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

The structure of Biphenyl-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase, PDB code: 6llf 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)	44.88 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.294, 89.684, 105.021, 90, 104.08, 90
R / Rfree (%)	15.8 / 20

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

Binding sites:

The binding sites of Iron atom in the Biphenyl-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase (pdb code 6llf). 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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase, PDB code: 6llf:
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-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.4 occ:1.00 FE1 A:FES401 0.0 12.4 1.0 S2 A:FES401 2.2 12.6 1.0 S1 A:FES401 2.2 13.0 1.0 SG A:CYS90 2.3 13.0 1.0 SG A:CYS69 2.4 13.3 1.0 FE2 A:FES401 2.7 13.1 1.0 CB A:CYS90 3.1 12.9 1.0 CB A:CYS69 3.1 13.2 1.0 CB A:TYR92 4.1 13.6 1.0 CG2 A:VAL74 4.1 13.5 1.0 CB A:HIS71 4.3 11.6 1.0 ND1 A:HIS71 4.4 11.1 1.0 N A:HIS93 4.5 12.5 1.0 ND1 A:HIS93 4.5 12.0 1.0 CA A:CYS90 4.5 12.4 1.0 CA A:CYS69 4.6 12.8 1.0 CB A:TRP95 4.8 11.7 1.0 N A:TYR92 4.8 12.2 1.0 CG A:HIS71 4.8 12.1 1.0 CG A:TRP95 4.9 10.6 1.0 CA A:TYR92 4.9 13.5 1.0 N A:ARG72 4.9 12.2 1.0

Iron binding site 2 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.1 occ:1.00 FE2 A:FES401 0.0 13.1 1.0 ND1 A:HIS71 2.1 11.1 1.0 ND1 A:HIS93 2.1 12.0 1.0 S1 A:FES401 2.2 13.0 1.0 S2 A:FES401 2.3 12.6 1.0 FE1 A:FES401 2.7 12.4 1.0 CE1 A:HIS71 3.0 12.9 1.0 CE1 A:HIS93 3.1 12.6 1.0 CG A:HIS71 3.1 12.1 1.0 CG A:HIS93 3.1 12.9 1.0 CB A:HIS71 3.5 11.6 1.0 CB A:HIS93 3.5 12.1 1.0 N A:HIS93 3.7 12.5 1.0 CB A:TYR92 4.0 13.6 1.0 CA A:HIS93 4.2 12.6 1.0 NE2 A:HIS93 4.2 11.7 1.0 NE2 A:HIS71 4.2 11.4 1.0 CD2 A:HIS71 4.2 11.2 1.0 CD2 A:HIS93 4.2 12.4 1.0 CG A:TYR92 4.3 14.1 1.0 CD2 A:TYR92 4.3 14.5 1.0 SG A:CYS69 4.4 13.3 1.0 N A:ARG72 4.4 12.2 1.0 CG A:ARG72 4.4 15.1 1.0 CD1 A:TRP95 4.5 10.8 1.0 C A:TYR92 4.5 13.1 1.0 SG A:CYS90 4.6 13.0 1.0 NE1 A:TRP95 4.6 10.8 1.0 CA A:HIS71 4.7 12.4 1.0 CB A:ARG72 4.8 13.7 1.0 CA A:TYR92 4.8 13.5 1.0 C A:HIS93 4.9 12.7 1.0 CG A:TRP95 4.9 10.6 1.0 C A:HIS71 5.0 11.4 1.0

