Iron in PDB 3gkq: Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1

The structure of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1, PDB code: 3gkq was solved by T.Umeda, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.07 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	117.147, 159.019, 167.774, 90.00, 94.45, 90.00
R / Rfree (%)	20.1 / 43.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 (pdb code 3gkq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1, PDB code: 3gkq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:16.6 occ:1.00 NE2 A:HIS186 1.7 18.4 1.0 O A:HOH2190 2.0 52.3 1.0 OD2 A:ASP334 2.2 29.5 1.0 OD1 A:ASP334 2.2 29.1 1.0 NE2 A:HIS190 2.3 33.8 1.0 O A:HOH2183 2.4 47.9 1.0 CG A:ASP334 2.5 29.4 1.0 CD2 A:HIS186 2.7 27.4 1.0 CE1 A:HIS186 2.8 29.2 1.0 CE1 A:HIS190 3.2 34.7 1.0 CD2 A:HIS190 3.3 31.0 1.0 ND1 A:HIS186 3.8 26.7 1.0 CG A:HIS186 3.9 26.9 1.0 CB A:ASP334 4.1 31.2 1.0 O A:HOH1263 4.1 49.0 1.0 ND2 A:ASN331 4.3 34.1 1.0 ND1 A:HIS190 4.3 32.1 1.0 O A:HOH1031 4.4 33.7 1.0 CD1 A:ILE189 4.4 43.0 1.0 CG A:HIS190 4.4 32.5 1.0 CE2 A:PHE330 4.4 36.9 1.0 OD1 A:ASN180 4.5 34.4 1.0 ND2 A:ASN180 4.6 26.0 1.0 O A:ASN180 4.8 33.8 1.0 CG A:ASN180 4.9 31.2 1.0 CA A:ASP334 5.0 33.2 1.0

Iron binding site 2 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:26.8 occ:1.00 FE1 A:FES502 0.0 26.8 1.0 S2 A:FES502 2.2 27.8 1.0 SG A:CYS72 2.3 25.1 1.0 SG A:CYS93 2.3 26.4 1.0 S1 A:FES502 2.3 32.1 1.0 FE2 A:FES502 2.8 26.5 1.0 CB A:CYS93 3.1 24.5 1.0 CB A:CYS72 3.1 27.1 1.0 CG2 A:VAL77 4.0 23.8 1.0 CB A:HIS74 4.0 26.0 1.0 CB A:TYR95 4.2 25.0 1.0 N A:HIS96 4.4 26.0 1.0 ND1 A:HIS96 4.5 22.9 1.0 ND1 A:HIS74 4.5 25.6 1.0 CA A:CYS93 4.5 26.4 1.0 CA A:CYS72 4.6 26.7 1.0 CG A:HIS74 4.8 25.2 1.0 N A:TYR95 4.8 26.9 1.0 CB A:TRP98 4.8 26.9 1.0 N A:ARG75 4.8 24.5 1.0 CA A:TYR95 4.9 26.8 1.0 N A:HIS74 5.0 26.5 1.0 C A:CYS93 5.0 26.6 1.0

Iron binding site 3 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:26.5 occ:1.00 FE2 A:FES502 0.0 26.5 1.0 ND1 A:HIS96 2.0 22.9 1.0 ND1 A:HIS74 2.1 25.6 1.0 S1 A:FES502 2.2 32.1 1.0 S2 A:FES502 2.3 27.8 1.0 FE1 A:FES502 2.8 26.8 1.0 CG A:HIS96 3.0 25.3 1.0 CG A:HIS74 3.0 25.2 1.0 CE1 A:HIS96 3.1 25.8 1.0 CE1 A:HIS74 3.2 25.4 1.0 CB A:HIS96 3.2 26.2 1.0 CB A:HIS74 3.3 26.0 1.0 N A:HIS96 3.7 26.0 1.0 CB A:TYR95 4.0 25.0 1.0 CA A:HIS96 4.0 26.6 1.0 CD2 A:HIS96 4.1 24.1 1.0 NE2 A:HIS96 4.1 25.3 1.0 CD2 A:HIS74 4.2 25.1 1.0 CG A:ARG75 4.2 22.8 1.0 NE2 A:HIS74 4.2 24.8 1.0 SG A:CYS72 4.3 25.1 1.0 N A:ARG75 4.4 24.5 1.0 CG A:TYR95 4.4 25.5 1.0 CD2 A:TYR95 4.5 27.5 1.0 C A:TYR95 4.5 25.9 1.0 CD1 A:TRP98 4.5 27.0 1.0 SG A:CYS93 4.6 26.4 1.0 NE1 A:TRP98 4.6 26.7 1.0 CA A:HIS74 4.7 26.4 1.0 CB A:ARG75 4.7 24.1 1.0 C A:HIS96 4.8 26.5 1.0 CA A:TYR95 4.9 26.8 1.0 C A:HIS74 4.9 26.5 1.0 CG A:TRP98 5.0 26.6 1.0

