Iron in PDB 4hm8: Naphthalene 1,2-Dioxygenase Bound to Thioanisole

All present enzymatic activity of Naphthalene 1,2-Dioxygenase Bound to Thioanisole:
1.14.12.12;

The structure of Naphthalene 1,2-Dioxygenase Bound to Thioanisole, PDB code: 4hm8 was solved by D.J.Ferraro, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.99 / 1.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	140.236, 140.236, 208.290, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.4

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase Bound to Thioanisole (pdb code 4hm8). 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 Bound to Thioanisole, PDB code: 4hm8:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Naphthalene 1,2-Dioxygenase Bound to Thioanisole


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 Bound to Thioanisole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:10.6 occ:1.00 FE1 A:FES1004 0.0 10.6 1.0 S1 A:FES1004 2.2 11.1 1.0 S2 A:FES1004 2.2 9.8 1.0 ND1 A:HIS83 2.2 10.5 1.0 ND1 A:HIS104 2.2 10.6 1.0 FE2 A:FES1004 2.7 9.9 1.0 CG A:HIS83 3.1 9.9 1.0 CG A:HIS104 3.2 10.5 1.0 CE1 A:HIS104 3.2 11.0 1.0 CE1 A:HIS83 3.2 10.3 1.0 CB A:HIS83 3.4 9.9 1.0 CB A:HIS104 3.5 9.6 1.0 N A:HIS104 3.7 10.3 1.0 N A:ARG84 4.0 11.9 1.0 CB A:TYR103 4.1 9.7 1.0 CA A:HIS104 4.2 10.4 1.0 NE2 A:HIS104 4.3 11.0 1.0 CD2 A:HIS104 4.3 11.4 1.0 CD2 A:HIS83 4.3 10.4 1.0 NE2 A:HIS83 4.3 9.9 1.0 CG A:TYR103 4.4 9.1 1.0 SG A:CYS81 4.4 9.8 1.0 SG A:CYS101 4.5 10.0 1.0 CD2 A:TYR103 4.6 9.5 1.0 CA A:HIS83 4.6 10.5 1.0 CB A:ARG84 4.6 13.6 1.0 C A:TYR103 4.7 9.4 1.0 C A:HIS83 4.8 12.2 1.0 CA A:ARG84 4.9 12.5 1.0 CA A:TYR103 4.9 9.3 1.0 C A:HIS104 4.9 10.9 1.0 CG A:ARG84 4.9 13.0 1.0

Iron binding site 2 out of 3 in the Naphthalene 1,2-Dioxygenase Bound to Thioanisole


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 Bound to Thioanisole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:9.9 occ:1.00 FE2 A:FES1004 0.0 9.9 1.0 S1 A:FES1004 2.2 11.1 1.0 S2 A:FES1004 2.2 9.8 1.0 SG A:CYS101 2.3 10.0 1.0 SG A:CYS81 2.4 9.8 1.0 FE1 A:FES1004 2.7 10.6 1.0 CB A:CYS101 3.1 10.2 1.0 CB A:CYS81 3.2 9.4 1.0 CB A:HIS83 4.1 9.9 1.0 CB A:TYR103 4.2 9.7 1.0 N A:HIS104 4.5 10.3 1.0 CB A:LYS86 4.5 13.3 1.0 ND1 A:HIS83 4.5 10.5 1.0 CA A:CYS101 4.6 10.1 1.0 ND1 A:HIS104 4.6 10.6 1.0 N A:ARG84 4.6 11.9 1.0 CA A:CYS81 4.6 9.5 1.0 CG A:HIS83 4.8 9.9 1.0 CB A:TRP106 4.9 11.0 1.0 N A:HIS83 4.9 11.0 1.0 N A:TYR103 4.9 10.4 1.0 N A:LYS86 5.0 10.1 1.0

Iron binding site 3 out of 3 in the Naphthalene 1,2-Dioxygenase Bound to Thioanisole


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 Bound to Thioanisole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:14.1 occ:1.00 O A:HOH1799 2.0 21.0 1.0 NE2 A:HIS213 2.1 13.0 1.0 OD1 A:ASP362 2.1 14.7 1.0 NE2 A:HIS208 2.1 11.8 1.0 OD2 A:ASP362 2.5 18.1 1.0 CG A:ASP362 2.6 15.1 1.0 CE1 A:HIS213 2.9 11.9 1.0 CD2 A:HIS208 3.0 10.6 1.0 CD2 A:HIS213 3.1 12.3 1.0 CE1 A:HIS208 3.2 12.4 1.0 ND2 A:ASN201 3.8 15.6 1.0 ND1 A:HIS213 4.1 11.6 1.0 CB A:ASP362 4.1 13.4 1.0 O A:HOH1482 4.1 20.3 1.0 CG A:HIS213 4.2 11.2 1.0 CG A:HIS208 4.2 10.4 1.0 ND1 A:HIS208 4.3 10.9 1.0 OD1 A:ASN201 4.3 16.3 1.0 O A:HOH1167 4.3 18.6 1.0 CG2 A:THR212 4.3 10.6 1.0 S7 A:16R1006 4.4 29.5 0.6 CG A:ASN201 4.4 13.6 1.0 C5 A:16R1006 4.5 27.1 0.5 C6 A:16R1006 4.7 29.0 0.5 O A:HOH1770 4.8 46.2 0.9 CA A:ASP362 5.0 11.8 1.0

D.J.Ferraro, S.Ramaswamy. Naphthalene 1,2-Dioxygenase Bound to Thioanisole To Be Published.