1.0 ND1 A:HIS93 2.1 22.3 1.0 ND1 A:HIS71 2.1 20.3 1.0 S1 A:FES401 2.3 22.8 1.0 S2 A:FES401 2.3 21.2 1.0 FE1 A:FES401 2.8 22.3 1.0 CE1 A:HIS93 3.0 22.5 1.0 CG A:HIS93 3.0 22.6 1.0 CG A:HIS71 3.0 21.0 1.0 CE1 A:HIS71 3.2 20.8 1.0 CB A:HIS71 3.3 21.0 1.0 CB A:HIS93 3.4 22.4 1.0 N A:HIS93 3.7 23.0 1.0 CB A:TYR92 3.8 23.3 1.0 CA A:HIS93 4.1 22.9 1.0 NE2 A:HIS93 4.1 22.7 1.0 CD2 A:HIS93 4.2 22.5 1.0 CG A:TYR92 4.2 23.7 1.0 CD2 A:HIS71 4.2 20.4 1.0 NE2 A:HIS71 4.3 20.4 1.0 CD2 A:TYR92 4.3 23.8 1.0 CG A:ARG72 4.3 23.2 1.0 N A:ARG72 4.4 22.1 1.0 SG A:CYS69 4.4 20.5 1.0 C A:TYR92 4.5 23.2 1.0 CD1 A:TRP95 4.6 21.2 1.0 NE1 A:TRP95 4.6 21.0 1.0 SG A:CYS90 4.6 22.2 1.0 CA A:HIS71 4.7 21.9 1.0 CB A:ARG72 4.7 22.7 1.0 CA A:TYR92 4.7 23.2 1.0 C A:HIS93 4.9 22.8 1.0 CG A:TRP95 4.9 21.4 1.0 C A:HIS71 4.9 21.9 1.0 CE2 A:TRP95 5.0 21.6 1.0

Iron binding site 4 out of 15 in the 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 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:34.1 occ:1.00 O2 B:OXY602 2.0 40.2 1.0 OD1 B:ASP333 2.0 28.3 1.0 NE2 B:HIS183 2.1 26.7 1.0 NE2 B:HIS187 2.2 29.4 1.0 O1 B:OXY602 2.5 41.5 1.0 CG B:ASP333 2.7 28.2 1.0 OD2 B:ASP333 2.7 28.5 1.0 CD2 B:HIS183 3.0 25.9 1.0 CE1 B:HIS187 3.1 30.0 1.0 CE1 B:HIS183 3.1 26.0 1.0 CD2 B:HIS187 3.2 30.1 1.0 O B:HOH1025 4.0 35.2 1.0 CB B:ASP333 4.1 28.3 1.0 CG B:HIS183 4.2 26.3 1.0 ND2 B:ASN177 4.2 26.0 1.0 ND1 B:HIS183 4.2 25.8 1.0 ND1 B:HIS187 4.2 30.0 1.0 O B:HOH497 4.2 26.0 1.0 CG B:HIS187 4.3 29.9 1.0 CE2 B:PHE329 4.5 29.2 1.0 ND2 B:ASN330 4.6 29.0 1.0 CD1 B:ILE186 4.6 27.9 1.0 CA B:ASP333 4.9 28.5 1.0 O B:ASN177 4.9 25.8 1.0 CG1 B:ILE186 5.0 27.5 1.0

Iron binding site 5 out of 15 in the 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 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:23.1 occ:1.00 FE1 B:FES401 0.0 23.1 1.0 S1 B:FES401 2.2 22.0 1.0 SG B:CYS69 2.3 19.8 1.0 SG B:CYS90 2.3 19.6 1.0 S2 B:FES401 2.3 23.8 1.0 FE2 B:FES401 2.8 22.7 1.0 CB B:CYS69 3.1 22.4 1.0 CB B:CYS90 3.1 24.0 1.0 CB B:TYR92 4.0 21.5 1.0 CB B:HIS71 4.1 19.4 1.0 CG2 B:VAL74 4.2 19.3 1.0 N B:HIS93 4.4 20.8 1.0 ND1 B:HIS93 4.5 19.7 1.0 CA B:CYS69 4.6 21.3 1.0 CA B:CYS90 4.6 22.9 1.0 ND1 B:HIS71 4.6 18.6 1.0 CB B:TRP95 4.7 20.8 1.0 N B:TYR92 4.8 21.3 1.0 CG B:HIS71 4.9 18.7 1.0 CA B:TYR92 4.9 21.6 1.0 CG B:TRP95 4.9 20.5 1.0 N B:ARG72 4.9 20.1 1.0 CD2 B:LEU76 5.0 24.8 1.0

