Iron in PDB 1o7m: Naphthalene 1,2-Dioxygenase, Binary Complex with Dioxygen

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

The structure of Naphthalene 1,2-Dioxygenase, Binary Complex with Dioxygen, PDB code: 1o7m 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 / 1.75
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	140.277, 140.277, 208.754, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 18.7

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase, Binary Complex with Dioxygen (pdb code 1o7m). 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, Binary Complex with Dioxygen, PDB code: 1o7m:
Jump to Iron binding site number: 1; 2; 3;

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


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, Binary Complex with Dioxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1453 b:14.1 occ:1.00 FE1 A:FES1453 0.0 14.1 1.0 ND1 A:HIS83 2.1 8.9 1.0 ND1 A:HIS104 2.2 14.7 1.0 S1 A:FES1453 2.2 13.2 1.0 S2 A:FES1453 2.2 11.0 1.0 FE2 A:FES1453 2.7 12.5 1.0 CG A:HIS83 3.1 11.4 1.0 CE1 A:HIS104 3.1 15.1 1.0 CE1 A:HIS83 3.1 12.0 1.0 CG A:HIS104 3.1 13.7 1.0 CB A:HIS83 3.3 12.2 1.0 CB A:HIS104 3.5 13.9 1.0 N A:HIS104 3.8 14.2 1.0 N A:ARG84 3.9 12.7 1.0 CB A:TYR103 4.1 13.5 1.0 CA A:HIS104 4.2 14.0 1.0 NE2 A:HIS104 4.2 15.2 1.0 CD2 A:HIS83 4.2 12.4 1.0 NE2 A:HIS83 4.2 9.9 1.0 CD2 A:HIS104 4.2 14.5 1.0 CG A:ARG84 4.3 15.8 1.0 SG A:CYS81 4.3 10.9 1.0 CG A:TYR103 4.3 13.2 1.0 CB A:ARG84 4.4 12.9 1.0 CD1 A:TYR103 4.4 14.3 1.0 SG A:CYS101 4.5 11.8 1.0 CA A:HIS83 4.6 12.2 1.0 C A:TYR103 4.7 13.9 1.0 C A:HIS83 4.7 12.5 1.0 CA A:ARG84 4.8 12.6 1.0 CD1 A:TRP106 5.0 14.0 1.0 CA A:TYR103 5.0 13.7 1.0 C A:HIS104 5.0 14.6 1.0

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


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, Binary Complex with Dioxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1453 b:12.5 occ:1.00 FE2 A:FES1453 0.0 12.5 1.0 S2 A:FES1453 2.2 11.0 1.0 S1 A:FES1453 2.2 13.2 1.0 SG A:CYS81 2.3 10.9 1.0 SG A:CYS101 2.3 11.8 1.0 FE1 A:FES1453 2.7 14.1 1.0 CB A:CYS81 3.1 11.2 1.0 CB A:CYS101 3.1 13.1 1.0 CB A:HIS83 4.0 12.2 1.0 CB A:TYR103 4.2 13.5 1.0 ND1 A:HIS83 4.4 8.9 1.0 N A:HIS104 4.5 14.2 1.0 ND1 A:HIS104 4.5 14.7 1.0 CB A:LYS86 4.5 13.9 1.0 CA A:CYS81 4.6 11.1 1.0 CA A:CYS101 4.6 13.0 1.0 N A:ARG84 4.6 12.7 1.0 CG A:HIS83 4.7 11.4 1.0 CB A:TRP106 4.8 13.0 1.0 N A:HIS83 4.9 12.4 1.0 N A:TYR103 5.0 13.4 1.0 CA A:HIS83 5.0 12.2 1.0

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


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, Binary Complex with Dioxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1454 b:22.4 occ:1.00 NE2 A:HIS213 2.0 15.1 1.0 NE2 A:HIS208 2.1 15.0 1.0 O1 A:OXY1451 2.1 36.1 1.0 OD2 A:ASP362 2.2 16.6 1.0 O2 A:OXY1451 2.3 38.9 1.0 OD1 A:ASP362 2.4 18.5 1.0 CG A:ASP362 2.7 16.5 1.0 CE1 A:HIS213 3.0 15.2 1.0 CD2 A:HIS213 3.1 16.8 1.0 CD2 A:HIS208 3.1 15.6 1.0 CE1 A:HIS208 3.1 16.1 1.0 ND2 A:ASN201 4.0 28.0 1.0 ND1 A:HIS213 4.1 11.2 1.0 O A:HOH2310 4.1 27.6 1.0 CG A:HIS213 4.2 14.4 1.0 CB A:ASP362 4.2 14.5 1.0 OD1 A:ASN201 4.2 24.6 1.0 ND1 A:HIS208 4.2 15.9 1.0 CG A:HIS208 4.3 16.1 1.0 CG A:ASN201 4.5 20.6 1.0 CG2 A:THR212 4.7 15.3 1.0 O A:HOH2306 4.7 27.4 1.0 O A:HOH2219 4.9 28.4 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