Iron in PDB 1o7w: Naphthalene 1,2-Dioxygenase, Fully Reduced Form

All present enzymatic activity of Naphthalene 1,2-Dioxygenase, Fully Reduced Form:
1.14.12.12;

The structure of Naphthalene 1,2-Dioxygenase, Fully Reduced Form, PDB code: 1o7w 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)	30.00 / 1.9
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.526, 139.526, 208.103, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 20.8

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase, Fully Reduced Form (pdb code 1o7w). 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, Fully Reduced Form, PDB code: 1o7w:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Naphthalene 1,2-Dioxygenase, Fully Reduced Form


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, Fully Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1452 b:22.6 occ:1.00 FE1 A:FES1452 0.0 22.6 1.0 ND1 A:HIS104 2.0 23.2 1.0 ND1 A:HIS83 2.2 21.6 1.0 S1 A:FES1452 2.2 23.3 1.0 S2 A:FES1452 2.3 21.8 1.0 FE2 A:FES1452 2.7 21.8 1.0 CE1 A:HIS104 2.9 23.6 1.0 CG A:HIS104 3.1 23.1 1.0 CG A:HIS83 3.1 21.8 1.0 CE1 A:HIS83 3.2 24.5 1.0 CB A:HIS83 3.4 22.8 1.0 CB A:HIS104 3.5 24.1 1.0 N A:HIS104 3.8 24.1 1.0 NE2 A:HIS104 4.0 22.2 1.0 CB A:TYR103 4.0 23.4 1.0 N A:ARG84 4.0 23.0 1.0 CD2 A:HIS104 4.1 23.8 1.0 CA A:HIS104 4.2 24.6 1.0 NE2 A:HIS83 4.3 21.8 1.0 CD2 A:HIS83 4.3 24.4 1.0 SG A:CYS81 4.3 22.9 1.0 CG A:ARG84 4.3 25.4 1.0 CG A:TYR103 4.3 22.9 1.0 CD1 A:TYR103 4.5 23.6 1.0 CB A:ARG84 4.5 23.2 1.0 SG A:CYS101 4.5 22.8 1.0 CA A:HIS83 4.6 23.4 1.0 C A:TYR103 4.7 24.1 1.0 C A:HIS83 4.8 23.5 1.0 CA A:ARG84 4.8 22.9 1.0 CA A:TYR103 4.9 23.6 1.0 CD1 A:TRP106 5.0 25.1 1.0 C A:HIS104 5.0 25.3 1.0

Iron binding site 2 out of 3 in the Naphthalene 1,2-Dioxygenase, Fully Reduced Form


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, Fully Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1452 b:21.8 occ:1.00 FE2 A:FES1452 0.0 21.8 1.0 S2 A:FES1452 2.2 21.8 1.0 S1 A:FES1452 2.2 23.3 1.0 SG A:CYS81 2.3 22.9 1.0 SG A:CYS101 2.3 22.8 1.0 FE1 A:FES1452 2.7 22.6 1.0 CB A:CYS101 3.1 23.8 1.0 CB A:CYS81 3.2 22.7 1.0 CB A:HIS83 4.1 22.8 1.0 CB A:TYR103 4.2 23.4 1.0 ND1 A:HIS104 4.4 23.2 1.0 ND1 A:HIS83 4.5 21.6 1.0 N A:HIS104 4.5 24.1 1.0 CA A:CYS101 4.6 24.0 1.0 CB A:LYS86 4.6 23.7 1.0 CA A:CYS81 4.6 22.2 1.0 N A:ARG84 4.7 23.0 1.0 CG A:HIS83 4.8 21.8 1.0 CB A:TRP106 4.9 24.8 1.0 N A:TYR103 4.9 23.8 1.0 N A:HIS83 5.0 23.5 1.0

Iron binding site 3 out of 3 in the Naphthalene 1,2-Dioxygenase, Fully Reduced Form


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, Fully Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1453 b:30.3 occ:1.00 NE2 A:HIS213 2.0 26.6 1.0 NE2 A:HIS208 2.1 27.2 1.0 OD2 A:ASP362 2.3 36.1 1.0 O A:HOH2144 2.3 43.2 1.0 OD1 A:ASP362 2.4 35.7 1.0 CG A:ASP362 2.7 31.7 1.0 CE1 A:HIS213 3.0 24.9 1.0 CD2 A:HIS208 3.0 27.8 1.0 CE1 A:HIS208 3.1 28.8 1.0 CD2 A:HIS213 3.1 26.4 1.0 OD1 A:ASN201 3.8 34.3 1.0 ND1 A:HIS213 4.1 25.5 1.0 ND1 A:HIS208 4.2 28.5 1.0 CG A:HIS208 4.2 28.3 1.0 CG A:HIS213 4.2 24.7 1.0 CB A:ASP362 4.2 30.0 1.0 ND2 A:ASN201 4.3 31.5 1.0 CG2 A:THR212 4.4 27.2 1.0 CG A:ASN201 4.5 29.4 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