Iron binding site 3 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:23.4 occ:1.00 O A:HOH501 1.7 26.4 1.0 OD1 A:ASP333 2.0 12.4 1.0 NE2 A:HIS183 2.1 12.5 1.0 NE2 A:HIS187 2.2 16.0 1.0 CG A:ASP333 2.6 12.8 1.0 OD2 A:ASP333 2.6 13.9 1.0 OA3 A:WBP403 2.8 45.6 0.5 OA2 A:WBP403 2.9 41.7 0.5 CD2 A:HIS183 2.9 12.0 1.0 CD2 A:HIS187 3.1 17.0 1.0 CE1 A:HIS187 3.2 19.0 1.0 CE1 A:HIS183 3.2 11.2 1.0 CA3 A:WBP403 3.4 45.3 0.5 CA2 A:WBP403 3.4 45.5 0.5 CB A:ASP333 4.1 12.5 1.0 OA2 A:WBP403 4.1 33.6 0.5 CG A:HIS183 4.1 12.1 1.0 ND2 A:ASN177 4.2 11.4 1.0 ND1 A:HIS183 4.2 12.2 1.0 CA2 A:WBP403 4.2 33.0 0.5 ND1 A:HIS187 4.3 17.9 1.0 CG A:HIS187 4.3 16.8 1.0 CE2 A:PHE329 4.4 16.7 1.0 O A:HOH591 4.4 17.6 1.0 CA3 A:WBP403 4.5 31.5 0.5 CD1 A:ILE186 4.5 13.8 1.0 ND2 A:ASN330 4.5 13.4 1.0 CA4 A:WBP403 4.6 50.0 0.5 OA3 A:WBP403 4.7 34.4 0.5 CA1 A:WBP403 4.7 48.5 0.5 CA A:ASP333 4.8 13.4 1.0 CA1 A:WBP403 4.8 31.8 0.5 CG1 A:ILE186 4.9 13.8 1.0 O A:ASN177 5.0 12.2 1.0 CD2 A:PHE329 5.0 16.3 1.0

Iron binding site 4 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:11.7 occ:1.00 FE1 B:FES401 0.0 11.7 1.0 S1 B:FES401 2.2 12.4 1.0 S2 B:FES401 2.2 12.4 1.0 SG B:CYS69 2.3 12.2 1.0 SG B:CYS90 2.3 11.9 1.0 FE2 B:FES401 2.7 11.9 1.0 CB B:CYS90 3.1 12.9 1.0 CB B:CYS69 3.1 13.2 1.0 CG2 B:VAL74 4.1 10.9 1.0 CB B:TYR92 4.1 11.1 1.0 CB B:HIS71 4.2 11.4 1.0 ND1 B:HIS93 4.5 10.3 1.0 ND1 B:HIS71 4.5 10.3 1.0 N B:HIS93 4.5 12.8 1.0 CA B:CYS90 4.5 12.7 1.0 CA B:CYS69 4.6 12.7 1.0 CB B:TRP95 4.7 12.9 1.0 N B:TYR92 4.8 11.9 1.0 CG B:HIS71 4.8 9.9 1.0 CG B:TRP95 4.9 12.7 1.0 CA B:TYR92 5.0 11.9 1.0 N B:ARG72 5.0 11.3 1.0

Iron binding site 5 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:11.9 occ:1.00 FE2 B:FES401 0.0 11.9 1.0 ND1 B:HIS93 2.1 10.3 1.0 ND1 B:HIS71 2.1 10.3 1.0 S1 B:FES401 2.2 12.4 1.0 S2 B:FES401 2.3 12.4 1.0 FE1 B:FES401 2.7 11.7 1.0 CE1 B:HIS93 3.0 9.9 1.0 CG B:HIS93 3.1 10.9 1.0 CG B:HIS71 3.1 9.9 1.0 CE1 B:HIS71 3.2 10.9 1.0 CB B:HIS71 3.3 11.4 1.0 CB B:HIS93 3.4 12.1 1.0 N B:HIS93 3.7 12.8 1.0 CB B:TYR92 4.0 11.1 1.0 NE2 B:HIS93 4.1 9.9 1.0 CA B:HIS93 4.1 12.3 1.0 CD2 B:HIS93 4.2 10.7 1.0 CD2 B:HIS71 4.2 10.6 1.0 NE2 B:HIS71 4.3 10.0 1.0 SG B:CYS69 4.3 12.2 1.0 CG B:TYR92 4.4 10.7 1.0 CG B:ARG72 4.4 13.3 1.0 CD2 B:TYR92 4.4 10.9 1.0 N B:ARG72 4.4 11.3 1.0 CD1 B:TRP95 4.6 13.0 1.0 C B:TYR92 4.6 12.1 1.0 SG B:CYS90 4.6 11.9 1.0 CA B:HIS71 4.6 12.8 1.0 NE1 B:TRP95 4.7 13.0 1.0 CB B:ARG72 4.8 12.8 1.0 CA B:TYR92 4.8 11.9 1.0 CG B:TRP95 4.8 12.7 1.0 C B:HIS93 4.9 12.5 1.0 C B:HIS71 4.9 11.2 1.0