Iron binding site 6 out of 15 in the 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 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:22.7 occ:1.00 FE2 B:FES401 0.0 22.7 1.0 ND1 B:HIS93 2.1 19.7 1.0 ND1 B:HIS71 2.2 18.6 1.0 S2 B:FES401 2.3 23.8 1.0 S1 B:FES401 2.3 22.0 1.0 FE1 B:FES401 2.8 23.1 1.0 CG B:HIS93 3.0 20.1 1.0 CE1 B:HIS93 3.1 18.9 1.0 CG B:HIS71 3.1 18.7 1.0 CB B:HIS71 3.3 19.4 1.0 CE1 B:HIS71 3.3 18.4 1.0 CB B:HIS93 3.4 20.4 1.0 N B:HIS93 3.7 20.8 1.0 CB B:TYR92 3.9 21.5 1.0 CA B:HIS93 4.1 20.6 1.0 NE2 B:HIS93 4.1 19.4 1.0 CD2 B:HIS93 4.2 19.6 1.0 CG B:TYR92 4.3 21.6 1.0 CD2 B:HIS71 4.3 18.6 1.0 CD2 B:TYR92 4.3 21.4 1.0 SG B:CYS69 4.3 19.8 1.0 N B:ARG72 4.3 20.1 1.0 CG B:ARG72 4.3 20.9 1.0 NE2 B:HIS71 4.3 18.1 1.0 C B:TYR92 4.5 21.0 1.0 CD1 B:TRP95 4.6 20.3 1.0 SG B:CYS90 4.6 19.6 1.0 CA B:HIS71 4.6 20.1 1.0 NE1 B:TRP95 4.6 20.6 1.0 CB B:ARG72 4.7 20.8 1.0 CA B:TYR92 4.8 21.6 1.0 C B:HIS93 4.9 20.6 1.0 C B:HIS71 4.9 19.9 1.0 CG B:TRP95 4.9 20.5 1.0

Iron binding site 7 out of 15 in the 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 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:30.5 occ:1.00 OD1 C:ASP333 2.0 25.6 1.0 O2 C:OXY603 2.0 34.9 1.0 NE2 C:HIS187 2.1 25.7 1.0 NE2 C:HIS183 2.1 24.5 1.0 CG C:ASP333 2.6 24.9 1.0 O1 C:OXY603 2.6 35.5 1.0 OD2 C:ASP333 2.6 25.6 1.0 CD2 C:HIS183 2.9 23.4 1.0 CE1 C:HIS187 3.0 26.0 1.0 CD2 C:HIS187 3.1 25.7 1.0 CE1 C:HIS183 3.2 23.9 1.0 O C:HOH432 4.1 41.6 1.0 CB C:ASP333 4.1 24.9 1.0 ND2 C:ASN177 4.1 24.6 1.0 ND1 C:HIS187 4.1 25.8 1.0 CG C:HIS183 4.1 23.4 1.0 CG C:HIS187 4.2 25.6 1.0 ND1 C:HIS183 4.3 23.3 1.0 O C:HOH445 4.3 26.1 1.0 CD1 C:ILE186 4.4 24.9 1.0 CE2 C:PHE329 4.4 26.4 1.0 ND2 C:ASN330 4.6 27.1 1.0 CA C:ASP333 4.8 24.5 1.0 CG1 C:ILE186 4.8 24.6 1.0

