Iron in PDB 1o7n: Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole

All present enzymatic activity of Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole:
1.14.12.12;

The structure of Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole, PDB code: 1o7n was solved by A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.827, 139.827, 208.876, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 20

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole (pdb code 1o7n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole, PDB code: 1o7n:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:14.7 occ:1.00 FE1 A:FES508 0.0 14.7 1.0 ND1 A:HIS104 2.1 16.8 1.0 ND1 A:HIS83 2.1 13.9 1.0 S2 A:FES508 2.2 13.3 1.0 S1 A:FES508 2.3 15.6 1.0 FE2 A:FES508 2.7 13.9 1.0 CE1 A:HIS104 3.0 14.7 1.0 CG A:HIS83 3.1 13.2 1.0 CG A:HIS104 3.1 14.2 1.0 CE1 A:HIS83 3.2 16.6 1.0 CB A:HIS83 3.3 15.2 1.0 CB A:HIS104 3.4 14.9 1.0 N A:HIS104 3.7 14.8 1.0 N A:ARG84 4.0 15.6 1.0 CB A:TYR103 4.0 12.8 1.0 NE2 A:HIS104 4.1 16.0 1.0 CA A:HIS104 4.2 15.6 1.0 CD2 A:HIS104 4.2 15.1 1.0 CD2 A:HIS83 4.3 14.6 1.0 NE2 A:HIS83 4.3 14.5 1.0 CG A:ARG84 4.3 21.4 1.0 CG A:TYR103 4.4 12.2 1.0 SG A:CYS81 4.4 13.6 1.0 CB A:ARG84 4.5 17.5 1.0 CD1 A:TYR103 4.5 14.6 1.0 SG A:CYS101 4.5 14.0 1.0 CA A:HIS83 4.6 15.4 1.0 C A:TYR103 4.6 14.8 1.0 C A:HIS83 4.8 15.7 1.0 CA A:ARG84 4.8 15.4 1.0 CA A:TYR103 4.9 14.2 1.0 C A:HIS104 5.0 16.8 1.0

Iron binding site 2 out of 3 in the Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:13.9 occ:1.00 FE2 A:FES508 0.0 13.9 1.0 S1 A:FES508 2.2 15.6 1.0 S2 A:FES508 2.2 13.3 1.0 SG A:CYS101 2.3 14.0 1.0 SG A:CYS81 2.3 13.6 1.0 FE1 A:FES508 2.7 14.7 1.0 CB A:CYS101 3.1 14.9 1.0 CB A:CYS81 3.2 12.6 1.0 CB A:HIS83 4.0 15.2 1.0 CB A:TYR103 4.2 12.8 1.0 ND1 A:HIS83 4.4 13.9 1.0 ND1 A:HIS104 4.5 16.8 1.0 N A:HIS104 4.5 14.8 1.0 CB A:LYS86 4.5 15.1 1.0 CA A:CYS101 4.6 14.8 1.0 CA A:CYS81 4.6 13.8 1.0 N A:ARG84 4.6 15.6 1.0 CG A:HIS83 4.7 13.2 1.0 CB A:TRP106 4.9 15.3 1.0 N A:HIS83 4.9 16.4 1.0 N A:TYR103 4.9 15.1 1.0 CA A:HIS83 5.0 15.4 1.0

Iron binding site 3 out of 3 in the Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Naphthalene 1,2-Dioxygenase, Ternary Complex with Dioxygen and Indole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe509 b:20.3 occ:1.00 O1 A:OXY506 1.7 39.0 1.0 O2 A:OXY506 2.0 32.8 1.0 NE2 A:HIS213 2.1 18.1 1.0 OD2 A:ASP362 2.1 20.8 1.0 NE2 A:HIS208 2.2 16.8 1.0 OD1 A:ASP362 2.4 25.9 1.0 CG A:ASP362 2.6 19.1 1.0 CE1 A:HIS213 3.0 16.5 1.0 CD2 A:HIS208 3.1 14.4 1.0 CD2 A:HIS213 3.1 17.9 1.0 CE1 A:HIS208 3.2 15.8 1.0 ND2 A:ASN201 3.8 21.6 1.0 ND1 A:HIS213 4.1 14.9 1.0 CB A:ASP362 4.1 17.2 1.0 O A:HOH636 4.2 28.8 1.0 CG A:HIS213 4.2 16.1 1.0 O A:HOH606 4.2 27.6 1.0 CG A:HIS208 4.3 16.3 1.0 OD1 A:ASN201 4.3 24.2 1.0 ND1 A:HIS208 4.3 16.1 1.0 C3 A:IND505 4.3 33.6 1.0 CG A:ASN201 4.5 18.7 1.0 CG2 A:THR212 4.5 15.8 1.0 C2 A:IND505 4.5 31.9 1.0 CA A:ASP362 5.0 17.1 1.0

A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, S.Ramaswamy. Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron Science V. 299 1039 2003.
ISSN: ISSN 0036-8075
PubMed: 12586937
DOI: 10.1126/SCIENCE.1078020