Iron in PDB 6llh: Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase

The structure of Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase, PDB code: 6llh 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)	36.59 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.257, 89.793, 105.445, 90, 103.99, 90
R / Rfree (%)	16.2 / 20.7

Pages:

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

Binding sites:

The binding sites of Iron atom in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase (pdb code 6llh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase, PDB code: 6llh:
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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.6 occ:1.00 OK1 A:BPY503 2.0 46.4 1.0 OD1 A:ASP333 2.0 19.7 1.0 OK2 A:BPY503 2.1 63.1 1.0 NE2 A:HIS183 2.1 15.5 1.0 NE2 A:HIS187 2.2 16.4 1.0 CG A:ASP333 2.6 18.2 1.0 OD2 A:ASP333 2.7 19.5 1.0 CK4 A:BPY503 2.8 59.0 1.0 CK3 A:BPY503 2.9 59.0 1.0 CD2 A:HIS183 3.0 15.1 1.0 CD2 A:HIS187 3.1 19.2 1.0 CE1 A:HIS187 3.1 19.7 1.0 CE1 A:HIS183 3.2 14.8 1.0 CB A:ASP333 4.1 17.6 1.0 CK5 A:BPY503 4.1 57.8 1.0 CG A:HIS183 4.2 14.7 1.0 ND2 A:ASN177 4.2 17.1 1.0 ND1 A:HIS183 4.2 14.4 1.0 ND1 A:HIS187 4.3 17.1 1.0 CG A:HIS187 4.3 18.0 1.0 CK2 A:BPY503 4.3 67.9 1.0 CE2 A:PHE329 4.3 19.3 1.0 O A:HOH622 4.4 24.8 1.0 CD1 A:ILE186 4.5 17.5 1.0 ND2 A:ASN330 4.6 19.0 1.0 CA A:ASP333 4.8 17.3 1.0 CG1 A:ILE186 4.9 17.7 1.0 CD2 A:PHE329 5.0 19.0 1.0

Iron binding site 2 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:15.3 occ:1.00 FE1 A:FES502 0.0 15.3 1.0 SG A:CYS90 2.3 15.6 1.0 S1 A:FES502 2.3 16.8 1.0 S2 A:FES502 2.3 16.8 1.0 SG A:CYS69 2.3 16.9 1.0 FE2 A:FES502 2.8 16.7 1.0 CB A:CYS90 3.1 16.7 1.0 CB A:CYS69 3.1 16.5 1.0 CB A:TYR92 4.2 17.2 1.0 CG2 A:VAL74 4.2 16.5 1.0 CB A:HIS71 4.3 13.9 1.0 ND1 A:HIS71 4.4 12.5 1.0 N A:HIS93 4.4 17.9 1.0 ND1 A:HIS93 4.5 16.8 1.0 CA A:CYS90 4.5 16.1 1.0 CA A:CYS69 4.6 15.8 1.0 CB A:TRP95 4.7 15.2 1.0 N A:TYR92 4.8 17.7 1.0 CG A:HIS71 4.9 14.4 1.0 CA A:TYR92 4.9 17.8 1.0 N A:ARG72 4.9 16.4 1.0 CG A:TRP95 5.0 14.0 1.0

