Iron in PDB 4hm3: Naphthalene 1,2-Dioxygenase Bound to Ethylbenzene

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

The structure of Naphthalene 1,2-Dioxygenase Bound to Ethylbenzene, PDB code: 4hm3 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)	15.95 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.940, 139.940, 208.253, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20.3

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase Bound to Ethylbenzene (pdb code 4hm3). 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 Ethylbenzene, PDB code: 4hm3:
Jump to Iron binding site number: 1; 2; 3;

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


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 Ethylbenzene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:12.1 occ:1.00 FE1 A:FES1004 0.0 12.1 1.0 S1 A:FES1004 2.2 13.4 1.0 S2 A:FES1004 2.2 11.6 1.0 ND1 A:HIS83 2.2 11.8 1.0 ND1 A:HIS104 2.3 11.4 1.0 FE2 A:FES1004 2.7 11.5 1.0 CG A:HIS83 3.1 11.6 1.0 CG A:HIS104 3.2 10.6 1.0 CE1 A:HIS104 3.2 12.4 1.0 CE1 A:HIS83 3.3 12.0 1.0 CB A:HIS83 3.3 10.4 1.0 CB A:HIS104 3.5 9.9 1.0 N A:HIS104 3.7 11.7 1.0 N A:ARG84 4.1 14.0 1.0 CB A:TYR103 4.1 9.9 1.0 CA A:HIS104 4.1 10.6 1.0 NE2 A:HIS104 4.3 11.8 1.0 CD2 A:HIS104 4.3 11.5 1.0 CD2 A:HIS83 4.3 11.4 1.0 NE2 A:HIS83 4.4 11.3 1.0 SG A:CYS81 4.4 11.1 1.0 CG A:TYR103 4.4 9.6 1.0 SG A:CYS101 4.6 10.7 1.0 CD2 A:TYR103 4.6 9.3 1.0 CB A:ARG84 4.6 13.8 1.0 CA A:HIS83 4.6 12.3 1.0 C A:TYR103 4.7 11.7 1.0 C A:HIS83 4.8 13.9 1.0 CG A:ARG84 4.8 13.9 1.0 CA A:ARG84 4.9 13.6 1.0 C A:HIS104 4.9 13.0 1.0 CA A:TYR103 4.9 10.1 1.0

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


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 Ethylbenzene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:11.5 occ:1.00 FE2 A:FES1004 0.0 11.5 1.0 S1 A:FES1004 2.2 13.4 1.0 S2 A:FES1004 2.2 11.6 1.0 SG A:CYS101 2.4 10.7 1.0 SG A:CYS81 2.4 11.1 1.0 FE1 A:FES1004 2.7 12.1 1.0 CB A:CYS101 3.1 9.9 1.0 CB A:CYS81 3.2 9.7 1.0 CB A:HIS83 4.1 10.4 1.0 CB A:TYR103 4.2 9.9 1.0 N A:HIS104 4.4 11.7 1.0 ND1 A:HIS83 4.5 11.8 1.0 CB A:LYS86 4.5 13.9 1.0 CA A:CYS101 4.6 10.4 1.0 ND1 A:HIS104 4.6 11.4 1.0 CA A:CYS81 4.6 11.4 1.0 N A:ARG84 4.6 14.0 1.0 CG A:HIS83 4.8 11.6 1.0 CB A:TRP106 4.8 12.9 1.0 N A:TYR103 4.9 10.7 1.0 N A:HIS83 4.9 12.7 1.0

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


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 Ethylbenzene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:17.4 occ:1.00 NE2 A:HIS213 2.0 12.1 1.0 O A:HOH1307 2.0 24.0 1.0 OD1 A:ASP362 2.1 17.1 1.0 NE2 A:HIS208 2.1 11.9 1.0 OD2 A:ASP362 2.5 20.1 1.0 CG A:ASP362 2.6 17.9 1.0 CE1 A:HIS213 2.9 13.1 1.0 CD2 A:HIS208 3.0 12.7 1.0 CD2 A:HIS213 3.0 13.5 1.0 CE1 A:HIS208 3.2 11.8 1.0 ND2 A:ASN201 3.8 16.8 1.0 ND1 A:HIS213 4.0 12.4 1.0 CB A:ASP362 4.1 16.1 1.0 CG A:HIS213 4.1 12.0 1.0 O A:HOH1288 4.2 23.1 1.0 CG A:HIS208 4.2 12.8 1.0 OD1 A:ASN201 4.2 18.6 1.0 ND1 A:HIS208 4.3 12.7 1.0 CG2 A:THR212 4.3 12.3 1.0 O A:HOH1276 4.4 22.6 1.0 CG A:ASN201 4.4 15.8 1.0 CB A:PYJ1006 4.5 17.6 0.5 CD1 A:PYJ1006 4.6 11.3 0.5 CE1 A:PYJ1006 4.6 12.1 0.5 CA A:ASP362 5.0 14.7 1.0 CX A:PYJ1006 5.0 15.8 0.5

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