Iron binding site 6 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:32.5 occ:1.00 O B:HOH569 1.7 40.9 1.0 NE2 B:HIS183 2.1 17.5 1.0 OD1 B:ASP333 2.2 20.6 1.0 NE2 B:HIS187 2.2 24.5 1.0 OD2 B:ASP333 2.6 23.7 1.0 CG B:ASP333 2.7 19.5 1.0 CD2 B:HIS183 3.1 16.7 1.0 CE1 B:HIS187 3.1 26.5 1.0 CE1 B:HIS183 3.2 16.3 1.0 CD2 B:HIS187 3.2 24.0 1.0 OA2 B:WBP403 3.5 53.0 1.0 CA2 B:WBP403 3.8 53.8 1.0 CA3 B:WBP403 4.1 51.4 1.0 OA3 B:WBP403 4.1 63.8 1.0 CB B:ASP333 4.2 19.8 1.0 ND2 B:ASN177 4.2 16.3 1.0 CG B:HIS183 4.2 16.0 1.0 ND1 B:HIS183 4.2 17.3 1.0 ND1 B:HIS187 4.3 26.1 1.0 CG B:HIS187 4.4 24.6 1.0 O B:HOH582 4.4 18.5 1.0 CE2 B:PHE329 4.5 20.8 1.0 CA1 B:WBP403 4.5 49.7 1.0 ND2 B:ASN330 4.6 21.0 1.0 CD1 B:ILE186 4.8 22.0 1.0 CA B:ASP333 4.9 19.9 1.0 CA4 B:WBP403 4.9 52.1 1.0 O B:ASN177 4.9 20.3 1.0 CG1 B:ILE186 5.0 20.8 1.0

Iron binding site 7 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:16.9 occ:1.00 FE1 C:FES401 0.0 16.9 1.0 SG C:CYS69 2.2 17.2 1.0 S1 C:FES401 2.2 18.7 1.0 S2 C:FES401 2.3 18.4 1.0 SG C:CYS90 2.3 17.6 1.0 FE2 C:FES401 2.8 16.3 1.0 CB C:CYS69 3.0 18.4 1.0 CB C:CYS90 3.1 18.1 1.0 CB C:TYR92 4.1 15.8 1.0 CB C:HIS71 4.2 13.4 1.0 CG2 C:VAL74 4.2 17.2 1.0 ND1 C:HIS93 4.4 16.3 1.0 CA C:CYS69 4.5 17.5 1.0 ND1 C:HIS71 4.5 13.5 1.0 CA C:CYS90 4.5 18.0 1.0 N C:HIS93 4.6 16.5 1.0 CB C:TRP95 4.7 16.8 1.0 N C:TYR92 4.8 17.2 1.0 CG C:HIS71 4.9 13.8 1.0 CA C:TYR92 4.9 18.1 1.0 CG C:TRP95 4.9 15.7 1.0 C C:CYS90 5.0 17.3 1.0 N C:ARG72 5.0 14.6 1.0