Iron binding site 3 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:16.7 occ:1.00 FE2 A:FES502 0.0 16.7 1.0 ND1 A:HIS71 2.0 12.5 1.0 ND1 A:HIS93 2.1 16.8 1.0 S1 A:FES502 2.2 16.8 1.0 S2 A:FES502 2.3 16.8 1.0 FE1 A:FES502 2.8 15.3 1.0 CE1 A:HIS93 3.0 17.0 1.0 CE1 A:HIS71 3.0 15.9 1.0 CG A:HIS93 3.1 16.9 1.0 CG A:HIS71 3.1 14.4 1.0 CB A:HIS71 3.4 13.9 1.0 CB A:HIS93 3.5 15.4 1.0 N A:HIS93 3.7 17.9 1.0 CB A:TYR92 4.0 17.2 1.0 NE2 A:HIS93 4.1 16.4 1.0 CA A:HIS93 4.1 16.7 1.0 NE2 A:HIS71 4.2 13.0 1.0 CD2 A:HIS93 4.2 19.0 1.0 CD2 A:HIS71 4.2 13.2 1.0 N A:ARG72 4.3 16.4 1.0 CG A:ARG72 4.4 20.2 1.0 CG A:TYR92 4.4 18.2 1.0 SG A:CYS69 4.4 16.9 1.0 CD2 A:TYR92 4.4 18.4 1.0 C A:TYR92 4.5 18.8 1.0 SG A:CYS90 4.6 15.6 1.0 CD1 A:TRP95 4.6 14.7 1.0 CA A:HIS71 4.7 16.3 1.0 NE1 A:TRP95 4.7 14.3 1.0 CB A:ARG72 4.7 19.8 1.0 CA A:TYR92 4.8 17.8 1.0 C A:HIS93 4.9 17.3 1.0 C A:HIS71 4.9 16.0 1.0

Iron binding site 4 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:33.8 occ:1.00 O B:HOH720 1.8 38.6 1.0 OD1 B:ASP333 2.1 30.2 1.0 NE2 B:HIS187 2.2 28.2 1.0 NE2 B:HIS183 2.2 20.6 1.0 OD2 B:ASP333 2.4 29.1 1.0 CG B:ASP333 2.6 25.2 1.0 CE1 B:HIS187 3.1 31.7 1.0 CD2 B:HIS183 3.1 20.6 1.0 CE1 B:HIS183 3.2 22.4 1.0 CD2 B:HIS187 3.2 30.1 1.0 OK2 B:BPY503 4.0 61.3 1.0 CK3 B:BPY503 4.0 60.7 1.0 CB B:ASP333 4.1 25.2 1.0 O B:HOH857 4.1 41.9 1.0 CK4 B:BPY503 4.1 60.2 1.0 ND2 B:ASN177 4.2 26.0 1.0 OK1 B:BPY503 4.2 66.0 1.0 ND1 B:HIS187 4.2 30.2 1.0 CG B:HIS183 4.2 20.0 1.0 ND1 B:HIS183 4.3 20.6 1.0 CG B:HIS187 4.3 29.1 1.0 O B:HOH688 4.4 28.1 1.0 ND2 B:ASN330 4.4 26.9 1.0 CE2 B:PHE329 4.5 26.0 1.0 CD1 B:ILE186 4.6 27.6 1.0 CK2 B:BPY503 4.7 59.2 1.0 CK5 B:BPY503 4.8 62.8 1.0 CA B:ASP333 4.8 23.9 1.0 O B:ASN177 5.0 27.8 1.0 CG1 B:ILE186 5.0 26.0 1.0

Iron binding site 5 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:14.1 occ:1.00 FE1 B:FES502 0.0 14.1 1.0 S1 B:FES502 2.2 13.8 1.0 SG B:CYS90 2.3 14.7 1.0 S2 B:FES502 2.3 14.7 1.0 SG B:CYS69 2.3 15.4 1.0 FE2 B:FES502 2.8 14.4 1.0 CB B:CYS90 3.0 15.6 1.0 CB B:CYS69 3.1 15.4 1.0 CG2 B:VAL74 4.1 14.8 1.0 CB B:TYR92 4.2 14.4 1.0 CB B:HIS71 4.2 13.2 1.0 ND1 B:HIS93 4.5 13.1 1.0 N B:HIS93 4.5 14.7 1.0 ND1 B:HIS71 4.5 13.6 1.0 CA B:CYS90 4.5 14.8 1.0 CA B:CYS69 4.6 15.2 1.0 CB B:TRP95 4.7 14.2 1.0 N B:TYR92 4.8 14.4 1.0 CG B:HIS71 4.9 12.6 1.0 CG B:TRP95 4.9 14.1 1.0 N B:ARG72 5.0 13.2 1.0 CA B:TYR92 5.0 14.6 1.0 N B:HIS71 5.0 14.7 1.0