Iron binding site 4 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:35.8 occ:1.00 NE2 A:HIS294 2.3 29.0 1.0 OD1 A:ASP171 3.1 44.6 1.0 CD2 A:HIS294 3.1 28.4 1.0 CE1 A:HIS294 3.4 31.7 1.0 CG A:ASP171 4.0 41.9 1.0 O A:HOH1444 4.1 53.5 1.0 CG A:HIS294 4.4 28.6 1.0 ND1 A:HIS294 4.4 31.2 1.0 OD2 A:ASP171 4.7 48.0 1.0 CB A:ASP171 4.7 36.2 1.0 O A:HOH1186 4.7 42.4 1.0

Iron binding site 5 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:11.4 occ:1.00 NE2 B:HIS190 2.2 30.3 1.0 NE2 B:HIS186 2.3 26.2 1.0 OD1 B:ASP334 2.3 29.4 1.0 O B:HOH2184 2.3 29.4 1.0 O B:HOH1158 2.4 44.2 1.0 OD2 B:ASP334 2.5 29.8 1.0 CG B:ASP334 2.7 29.3 1.0 CD2 B:HIS186 3.1 26.6 1.0 CE1 B:HIS190 3.2 30.5 1.0 CD2 B:HIS190 3.3 29.2 1.0 CE1 B:HIS186 3.3 25.6 1.0 CB B:ASP334 4.3 26.2 1.0 ND1 B:HIS190 4.3 29.8 1.0 CG B:HIS186 4.3 27.4 1.0 O B:HOH1027 4.4 30.7 1.0 ND1 B:HIS186 4.4 25.9 1.0 CG B:HIS190 4.4 29.4 1.0 ND2 B:ASN331 4.4 26.9 1.0 ND2 B:ASN180 4.5 24.2 1.0 CE2 B:PHE330 4.6 33.8 1.0 O B:HOH710 4.6 45.4 1.0 O B:ASN180 4.8 26.6 1.0 CG2 B:ILE189 4.8 24.8 1.0 OD1 B:ASN180 4.8 24.8 1.0 CG B:ASN180 5.0 25.7 1.0

Iron binding site 6 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:26.1 occ:1.00 FE1 B:FES502 0.0 26.1 1.0 SG B:CYS72 2.3 24.9 1.0 S1 B:FES502 2.3 29.5 1.0 SG B:CYS93 2.3 25.6 1.0 S2 B:FES502 2.3 27.6 1.0 FE2 B:FES502 2.7 26.1 1.0 CB B:CYS93 3.1 24.2 1.0 CB B:CYS72 3.1 25.0 1.0 CB B:HIS74 4.0 25.3 1.0 CG2 B:VAL77 4.0 23.6 1.0 CB B:TYR95 4.2 27.9 1.0 N B:HIS96 4.4 24.9 1.0 ND1 B:HIS74 4.5 25.6 1.0 ND1 B:HIS96 4.5 22.0 1.0 CA B:CYS93 4.5 23.8 1.0 CA B:CYS72 4.6 25.7 1.0 CB B:TRP98 4.7 26.0 1.0 CG B:HIS74 4.7 26.3 1.0 N B:ARG75 4.8 25.8 1.0 N B:TYR95 4.8 25.6 1.0 CG B:TRP98 4.9 26.5 1.0 N B:HIS74 4.9 25.9 1.0 CA B:TYR95 5.0 25.8 1.0 C B:CYS93 5.0 24.0 1.0

Iron binding site 7 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:26.1 occ:1.00 FE2 B:FES502 0.0 26.1 1.0 ND1 B:HIS96 2.1 22.0 1.0 ND1 B:HIS74 2.1 25.6 1.0 S1 B:FES502 2.3 29.5 1.0 S2 B:FES502 2.3 27.6 1.0 FE1 B:FES502 2.7 26.1 1.0 CG B:HIS96 3.0 26.2 1.0 CG B:HIS74 3.0 26.3 1.0 CE1 B:HIS96 3.1 25.2 1.0 CE1 B:HIS74 3.2 26.1 1.0 CB B:HIS74 3.2 25.3 1.0 CB B:HIS96 3.3 24.2 1.0 N B:HIS96 3.7 24.9 1.0 CB B:TYR95 4.0 27.9 1.0 CA B:HIS96 4.1 25.6 1.0 CD2 B:HIS96 4.1 24.9 1.0 NE2 B:HIS96 4.2 25.0 1.0 CG B:ARG75 4.2 28.0 1.0 CD2 B:HIS74 4.2 25.3 1.0 NE2 B:HIS74 4.3 24.9 1.0 N B:ARG75 4.3 25.8 1.0 SG B:CYS72 4.3 24.9 1.0 CG B:TYR95 4.4 31.8 1.0 CD2 B:TYR95 4.5 33.6 1.0 C B:TYR95 4.5 25.5 1.0 CD1 B:TRP98 4.6 25.6 1.0 SG B:CYS93 4.6 25.6 1.0 CA B:HIS74 4.6 26.5 1.0 NE1 B:TRP98 4.7 24.8 1.0 CB B:ARG75 4.7 25.8 1.0 CA B:TYR95 4.8 25.8 1.0 C B:HIS96 4.9 25.8 1.0 C B:HIS74 4.9 25.8 1.0 CG B:TRP98 5.0 26.5 1.0

