Iron in PDB 1o7p: Naphthalene 1,2-Dioxygenase, Product Complex

All present enzymatic activity of Naphthalene 1,2-Dioxygenase, Product Complex:
1.14.12.12;

The structure of Naphthalene 1,2-Dioxygenase, Product Complex, PDB code: 1o7p 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 / 1.95
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.673, 139.673, 208.439, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 21.9

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase, Product Complex (pdb code 1o7p). 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, Product Complex, PDB code: 1o7p:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Naphthalene 1,2-Dioxygenase, Product Complex


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, Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1452 b:26.9 occ:1.00 FE1 A:FES1452 0.0 26.9 1.0 ND1 A:HIS104 2.0 30.0 1.0 ND1 A:HIS83 2.1 25.2 1.0 S1 A:FES1452 2.2 28.2 1.0 S2 A:FES1452 2.3 26.8 1.0 FE2 A:FES1452 2.7 25.0 1.0 CE1 A:HIS104 2.9 29.6 1.0 CG A:HIS104 3.0 27.8 1.0 CE1 A:HIS83 3.1 28.9 1.0 CG A:HIS83 3.1 25.6 1.0 CB A:HIS104 3.4 28.8 1.0 CB A:HIS83 3.4 26.3 1.0 N A:HIS104 3.8 29.5 1.0 NE2 A:HIS104 4.0 28.4 1.0 N A:ARG84 4.0 27.9 1.0 CB A:TYR103 4.1 28.0 1.0 CD2 A:HIS104 4.1 29.5 1.0 CA A:HIS104 4.2 29.7 1.0 NE2 A:HIS83 4.2 23.9 1.0 CD2 A:HIS83 4.2 28.2 1.0 CG A:ARG84 4.3 31.3 1.0 SG A:CYS81 4.3 24.9 1.0 CG A:TYR103 4.4 27.9 1.0 CB A:ARG84 4.4 28.1 1.0 CD1 A:TYR103 4.5 28.4 1.0 SG A:CYS101 4.5 26.3 1.0 C A:TYR103 4.7 29.1 1.0 CA A:HIS83 4.7 27.3 1.0 CA A:ARG84 4.8 28.2 1.0 C A:HIS83 4.8 27.6 1.0 CD1 A:TRP106 4.9 30.3 1.0 CA A:TYR103 4.9 29.1 1.0 C A:HIS104 4.9 30.8 1.0 NE1 A:TRP106 5.0 29.4 1.0

Iron binding site 2 out of 3 in the Naphthalene 1,2-Dioxygenase, Product Complex


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, Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1452 b:25.0 occ:1.00 FE2 A:FES1452 0.0 25.0 1.0 S2 A:FES1452 2.2 26.8 1.0 SG A:CYS81 2.2 24.9 1.0 S1 A:FES1452 2.3 28.2 1.0 SG A:CYS101 2.3 26.3 1.0 FE1 A:FES1452 2.7 26.9 1.0 CB A:CYS101 3.1 28.1 1.0 CB A:CYS81 3.2 26.7 1.0 CB A:HIS83 4.1 26.3 1.0 CB A:TYR103 4.2 28.0 1.0 ND1 A:HIS104 4.4 30.0 1.0 ND1 A:HIS83 4.4 25.2 1.0 N A:HIS104 4.5 29.5 1.0 CB A:LYS86 4.5 25.9 1.0 CA A:CYS101 4.6 28.4 1.0 N A:ARG84 4.6 27.9 1.0 CA A:CYS81 4.6 25.6 1.0 CG A:HIS83 4.8 25.6 1.0 CB A:TRP106 4.9 29.3 1.0 N A:TYR103 4.9 29.2 1.0

Iron binding site 3 out of 3 in the Naphthalene 1,2-Dioxygenase, Product Complex


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, Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1453 b:37.9 occ:1.00 NE2 A:HIS213 2.0 31.9 1.0 NE2 A:HIS208 2.0 34.5 1.0 OD2 A:ASP362 2.1 39.8 1.0 OD1 A:ASP362 2.2 39.4 1.0 CG A:ASP362 2.5 35.5 1.0 OH2 A:NDH1450 2.8 52.4 1.0 OH1 A:NDH1450 2.8 53.4 1.0 CE1 A:HIS213 3.0 31.2 1.0 CE1 A:HIS208 3.0 35.4 1.0 CD2 A:HIS208 3.0 35.0 1.0 CD2 A:HIS213 3.1 33.2 1.0 ND2 A:ASN201 3.8 35.1 1.0 C1 A:NDH1450 4.0 49.6 1.0 C2 A:NDH1450 4.0 49.9 1.0 CB A:ASP362 4.0 33.3 1.0 ND1 A:HIS213 4.1 31.9 1.0 ND1 A:HIS208 4.2 33.1 1.0 O A:HOH2224 4.2 43.5 1.0 CG A:HIS213 4.2 31.4 1.0 CG A:HIS208 4.2 35.2 1.0 OD1 A:ASN201 4.3 38.9 1.0 CG2 A:THR212 4.4 34.6 1.0 CG A:ASN201 4.5 35.0 1.0 C3 A:NDH1450 4.9 47.4 1.0 CA A:ASP362 4.9 32.5 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