Iron in PDB 4hkv: Naphthalene 1,2-Dioxygenase Bound to Benzamide

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

The structure of Naphthalene 1,2-Dioxygenase Bound to Benzamide, PDB code: 4hkv 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)	47.89 / 1.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	140.102, 140.102, 208.495, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 20.2

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

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


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 Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:15.5 occ:1.00 FE1 A:FES1004 0.0 15.5 1.0 S1 A:FES1004 2.2 16.9 1.0 ND1 A:HIS83 2.2 14.0 1.0 S2 A:FES1004 2.2 14.3 1.0 ND1 A:HIS104 2.2 18.1 1.0 FE2 A:FES1004 2.7 14.8 1.0 CG A:HIS83 3.1 17.1 1.0 CE1 A:HIS104 3.2 16.4 1.0 CG A:HIS104 3.2 16.5 1.0 CE1 A:HIS83 3.2 19.8 1.0 CB A:HIS83 3.3 15.1 1.0 CB A:HIS104 3.5 15.2 1.0 N A:HIS104 3.7 16.1 1.0 CB A:TYR103 4.0 14.3 1.0 N A:ARG84 4.0 13.9 1.0 CA A:HIS104 4.2 15.6 1.0 NE2 A:HIS104 4.3 17.3 1.0 CD2 A:HIS83 4.3 17.0 1.0 CG A:ARG84 4.3 25.7 1.0 CD2 A:HIS104 4.3 15.7 1.0 NE2 A:HIS83 4.3 15.1 1.0 CG A:TYR103 4.3 14.2 1.0 SG A:CYS81 4.4 14.6 1.0 CB A:ARG84 4.5 17.7 1.0 CD2 A:TYR103 4.5 15.8 1.0 SG A:CYS101 4.5 14.9 1.0 CA A:HIS83 4.6 15.7 1.0 C A:TYR103 4.6 15.5 1.0 C A:HIS83 4.8 17.8 1.0 CA A:ARG84 4.8 16.0 1.0 CA A:TYR103 4.9 14.1 1.0 C A:HIS104 4.9 17.2 1.0

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


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 Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:14.8 occ:1.00 FE2 A:FES1004 0.0 14.8 1.0 S2 A:FES1004 2.2 14.3 1.0 S1 A:FES1004 2.2 16.9 1.0 SG A:CYS101 2.4 14.9 1.0 SG A:CYS81 2.4 14.6 1.0 FE1 A:FES1004 2.7 15.5 1.0 CB A:CYS101 3.1 14.9 1.0 CB A:CYS81 3.2 13.6 1.0 CB A:HIS83 4.0 15.1 1.0 CB A:TYR103 4.2 14.3 1.0 N A:HIS104 4.5 16.1 1.0 ND1 A:HIS83 4.5 14.0 1.0 CB A:LYS86 4.6 16.0 1.0 CA A:CYS101 4.6 15.1 1.0 ND1 A:HIS104 4.6 18.1 1.0 N A:ARG84 4.6 13.9 1.0 CA A:CYS81 4.6 12.7 1.0 CG A:HIS83 4.8 17.1 1.0 CB A:TRP106 4.9 15.9 1.0 N A:TYR103 4.9 15.6 1.0 N A:HIS83 4.9 15.6 1.0 CA A:HIS83 5.0 15.7 1.0

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


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 Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:18.8 occ:1.00 NE2 A:HIS213 2.0 16.5 1.0 O A:HOH1493 2.0 26.8 1.0 NE2 A:HIS208 2.2 18.2 1.0 OD1 A:ASP362 2.3 24.1 1.0 OD2 A:ASP362 2.5 28.1 1.0 CG A:ASP362 2.7 23.1 1.0 CE1 A:HIS213 2.9 17.7 1.0 CD2 A:HIS208 3.1 15.7 1.0 CD2 A:HIS213 3.1 18.0 1.0 CE1 A:HIS208 3.2 17.1 1.0 OD1 A:ASN201 3.8 25.4 1.0 O08 A:UNU1006 4.0 33.2 1.0 ND1 A:HIS213 4.1 16.1 1.0 CG A:HIS213 4.2 15.8 1.0 O A:HOH1173 4.2 29.7 1.0 CB A:ASP362 4.2 19.4 1.0 CG A:HIS208 4.3 18.2 1.0 ND2 A:ASN201 4.3 21.5 1.0 ND1 A:HIS208 4.3 16.8 1.0 O A:HOH1492 4.4 28.7 1.0 CG A:ASN201 4.4 22.8 1.0 CG2 A:THR212 4.5 16.9 1.0 C07 A:UNU1006 4.6 29.4 1.0 O A:HOH1745 4.7 36.4 1.0

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