Iron in PDB 4hm5: Naphthalene 1,2-Dioxygenase Bound to Indene

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

The structure of Naphthalene 1,2-Dioxygenase Bound to Indene, PDB code: 4hm5 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)	16.00 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.982, 139.982, 208.209, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20.4

The binding sites of Iron atom in the Naphthalene 1,2-Dioxygenase Bound to Indene (pdb code 4hm5). 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 Indene, PDB code: 4hm5:
Jump to Iron binding site number: 1; 2; 3;

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


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 Indene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:16.4 occ:1.00 FE1 A:FES1004 0.0 16.4 1.0 S1 A:FES1004 2.2 17.3 1.0 S2 A:FES1004 2.2 15.5 1.0 ND1 A:HIS104 2.3 17.6 1.0 ND1 A:HIS83 2.3 16.4 1.0 FE2 A:FES1004 2.6 15.4 1.0 CG A:HIS83 3.2 16.8 1.0 CG A:HIS104 3.2 16.4 1.0 CE1 A:HIS104 3.2 17.7 1.0 CE1 A:HIS83 3.3 16.9 1.0 CB A:HIS83 3.4 15.4 1.0 CB A:HIS104 3.5 17.0 1.0 N A:HIS104 3.7 16.8 1.0 N A:ARG84 4.0 16.8 1.0 CB A:TYR103 4.0 15.6 1.0 CA A:HIS104 4.2 17.5 1.0 NE2 A:HIS104 4.3 16.6 1.0 CG A:ARG84 4.3 22.5 1.0 CD2 A:HIS104 4.3 16.3 1.0 CG A:TYR103 4.4 15.0 1.0 CD2 A:HIS83 4.4 16.8 1.0 SG A:CYS81 4.4 14.8 1.0 NE2 A:HIS83 4.4 17.8 1.0 CB A:ARG84 4.5 18.6 1.0 SG A:CYS101 4.6 15.6 1.0 CA A:HIS83 4.6 16.4 1.0 CD2 A:TYR103 4.6 15.1 1.0 C A:TYR103 4.6 15.7 1.0 C A:HIS83 4.7 17.6 1.0 CA A:ARG84 4.8 18.6 1.0 CA A:TYR103 4.9 14.9 1.0 C A:HIS104 5.0 19.8 1.0

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


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 Indene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:15.4 occ:1.00 FE2 A:FES1004 0.0 15.4 1.0 S1 A:FES1004 2.2 17.3 1.0 S2 A:FES1004 2.2 15.5 1.0 SG A:CYS101 2.4 15.6 1.0 SG A:CYS81 2.4 14.8 1.0 FE1 A:FES1004 2.6 16.4 1.0 CB A:CYS101 3.1 16.1 1.0 CB A:CYS81 3.2 14.1 1.0 CB A:HIS83 4.1 15.4 1.0 CB A:TYR103 4.2 15.6 1.0 N A:HIS104 4.5 16.8 1.0 ND1 A:HIS83 4.6 16.4 1.0 CB A:LYS86 4.6 19.3 1.0 ND1 A:HIS104 4.6 17.6 1.0 N A:ARG84 4.6 16.8 1.0 CA A:CYS101 4.6 14.6 1.0 CA A:CYS81 4.7 13.7 1.0 CG A:HIS83 4.8 16.8 1.0 CB A:TRP106 4.9 16.2 1.0 N A:TYR103 4.9 15.3 1.0 N A:HIS83 4.9 16.6 1.0 CA A:HIS83 5.0 16.4 1.0 CA A:TYR103 5.0 14.9 1.0

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


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 Indene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:22.5 occ:1.00 O A:HOH1551 2.0 53.8 1.0 NE2 A:HIS213 2.1 19.4 1.0 OD1 A:ASP362 2.1 21.5 1.0 NE2 A:HIS208 2.2 19.1 1.0 OD2 A:ASP362 2.4 27.1 1.0 CG A:ASP362 2.6 22.5 1.0 CE1 A:HIS213 2.9 19.0 1.0 CD2 A:HIS208 3.1 17.8 1.0 CD2 A:HIS213 3.2 20.1 1.0 CE1 A:HIS208 3.2 19.0 1.0 ND2 A:ASN201 3.8 19.8 1.0 O A:HOH1370 4.0 29.8 1.0 ND1 A:HIS213 4.1 17.0 1.0 CB A:ASP362 4.1 21.0 1.0 O A:HOH1155 4.2 33.6 1.0 CG A:HIS213 4.2 18.1 1.0 CG A:HIS208 4.2 17.8 1.0 OD1 A:ASN201 4.2 22.7 1.0 ND1 A:HIS208 4.3 19.0 1.0 C7 A:16N1006 4.3 25.8 1.0 CG2 A:THR212 4.3 16.5 1.0 CG A:ASN201 4.4 19.5 1.0 C8 A:16N1006 4.5 24.2 1.0 CA A:ASP362 4.9 21.1 1.0 CB A:THR212 5.0 16.4 1.0

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