Iron binding site 8 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:16.3 occ:1.00 FE2 C:FES401 0.0 16.3 1.0 ND1 C:HIS93 2.0 16.3 1.0 ND1 C:HIS71 2.2 13.5 1.0 S1 C:FES401 2.2 18.7 1.0 S2 C:FES401 2.3 18.4 1.0 FE1 C:FES401 2.8 16.9 1.0 CE1 C:HIS93 2.9 17.1 1.0 CG C:HIS93 3.1 18.1 1.0 CG C:HIS71 3.1 13.8 1.0 CE1 C:HIS71 3.2 13.9 1.0 CB C:HIS71 3.4 13.4 1.0 CB C:HIS93 3.5 17.0 1.0 N C:HIS93 3.8 16.5 1.0 CB C:TYR92 3.9 15.8 1.0 NE2 C:HIS93 4.1 16.4 1.0 CD2 C:HIS93 4.1 17.5 1.0 CA C:HIS93 4.2 17.6 1.0 SG C:CYS69 4.3 17.2 1.0 NE2 C:HIS71 4.3 14.0 1.0 CD2 C:HIS71 4.3 13.9 1.0 CD2 C:TYR92 4.3 15.7 1.0 CG C:TYR92 4.3 16.4 1.0 CG C:ARG72 4.4 16.2 1.0 N C:ARG72 4.4 14.6 1.0 CD1 C:TRP95 4.6 16.9 1.0 C C:TYR92 4.6 16.8 1.0 SG C:CYS90 4.6 17.6 1.0 CA C:HIS71 4.6 15.7 1.0 NE1 C:TRP95 4.6 15.9 1.0 CB C:ARG72 4.7 14.8 1.0 CA C:TYR92 4.8 18.1 1.0 C C:HIS93 4.9 18.1 1.0 C C:HIS71 5.0 14.5 1.0 CG C:TRP95 5.0 15.7 1.0

Iron binding site 9 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-Soaked Resting Complex of Oxy and Fd in Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:25.0 occ:1.00 O C:HOH501 1.9 29.0 1.0 OD1 C:ASP333 2.1 16.1 1.0 NE2 C:HIS183 2.1 15.8 1.0 NE2 C:HIS187 2.2 13.9 1.0 CG C:ASP333 2.7 14.9 1.0 OD2 C:ASP333 2.7 16.8 1.0 CD2 C:HIS183 3.0 12.9 1.0 CE1 C:HIS187 3.1 15.9 1.0 CD2 C:HIS187 3.1 14.9 1.0 CE1 C:HIS183 3.2 15.4 1.0 OA2 C:WBP403 3.5 50.4 1.0 CA2 C:WBP403 3.9 48.5 1.0 O C:HOH835 4.0 36.0 1.0 CB C:ASP333 4.2 14.9 1.0 OA3 C:WBP403 4.2 60.8 1.0 ND2 C:ASN177 4.2 15.9 1.0 CG C:HIS183 4.2 13.8 1.0 CA3 C:WBP403 4.2 49.8 1.0 ND1 C:HIS187 4.3 15.4 1.0 ND1 C:HIS183 4.3 13.4 1.0 CG C:HIS187 4.3 14.3 1.0 CE2 C:PHE329 4.4 16.9 1.0 O C:HOH638 4.5 16.6 1.0 ND2 C:ASN330 4.5 14.9 1.0 CD1 C:ILE186 4.7 15.6 1.0 CA1 C:WBP403 4.7 44.6 1.0 CA C:ASP333 4.9 14.0 1.0 O C:ASN177 5.0 15.4 1.0 CG1 C:ILE186 5.0 15.2 1.0 CD2 C:PHE329 5.0 16.5 1.0

Iron binding site 10 out of 15 in the Biphenyl-2,2',3-Triol-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-2,2',3-Triol-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:16.9 occ:1.00 FE1 D:FES201 0.0 16.9 1.0 S1 D:FES201 2.2 19.4 1.0 S2 D:FES201 2.2 17.4 1.0 SG D:CYS65 2.3 18.8 1.0 SG D:CYS46 2.3 19.1 1.0 FE2 D:FES201 2.7 16.5 1.0 CB D:CYS46 3.1 19.9 1.0 CB D:CYS65 3.1 20.8 1.0 CB D:HIS48 4.1 16.8 1.0 CB D:ALA51 4.1 19.3 1.0 CB D:PHE67 4.3 19.1 1.0 ND1 D:HIS48 4.3 15.2 1.0 ND1 D:HIS68 4.4 14.0 1.0 CA D:CYS46 4.5 21.5 1.0 SG D:CYS84 4.5 23.6 1.0 CA D:CYS65 4.6 19.6 1.0 CG D:HIS48 4.7 15.6 1.0 N D:HIS68 4.7 15.9 1.0 CA D:HIS48 4.9 17.1 1.0 N D:HIS48 4.9 18.4 1.0 N D:GLY49 4.9 19.2 1.0 C D:HIS48 4.9 17.8 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.