Iron binding site 8 out of 15 in the 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 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:26.0 occ:1.00 FE1 C:FES401 0.0 26.0 1.0 S1 C:FES401 2.2 25.2 1.0 SG C:CYS69 2.3 26.5 1.0 S2 C:FES401 2.3 24.5 1.0 SG C:CYS90 2.3 26.1 1.0 FE2 C:FES401 2.7 26.9 1.0 CB C:CYS69 3.1 25.3 1.0 CB C:CYS90 3.1 26.6 1.0 CB C:TYR92 4.0 24.9 1.0 CB C:HIS71 4.1 22.9 1.0 CG2 C:VAL74 4.3 22.5 1.0 N C:HIS93 4.4 26.0 1.0 ND1 C:HIS93 4.5 25.3 1.0 CA C:CYS69 4.6 25.1 1.0 CA C:CYS90 4.6 26.6 1.0 ND1 C:HIS71 4.6 22.6 1.0 CB C:TRP95 4.8 25.4 1.0 N C:TYR92 4.8 25.4 1.0 CG C:HIS71 4.8 22.6 1.0 CA C:TYR92 4.9 25.9 1.0 N C:ARG72 4.9 23.2 1.0 CG C:TRP95 4.9 24.6 1.0

Iron binding site 9 out of 15 in the 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 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:26.9 occ:1.00 FE2 C:FES401 0.0 26.9 1.0 ND1 C:HIS93 2.1 25.3 1.0 ND1 C:HIS71 2.2 22.6 1.0 S1 C:FES401 2.3 25.2 1.0 S2 C:FES401 2.3 24.5 1.0 FE1 C:FES401 2.7 26.0 1.0 CG C:HIS71 3.1 22.6 1.0 CE1 C:HIS93 3.1 24.5 1.0 CG C:HIS93 3.1 25.4 1.0 CB C:HIS71 3.2 22.9 1.0 CE1 C:HIS71 3.3 21.8 1.0 CB C:HIS93 3.4 25.8 1.0 N C:HIS93 3.7 26.0 1.0 CB C:TYR92 3.9 24.9 1.0 CA C:HIS93 4.2 26.0 1.0 NE2 C:HIS93 4.2 25.0 1.0 CD2 C:HIS93 4.2 25.4 1.0 CD2 C:HIS71 4.3 22.3 1.0 SG C:CYS69 4.3 26.5 1.0 CG C:TYR92 4.3 25.1 1.0 CD2 C:TYR92 4.3 24.3 1.0 N C:ARG72 4.3 23.2 1.0 NE2 C:HIS71 4.3 22.1 1.0 CG C:ARG72 4.4 24.5 1.0 C C:TYR92 4.6 25.6 1.0 CD1 C:TRP95 4.6 24.9 1.0 CA C:HIS71 4.6 23.3 1.0 SG C:CYS90 4.6 26.1 1.0 NE1 C:TRP95 4.6 24.8 1.0 CB C:ARG72 4.7 23.3 1.0 CA C:TYR92 4.8 25.9 1.0 C C:HIS71 4.9 23.3 1.0 C C:HIS93 4.9 26.3 1.0 CG C:TRP95 4.9 24.6 1.0

Iron binding site 10 out of 15 in the 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 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:25.4 occ:1.00 FE1 D:FES201 0.0 25.4 1.0 ND1 D:HIS48 2.1 25.4 1.0 ND1 D:HIS68 2.1 23.9 1.0 S1 D:FES201 2.2 26.0 1.0 S2 D:FES201 2.3 27.2 1.0 FE2 D:FES201 2.7 26.5 1.0 CE1 D:HIS48 3.0 25.4 1.0 CE1 D:HIS68 3.0 23.9 1.0 CG D:HIS48 3.1 25.9 1.0 CG D:HIS68 3.2 24.0 1.0 CB D:HIS68 3.5 24.4 1.0 CB D:HIS48 3.5 26.4 1.0 O D:HOH116 3.9 23.9 1.0 NE2 D:HIS48 4.1 24.9 1.0 N D:HIS68 4.1 25.7 1.0 NE2 D:HIS68 4.2 24.1 1.0 CB D:PHE67 4.2 27.0 1.0 O D:HIS48 4.2 26.9 1.0 CD2 D:HIS48 4.2 25.7 1.0 C D:HIS48 4.2 27.1 1.0 CD2 D:HIS68 4.3 23.5 1.0 CA D:HIS68 4.5 25.1 1.0 SG D:CYS65 4.5 27.0 1.0 SG D:CYS46 4.5 27.3 1.0 CG D:PRO83 4.5 28.1 1.0 CA D:HIS48 4.5 26.9 1.0 N D:GLY49 4.6 27.1 1.0 O A:VAL351 4.8 21.8 1.0 O A:GLU353 4.9 20.0 1.0 C D:PHE67 5.0 26.1 1.0

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