Iron in PDB 4hm1: Naphthalene 1,2-Dioxygenase Bound to 1-Indanone

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

The structure of Naphthalene 1,2-Dioxygenase Bound to 1-Indanone, PDB code: 4hm1 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)	15.99 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.935, 139.935, 208.238, 90.00, 90.00, 120.00
R / Rfree (%)	14.9 / 19

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase Bound to 1-Indanone (pdb code 4hm1). 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 1-Indanone, PDB code: 4hm1:
Jump to Iron binding site number: 1; 2; 3;

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


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 1-Indanone 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 10.2 1.0 ND1 A:HIS104 2.3 11.8 1.0 FE2 A:FES1004 2.6 11.5 1.0 CG A:HIS83 3.1 11.2 1.0 CG A:HIS104 3.2 11.1 1.0 CE1 A:HIS104 3.2 12.7 1.0 CE1 A:HIS83 3.3 11.1 1.0 CB A:HIS83 3.3 10.8 1.0 CB A:HIS104 3.5 10.3 1.0 N A:HIS104 3.7 11.4 1.0 CB A:TYR103 4.0 10.9 1.0 N A:ARG84 4.0 12.6 1.0 CA A:HIS104 4.1 11.3 1.0 CD2 A:HIS83 4.3 11.7 1.0 NE2 A:HIS104 4.3 12.5 1.0 CD2 A:HIS104 4.4 12.2 1.0 NE2 A:HIS83 4.4 10.3 1.0 CG A:TYR103 4.4 9.5 1.0 SG A:CYS81 4.4 10.5 1.0 SG A:CYS101 4.5 11.5 1.0 CD2 A:TYR103 4.6 9.4 1.0 CB A:ARG84 4.6 14.1 1.0 CA A:HIS83 4.6 11.4 1.0 C A:TYR103 4.6 11.3 1.0 C A:HIS83 4.8 13.1 1.0 CA A:ARG84 4.8 12.9 1.0 CG A:ARG84 4.9 15.3 1.0 CA A:TYR103 4.9 10.3 1.0 C A:HIS104 4.9 13.2 1.0

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


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 1-Indanone 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 11.5 1.0 SG A:CYS81 2.4 10.5 1.0 FE1 A:FES1004 2.6 12.1 1.0 CB A:CYS101 3.1 11.1 1.0 CB A:CYS81 3.2 9.1 1.0 CB A:HIS83 4.1 10.8 1.0 CB A:TYR103 4.2 10.9 1.0 N A:HIS104 4.4 11.4 1.0 ND1 A:HIS83 4.5 10.2 1.0 CB A:LYS86 4.5 14.1 1.0 CA A:CYS101 4.6 10.3 1.0 N A:ARG84 4.6 12.6 1.0 ND1 A:HIS104 4.6 11.8 1.0 CA A:CYS81 4.6 10.0 1.0 CG A:HIS83 4.8 11.2 1.0 CB A:TRP106 4.9 12.2 1.0 N A:TYR103 4.9 11.1 1.0 N A:HIS83 4.9 11.6 1.0 CA A:TYR103 5.0 10.3 1.0 N A:LYS86 5.0 12.6 1.0

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


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 1-Indanone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:17.4 occ:1.00 NE2 A:HIS213 2.0 12.6 1.0 O A:HOH1308 2.1 24.0 1.0 NE2 A:HIS208 2.1 12.6 1.0 OD1 A:ASP362 2.2 19.1 1.0 OD2 A:ASP362 2.5 21.6 1.0 CG A:ASP362 2.7 18.5 1.0 CE1 A:HIS213 2.9 12.2 1.0 CD2 A:HIS208 3.0 11.9 1.0 CD2 A:HIS213 3.1 13.4 1.0 CE1 A:HIS208 3.2 12.1 1.0 O10 A:1ON1006 3.7 44.2 0.5 ND2 A:ASN201 3.8 17.6 1.0 ND1 A:HIS213 4.1 12.8 1.0 CG A:HIS213 4.2 12.9 1.0 CB A:ASP362 4.2 15.0 1.0 O A:HOH1289 4.2 23.1 1.0 CG A:HIS208 4.2 11.3 1.0 ND1 A:HIS208 4.2 12.6 1.0 OD1 A:ASN201 4.3 18.3 1.0 O A:HOH1277 4.3 22.6 1.0 C1 A:1ON1006 4.3 41.6 0.5 C7 A:1ON1006 4.3 41.6 0.5 C2 A:1ON1006 4.4 41.5 0.5 CG A:ASN201 4.4 16.0 1.0 CG2 A:THR212 4.4 12.2 1.0 C8 A:1ON1006 4.7 41.4 0.5

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