Iron in PDB 1o7g: Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site.

All present enzymatic activity of Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site.:
1.14.12.12;

The structure of Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site., PDB code: 1o7g 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)	25.00 / 1.7
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.670, 139.670, 208.109, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 18.7

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site. (pdb code 1o7g). 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 with Naphthalene Bound in the Active Site., PDB code: 1o7g:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site.


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 with Naphthalene Bound in the Active Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1452 b:17.1 occ:1.00 FE1 A:FES1452 0.0 17.1 1.0 ND1 A:HIS104 2.1 18.8 1.0 ND1 A:HIS83 2.1 15.9 1.0 S2 A:FES1452 2.2 14.9 1.0 S1 A:FES1452 2.2 17.4 1.0 FE2 A:FES1452 2.7 15.5 1.0 CE1 A:HIS104 3.0 18.7 1.0 CG A:HIS104 3.1 16.9 1.0 CG A:HIS83 3.1 16.0 1.0 CE1 A:HIS83 3.1 20.4 1.0 CB A:HIS83 3.3 17.1 1.0 CB A:HIS104 3.4 18.0 1.0 N A:HIS104 3.8 17.8 1.0 CB A:TYR103 4.0 16.7 1.0 N A:ARG84 4.1 17.0 1.0 NE2 A:HIS104 4.1 18.5 1.0 CD2 A:HIS104 4.2 17.0 1.0 CA A:HIS104 4.2 17.9 1.0 CD2 A:HIS83 4.2 19.8 1.0 NE2 A:HIS83 4.2 17.0 1.0 CG A:TYR103 4.3 15.6 1.0 SG A:CYS81 4.4 16.8 1.0 CG A:ARG84 4.4 22.1 1.0 CD1 A:TYR103 4.5 17.7 1.0 CB A:ARG84 4.5 18.0 1.0 SG A:CYS101 4.5 16.3 1.0 CA A:HIS83 4.6 17.0 1.0 C A:TYR103 4.6 17.1 1.0 C A:HIS83 4.8 18.0 1.0 CA A:ARG84 4.9 17.5 1.0 CA A:TYR103 4.9 15.8 1.0 C A:HIS104 5.0 19.3 1.0

Iron binding site 2 out of 3 in the Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site.


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 with Naphthalene Bound in the Active Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1452 b:15.5 occ:1.00 FE2 A:FES1452 0.0 15.5 1.0 S2 A:FES1452 2.2 14.9 1.0 S1 A:FES1452 2.2 17.4 1.0 SG A:CYS101 2.3 16.3 1.0 SG A:CYS81 2.3 16.8 1.0 FE1 A:FES1452 2.7 17.1 1.0 CB A:CYS101 3.1 16.3 1.0 CB A:CYS81 3.2 14.9 1.0 CB A:HIS83 4.0 17.1 1.0 CB A:TYR103 4.2 16.7 1.0 ND1 A:HIS83 4.4 15.9 1.0 ND1 A:HIS104 4.4 18.8 1.0 N A:HIS104 4.5 17.8 1.0 CA A:CYS101 4.6 16.7 1.0 CA A:CYS81 4.6 15.5 1.0 CB A:LYS86 4.6 17.4 1.0 N A:ARG84 4.7 17.0 1.0 CG A:HIS83 4.7 16.0 1.0 CB A:TRP106 4.8 18.4 1.0 N A:HIS83 4.9 17.5 1.0 N A:TYR103 4.9 16.5 1.0 CA A:HIS83 5.0 17.0 1.0

Iron binding site 3 out of 3 in the Naphthalene 1,2-Dioxygenase with Naphthalene Bound in the Active Site.


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 with Naphthalene Bound in the Active Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1453 b:23.0 occ:1.00 NE2 A:HIS213 2.0 19.3 1.0 O A:HOH2203 2.1 34.3 1.0 NE2 A:HIS208 2.1 19.8 1.0 OD2 A:ASP362 2.3 29.5 1.0 OD1 A:ASP362 2.4 32.0 1.0 CG A:ASP362 2.7 25.4 1.0 CE1 A:HIS213 2.9 18.2 1.0 CD2 A:HIS208 3.0 19.8 1.0 CD2 A:HIS213 3.1 21.4 1.0 CE1 A:HIS208 3.1 20.2 1.0 ND2 A:ASN201 3.8 23.6 1.0 ND1 A:HIS213 4.0 19.2 1.0 O A:HOH2289 4.1 36.1 1.0 CG A:HIS213 4.2 19.2 1.0 CB A:ASP362 4.2 21.4 1.0 CG A:HIS208 4.2 20.2 1.0 ND1 A:HIS208 4.2 20.3 1.0 OD1 A:ASN201 4.2 27.3 1.0 C1 A:NPY1450 4.3 38.1 1.0 CG A:ASN201 4.5 22.9 1.0 CG2 A:THR212 4.5 19.6 1.0 C2 A:NPY1450 4.5 39.9 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