Iron in PDB 2hml: Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene.

All present enzymatic activity of Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene.:
1.14.12.12;

The structure of Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene., PDB code: 2hml 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)	17.97 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.865, 139.865, 208.431, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 19

The binding sites of Iron atom in the Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene. (pdb code 2hml). 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 the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene., PDB code: 2hml:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant 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 the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe450 b:25.6 occ:1.00 O A:HOH753 1.7 23.5 0.5 NE2 A:HIS213 2.1 16.9 1.0 OD1 A:ASP362 2.1 20.8 1.0 NE2 A:HIS208 2.3 18.9 1.0 OD2 A:ASP362 2.4 22.4 1.0 CG A:ASP362 2.6 18.9 1.0 CE1 A:HIS213 2.9 15.8 1.0 CD2 A:HIS208 3.1 19.1 1.0 CD2 A:HIS213 3.2 16.8 1.0 CE1 A:HIS208 3.3 18.0 1.0 C14 A:PEY701 3.4 17.3 0.7 C13 A:PEY701 3.7 17.0 0.7 OD1 A:ASN201 3.8 25.0 1.0 C8 A:PEY701 3.9 16.5 0.7 O A:HOH734 4.0 13.5 0.3 ND1 A:HIS213 4.1 15.1 1.0 CB A:ASP362 4.1 17.9 1.0 CG A:HIS213 4.2 16.2 1.0 CG A:HIS208 4.3 18.5 1.0 O A:HOH908 4.3 29.1 1.0 C12 A:PEY701 4.4 17.0 0.7 C9 A:PEY701 4.4 16.6 0.7 ND2 A:ASN201 4.4 19.2 1.0 ND1 A:HIS208 4.4 18.5 1.0 CG2 A:THR212 4.4 16.4 1.0 CG A:ASN201 4.5 17.8 1.0 C7 A:PEY701 4.6 16.6 0.7 C11 A:PEY701 4.7 17.2 0.7 CA A:ASP362 4.9 17.6 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant 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 the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe714 b:15.1 occ:1.00 FE1 A:FES714 0.0 15.1 1.0 ND1 A:HIS104 2.1 14.6 1.0 ND1 A:HIS83 2.1 15.9 1.0 S1 A:FES714 2.2 17.1 1.0 S2 A:FES714 2.2 14.3 1.0 FE2 A:FES714 2.7 14.0 1.0 CE1 A:HIS104 3.1 14.2 1.0 CG A:HIS104 3.1 13.9 1.0 CG A:HIS83 3.1 16.2 1.0 CE1 A:HIS83 3.1 17.4 1.0 CB A:HIS83 3.4 16.4 1.0 CB A:HIS104 3.4 15.2 1.0 N A:HIS104 3.8 15.2 1.0 N A:ARG84 4.1 16.6 1.0 CB A:TYR103 4.1 14.6 1.0 CA A:HIS104 4.2 15.6 1.0 NE2 A:HIS104 4.2 13.6 1.0 CD2 A:HIS104 4.2 13.7 1.0 NE2 A:HIS83 4.2 15.3 1.0 CD2 A:HIS83 4.3 16.1 1.0 CG A:ARG84 4.3 18.2 1.0 SG A:CYS81 4.4 14.7 1.0 CG A:TYR103 4.4 14.0 1.0 CD2 A:TYR103 4.5 14.8 1.0 SG A:CYS101 4.6 14.9 1.0 CB A:ARG84 4.6 16.9 1.0 CA A:HIS83 4.6 16.7 1.0 C A:TYR103 4.7 15.2 1.0 C A:HIS83 4.8 16.7 1.0 CA A:ARG84 4.9 16.4 1.0 CA A:TYR103 5.0 14.9 1.0 C A:HIS104 5.0 16.5 1.0 CD1 A:TRP106 5.0 16.9 1.0

Iron binding site 3 out of 3 in the Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant 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 the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe714 b:14.0 occ:1.00 FE2 A:FES714 0.0 14.0 1.0 S2 A:FES714 2.2 14.3 1.0 S1 A:FES714 2.2 17.1 1.0 SG A:CYS81 2.3 14.7 1.0 SG A:CYS101 2.3 14.9 1.0 FE1 A:FES714 2.7 15.1 1.0 CB A:CYS101 3.1 15.5 1.0 CB A:CYS81 3.1 15.1 1.0 CB A:HIS83 4.1 16.4 1.0 CB A:TYR103 4.2 14.6 1.0 ND1 A:HIS83 4.5 15.9 1.0 CB A:LYS86 4.5 16.1 1.0 N A:HIS104 4.5 15.2 1.0 ND1 A:HIS104 4.5 14.6 1.0 CA A:CYS101 4.6 15.3 1.0 CA A:CYS81 4.6 14.8 1.0 N A:ARG84 4.7 16.6 1.0 CG A:HIS83 4.8 16.2 1.0 CB A:TRP106 4.8 16.6 1.0 N A:TYR103 4.9 14.8 1.0 N A:HIS83 5.0 16.9 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