Iron in PDB 2hmk: Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene

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

The structure of Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene, PDB code: 2hmk was solved by D.J.Ferraro, A.L.Okerlund, J.C.Mowers, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.51 / 1.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.947, 139.947, 208.464, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 18.3

The binding sites of Iron atom in the Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene (pdb code 2hmk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene, PDB code: 2hmk:
Jump to Iron binding site number: 1; 2; 3;

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe451 b:23.2 occ:1.00 O A:HOH923 2.0 10.4 1.0 NE2 A:HIS213 2.0 19.1 1.0 NE2 A:HIS208 2.1 17.9 1.0 OD2 A:ASP362 2.2 21.2 1.0 OD1 A:ASP362 2.6 25.7 1.0 CG A:ASP362 2.7 20.8 1.0 CE1 A:HIS213 2.9 19.0 1.0 CD2 A:HIS208 3.0 18.0 1.0 CD2 A:HIS213 3.1 19.3 1.0 CE1 A:HIS208 3.2 19.0 1.0 OD1 A:ASN201 3.8 24.3 1.0 ND1 A:HIS213 4.0 18.4 1.0 O A:HOH900 4.1 9.9 1.0 CB A:ASP362 4.2 20.4 1.0 C2 A:PEY701 4.2 37.6 1.0 CG A:HIS213 4.2 18.9 1.0 CG A:HIS208 4.2 18.3 1.0 ND1 A:HIS208 4.3 18.7 1.0 ND2 A:ASN201 4.3 19.5 1.0 O A:HOH893 4.3 9.7 1.0 CG2 A:THR212 4.4 19.2 1.0 CG A:ASN201 4.4 18.5 1.0 C3 A:PEY701 4.6 38.9 1.0 C1 A:PEY701 4.7 36.6 1.0 CA A:ASP362 5.0 19.6 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe454 b:17.4 occ:1.00 FE1 A:FES454 0.0 17.4 1.0 ND1 A:HIS104 2.1 18.8 1.0 ND1 A:HIS83 2.1 17.0 1.0 S1 A:FES454 2.2 18.9 1.0 S2 A:FES454 2.2 17.0 1.0 FE2 A:FES454 2.7 16.9 1.0 CE1 A:HIS104 3.1 18.8 1.0 CG A:HIS104 3.1 16.6 1.0 CG A:HIS83 3.1 17.4 1.0 CE1 A:HIS83 3.2 18.7 1.0 CB A:HIS83 3.3 17.5 1.0 CB A:HIS104 3.4 17.5 1.0 N A:HIS104 3.7 17.3 1.0 CB A:TYR103 4.1 17.5 1.0 N A:ARG84 4.1 18.0 1.0 CA A:HIS104 4.1 17.8 1.0 NE2 A:HIS104 4.2 18.0 1.0 CD2 A:HIS104 4.2 18.0 1.0 CD2 A:HIS83 4.3 18.4 1.0 NE2 A:HIS83 4.3 17.9 1.0 CG A:ARG84 4.3 21.8 1.0 CG A:TYR103 4.4 17.5 1.0 SG A:CYS81 4.4 16.4 1.0 CB A:ARG84 4.5 19.0 1.0 CD1 A:TYR103 4.5 17.6 1.0 SG A:CYS101 4.6 17.3 1.0 CA A:HIS83 4.6 17.8 1.0 C A:TYR103 4.6 17.2 1.0 C A:HIS83 4.8 18.1 1.0 CA A:ARG84 4.8 18.2 1.0 C A:HIS104 4.9 18.8 1.0 CA A:TYR103 4.9 17.2 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe454 b:16.9 occ:1.00 FE2 A:FES454 0.0 16.9 1.0 S1 A:FES454 2.2 18.9 1.0 S2 A:FES454 2.2 17.0 1.0 SG A:CYS81 2.4 16.4 1.0 SG A:CYS101 2.4 17.3 1.0 FE1 A:FES454 2.7 17.4 1.0 CB A:CYS101 3.1 16.8 1.0 CB A:CYS81 3.1 16.4 1.0 CB A:HIS83 4.1 17.5 1.0 CB A:TYR103 4.2 17.5 1.0 ND1 A:HIS83 4.4 17.0 1.0 N A:HIS104 4.5 17.3 1.0 ND1 A:HIS104 4.5 18.8 1.0 CB A:LYS86 4.5 18.4 1.0 CA A:CYS101 4.5 17.6 1.0 CA A:CYS81 4.6 16.5 1.0 N A:ARG84 4.7 18.0 1.0 CG A:HIS83 4.8 17.4 1.0 CB A:TRP106 4.8 19.0 1.0 N A:HIS83 4.9 17.8 1.0 N A:TYR103 4.9 17.5 1.0

D.J.Ferraro, A.L.Okerlund, J.C.Mowers, S.Ramaswamy. Structural Basis For Regioselectivity and Stereoselectivity of Product Formation By Naphthalene 1,2-Dioxygenase. J.Bacteriol. V. 188 6986 2006.
ISSN: ISSN 0021-9193
PubMed: 16980501
DOI: 10.1128/JB.00707-06