Iron binding site 6 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:14.4 occ:1.00 FE2 B:FES502 0.0 14.4 1.0 ND1 B:HIS93 2.0 13.1 1.0 ND1 B:HIS71 2.1 13.6 1.0 S2 B:FES502 2.3 14.7 1.0 S1 B:FES502 2.3 13.8 1.0 FE1 B:FES502 2.8 14.1 1.0 CE1 B:HIS93 3.0 12.6 1.0 CG B:HIS93 3.1 13.7 1.0 CG B:HIS71 3.1 12.6 1.0 CE1 B:HIS71 3.1 14.2 1.0 CB B:HIS71 3.3 13.2 1.0 CB B:HIS93 3.4 14.2 1.0 N B:HIS93 3.7 14.7 1.0 CB B:TYR92 4.0 14.4 1.0 NE2 B:HIS93 4.1 12.2 1.0 CD2 B:HIS93 4.1 13.5 1.0 CA B:HIS93 4.2 14.0 1.0 CD2 B:HIS71 4.2 12.8 1.0 NE2 B:HIS71 4.2 12.1 1.0 SG B:CYS69 4.3 15.4 1.0 CG B:ARG72 4.4 18.0 1.0 N B:ARG72 4.4 13.2 1.0 CG B:TYR92 4.4 15.2 1.0 CD2 B:TYR92 4.4 15.7 1.0 SG B:CYS90 4.6 14.7 1.0 C B:TYR92 4.6 13.7 1.0 CA B:HIS71 4.6 14.5 1.0 CD1 B:TRP95 4.7 14.4 1.0 CB B:ARG72 4.7 16.4 1.0 NE1 B:TRP95 4.7 13.8 1.0 C B:HIS93 4.9 13.8 1.0 CA B:TYR92 4.9 14.6 1.0 C B:HIS71 4.9 13.4 1.0 CG B:TRP95 5.0 14.1 1.0

Iron binding site 7 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:27.9 occ:1.00 O C:HOH700 1.8 39.5 1.0 OD1 C:ASP333 2.1 24.7 1.0 NE2 C:HIS187 2.1 16.9 1.0 NE2 C:HIS183 2.2 20.7 1.0 CG C:ASP333 2.7 24.5 1.0 OD2 C:ASP333 2.7 23.2 1.0 CD2 C:HIS183 3.0 18.0 1.0 CE1 C:HIS187 3.1 19.1 1.0 CD2 C:HIS187 3.1 18.0 1.0 CE1 C:HIS183 3.3 19.6 1.0 OK2 C:BPY503 4.0 54.8 1.0 CK3 C:BPY503 4.1 54.7 1.0 ND2 C:ASN177 4.2 25.8 1.0 CB C:ASP333 4.2 21.7 1.0 CG C:HIS183 4.2 18.0 1.0 ND1 C:HIS187 4.2 17.7 1.0 CG C:HIS187 4.3 17.7 1.0 ND1 C:HIS183 4.3 18.2 1.0 CK4 C:BPY503 4.3 49.0 1.0 OK1 C:BPY503 4.3 54.8 1.0 O C:HOH681 4.4 28.3 1.0 CE2 C:PHE329 4.5 21.2 1.0 ND2 C:ASN330 4.5 22.2 1.0 CD1 C:ILE186 4.5 21.2 1.0 CK2 C:BPY503 4.9 52.5 1.0 CG1 C:ILE186 4.9 19.1 1.0 CA C:ASP333 4.9 19.7 1.0 O C:ASN177 5.0 22.2 1.0

