Iron in PDB 4hm0: Naphthalene 1,2-Dioxygenase Bound to Indole-3-Acetate

All present enzymatic activity of Naphthalene 1,2-Dioxygenase Bound to Indole-3-Acetate:
1.14.12.12;

The structure of Naphthalene 1,2-Dioxygenase Bound to Indole-3-Acetate, PDB code: 4hm0 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)	40.61 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	140.682, 140.682, 207.829, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.4

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase Bound to Indole-3-Acetate (pdb code 4hm0). 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 Indole-3-Acetate, PDB code: 4hm0:
Jump to Iron binding site number: 1; 2; 3;

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


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 Indole-3-Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:31.6 occ:1.00 NE2 A:HIS213 2.3 33.0 1.0 OD1 A:ASP362 2.3 33.5 1.0 O3 A:IAC505 2.3 37.4 1.0 NE2 A:HIS208 2.4 30.5 1.0 OD2 A:ASP362 2.4 36.5 1.0 O2 A:IAC505 2.4 34.0 1.0 CG A:ASP362 2.7 34.5 1.0 C18 A:IAC505 2.7 36.5 1.0 CE1 A:HIS213 3.1 28.7 1.0 CD2 A:HIS208 3.2 28.6 1.0 CD2 A:HIS213 3.3 28.8 1.0 CE1 A:HIS208 3.4 29.0 1.0 ND2 A:ASN201 3.9 32.1 1.0 O A:HOH814 4.0 30.0 1.0 CB A:ASP362 4.1 32.5 1.0 ND1 A:HIS213 4.2 29.4 1.0 C17 A:IAC505 4.2 30.8 1.0 CG A:HIS213 4.3 26.8 1.0 CG A:HIS208 4.4 28.6 1.0 O A:HOH769 4.5 35.1 1.0 ND1 A:HIS208 4.5 28.9 1.0 CG2 A:THR212 4.5 29.3 1.0 OD1 A:ASN201 4.6 31.1 1.0 CG A:ASN201 4.7 27.6 1.0 C7 A:IAC505 4.9 31.7 1.0 CE2 A:PHE352 4.9 26.1 1.0 CA A:ASP362 5.0 30.5 1.0 O A:TRP358 5.0 26.2 1.0

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


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 Indole-3-Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:25.0 occ:1.00 FE1 A:FES508 0.0 25.0 1.0 S1 A:FES508 2.2 26.4 1.0 S2 A:FES508 2.2 24.2 1.0 ND1 A:HIS104 2.3 26.9 1.0 ND1 A:HIS83 2.4 30.8 1.0 FE2 A:FES508 2.6 22.5 1.0 CG A:HIS104 3.2 27.0 1.0 CG A:HIS83 3.2 26.8 1.0 CE1 A:HIS104 3.3 25.5 1.0 CB A:HIS83 3.3 24.5 1.0 CB A:HIS104 3.4 22.5 1.0 CE1 A:HIS83 3.5 30.9 1.0 N A:HIS104 3.7 24.2 1.0 CB A:TYR103 4.0 25.7 1.0 N A:ARG84 4.1 23.8 1.0 CA A:HIS104 4.1 26.8 1.0 CG A:TYR103 4.3 25.0 1.0 CD2 A:HIS104 4.3 27.1 1.0 NE2 A:HIS104 4.4 27.0 1.0 CD2 A:HIS83 4.4 29.6 1.0 SG A:CYS81 4.4 23.4 1.0 CG A:ARG84 4.4 31.3 1.0 CD2 A:TYR103 4.5 24.6 1.0 NE2 A:HIS83 4.5 28.9 1.0 CB A:ARG84 4.5 26.7 1.0 C A:TYR103 4.6 26.9 1.0 CA A:HIS83 4.6 25.6 1.0 SG A:CYS101 4.7 24.8 1.0 C A:HIS83 4.8 28.2 1.0 CA A:ARG84 4.9 24.0 1.0 CA A:TYR103 4.9 25.8 1.0 C A:HIS104 5.0 29.8 1.0

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


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 Indole-3-Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:22.5 occ:1.00 FE2 A:FES508 0.0 22.5 1.0 S2 A:FES508 2.2 24.2 1.0 S1 A:FES508 2.2 26.4 1.0 SG A:CYS81 2.4 23.4 1.0 SG A:CYS101 2.5 24.8 1.0 FE1 A:FES508 2.6 25.0 1.0 CB A:CYS101 3.2 25.9 1.0 CB A:CYS81 3.2 25.1 1.0 CB A:HIS83 4.1 24.5 1.0 CB A:TYR103 4.2 25.7 1.0 N A:HIS104 4.5 24.2 1.0 CA A:CYS101 4.6 26.4 1.0 ND1 A:HIS104 4.6 26.9 1.0 ND1 A:HIS83 4.6 30.8 1.0 N A:ARG84 4.6 23.8 1.0 CA A:CYS81 4.7 24.8 1.0 CB A:LYS86 4.7 26.3 1.0 CB A:TRP106 4.8 25.6 1.0 CG A:HIS83 4.8 26.8 1.0 N A:TYR103 4.9 24.7 1.0 N A:HIS83 4.9 24.2 1.0

D.J.Ferraro, S.Ramaswamy. Naphthalene 1,2-Dioxygenase Bound to Indole-3-Acetate To Be Published.