Iron binding site 8 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe503 b:35.4 occ:1.00 NE2 B:HIS294 2.2 28.0 1.0 CE1 B:HIS294 3.2 28.1 1.0 CD2 B:HIS294 3.2 24.5 1.0 OD1 B:ASP171 3.5 34.6 1.0 CG B:ASP171 4.0 33.3 1.0 ND1 B:HIS294 4.3 28.7 1.0 OD2 B:ASP171 4.4 35.5 1.0 CG B:HIS294 4.4 26.3 1.0 O B:HOH1986 4.5 37.3 1.0 CB B:ASP171 4.8 29.2 1.0

Iron binding site 9 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:16.2 occ:1.00 O C:HOH2088 2.2 44.1 1.0 NE2 C:HIS186 2.2 25.8 1.0 NE2 C:HIS190 2.3 34.6 1.0 OD1 C:ASP334 2.4 30.0 1.0 OD2 C:ASP334 2.5 31.6 1.0 O C:HOH2185 2.5 29.9 1.0 CG C:ASP334 2.8 30.6 1.0 CE1 C:HIS186 3.2 24.4 1.0 CD2 C:HIS186 3.2 27.8 1.0 CE1 C:HIS190 3.3 34.8 1.0 CD2 C:HIS190 3.3 34.1 1.0 CB C:ASP334 4.3 27.1 1.0 ND1 C:HIS186 4.3 28.0 1.0 CG C:HIS186 4.4 27.9 1.0 O C:HOH1047 4.4 36.6 1.0 ND2 C:ASN331 4.4 30.5 1.0 ND1 C:HIS190 4.4 33.7 1.0 CG C:HIS190 4.4 34.6 1.0 ND2 C:ASN180 4.4 25.8 1.0 CE2 C:PHE330 4.6 36.9 1.0 OD1 C:ASN180 4.7 27.3 1.0 O C:ASN180 4.8 29.5 1.0 CG2 C:ILE189 4.8 26.6 1.0 CG C:ASN180 4.9 27.1 1.0

Iron binding site 10 out of 24 in the Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Terminal Oxygenase of Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:23.9 occ:1.00 FE1 C:FES502 0.0 23.9 1.0 SG C:CYS93 2.2 23.6 1.0 SG C:CYS72 2.3 25.3 1.0 S2 C:FES502 2.3 24.7 1.0 S1 C:FES502 2.3 28.6 1.0 FE2 C:FES502 2.8 24.0 1.0 CB C:CYS93 3.0 23.2 1.0 CB C:CYS72 3.1 23.2 1.0 CB C:HIS74 4.0 21.8 1.0 CG2 C:VAL77 4.0 23.5 1.0 CB C:TYR95 4.2 23.4 1.0 N C:HIS96 4.4 24.5 1.0 ND1 C:HIS74 4.5 20.1 1.0 ND1 C:HIS96 4.5 23.5 1.0 CA C:CYS93 4.5 24.0 1.0 CA C:CYS72 4.6 25.6 1.0 CB C:TRP98 4.7 24.9 1.0 CG C:HIS74 4.7 21.2 1.0 N C:TYR95 4.8 23.3 1.0 N C:ARG75 4.8 22.8 1.0 CG C:TRP98 4.9 24.1 1.0 C C:CYS93 4.9 24.1 1.0 CA C:TYR95 4.9 23.8 1.0 N C:HIS74 5.0 23.9 1.0

T.Umeda, J.Katsuki, Y.Ashikawa, K.Inoue, Y.Usami, H.Noguchi, T.Terada, M.Abo, Z.Fujimoto, H.Yamane, H.Nojiri. Specific Interaction Via Putidaredoxin-Type Ferredoxin in Carbazole 1,9A-Dioxygenase From Novosphingobium Sp. KA1 To Be Published.