Iron binding site 8 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:19.8 occ:1.00 FE1 C:FES502 0.0 19.8 1.0 SG C:CYS69 2.1 20.7 1.0 S2 C:FES502 2.2 21.2 1.0 S1 C:FES502 2.3 21.6 1.0 SG C:CYS90 2.3 21.4 1.0 FE2 C:FES502 2.8 20.0 1.0 CB C:CYS69 3.1 21.1 1.0 CB C:CYS90 3.1 23.5 1.0 CB C:TYR92 4.1 17.5 1.0 CB C:HIS71 4.3 17.4 1.0 CG2 C:VAL74 4.3 21.5 1.0 ND1 C:HIS93 4.4 20.4 1.0 CA C:CYS69 4.5 19.9 1.0 ND1 C:HIS71 4.5 20.1 1.0 CA C:CYS90 4.6 20.8 1.0 N C:HIS93 4.6 18.6 1.0 N C:TYR92 4.8 19.2 1.0 CB C:TRP95 4.9 20.3 1.0 CG C:HIS71 4.9 17.5 1.0 CA C:TYR92 4.9 20.6 1.0

Iron binding site 9 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:20.0 occ:1.00 FE2 C:FES502 0.0 20.0 1.0 ND1 C:HIS93 2.0 20.4 1.0 ND1 C:HIS71 2.1 20.1 1.0 S1 C:FES502 2.2 21.6 1.0 S2 C:FES502 2.3 21.2 1.0 FE1 C:FES502 2.8 19.8 1.0 CE1 C:HIS93 3.0 22.6 1.0 CG C:HIS93 3.0 21.5 1.0 CE1 C:HIS71 3.1 20.2 1.0 CG C:HIS71 3.1 17.5 1.0 CB C:HIS93 3.4 21.3 1.0 CB C:HIS71 3.4 17.4 1.0 N C:HIS93 3.8 18.6 1.0 CB C:TYR92 3.9 17.5 1.0 NE2 C:HIS93 4.1 19.2 1.0 CD2 C:HIS93 4.1 23.5 1.0 CA C:HIS93 4.2 21.9 1.0 NE2 C:HIS71 4.2 17.6 1.0 SG C:CYS69 4.2 20.7 1.0 CD2 C:HIS71 4.2 18.0 1.0 CG C:ARG72 4.3 23.5 1.0 CG C:TYR92 4.3 19.5 1.0 CD2 C:TYR92 4.3 19.5 1.0 N C:ARG72 4.4 17.6 1.0 C C:TYR92 4.6 18.6 1.0 SG C:CYS90 4.6 21.4 1.0 CD1 C:TRP95 4.7 21.2 1.0 CA C:HIS71 4.7 20.3 1.0 CB C:ARG72 4.7 20.9 1.0 NE1 C:TRP95 4.7 21.5 1.0 CA C:TYR92 4.8 20.6 1.0 C C:HIS93 4.9 22.2 1.0 C C:HIS71 5.0 18.2 1.0

Iron binding site 10 out of 15 in the Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd 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 Biphenyl-2,3-Diol-Soaked Resting Complex of Oxy and Fd in Carbazole 1, 9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:21.9 occ:1.00 FE1 D:FES201 0.0 21.9 1.0 S1 D:FES201 2.2 23.7 1.0 S2 D:FES201 2.2 22.9 1.0 SG D:CYS65 2.3 23.9 1.0 SG D:CYS46 2.3 23.4 1.0 FE2 D:FES201 2.8 22.3 1.0 CB D:CYS46 3.1 23.1 1.0 CB D:CYS65 3.1 24.1 1.0 CB D:ALA51 4.1 21.8 1.0 CB D:HIS48 4.1 22.8 1.0 ND1 D:HIS48 4.4 23.0 1.0 CB D:PHE67 4.5 24.0 1.0 ND1 D:HIS68 4.6 20.3 1.0 SG D:CYS84 4.6 30.8 1.0 CA D:CYS46 4.6 25.9 1.0 CA D:CYS65 4.6 22.4 1.0 CG D:HIS48 4.7 21.1 1.0 N D:HIS68 4.7 21.4 1.0 N D:HIS48 4.9 24.6 1.0 CA D:HIS48 4.9 22.6 1.0 N D:GLY49 4.9 24.8 1.0

Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri. Biphenyl-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase To Be Published.