Iron in PDB 2hmm: Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene

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

The structure of Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene, PDB code: 2hmm 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)	15.97 / 1.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	139.725, 139.725, 208.113, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 19.8

The binding sites of Iron atom in the Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene (pdb code 2hmm). 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 Anthracene, PDB code: 2hmm:
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 Anthracene


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 Anthracene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe450 b:24.3 occ:1.00 O A:HOH1055 1.9 32.6 1.0 NE2 A:HIS213 2.0 21.0 1.0 NE2 A:HIS208 2.1 20.5 1.0 OD1 A:ASP362 2.2 23.6 1.0 OD2 A:ASP362 2.4 26.2 1.0 CG A:ASP362 2.6 21.6 1.0 CE1 A:HIS213 3.0 19.2 1.0 CD2 A:HIS208 3.0 20.9 1.0 CD2 A:HIS213 3.1 21.2 1.0 CE1 A:HIS208 3.2 21.4 1.0 ND2 A:ASN201 3.7 20.9 1.0 ND1 A:HIS213 4.1 19.1 1.0 CB A:ASP362 4.1 20.2 1.0 C2 A:AN3801 4.1 50.4 0.7 CG A:HIS213 4.2 19.1 1.0 CG A:HIS208 4.2 20.5 1.0 O A:HOH1004 4.2 28.6 1.0 ND1 A:HIS208 4.3 21.7 1.0 C4 A:AN3801 4.3 49.9 0.7 OD1 A:ASN201 4.3 23.3 1.0 O A:HOH995 4.4 28.2 1.0 CG2 A:THR212 4.4 19.2 1.0 CG A:ASN201 4.4 18.6 1.0 C1 A:AN3801 5.0 51.3 0.7 CA A:ASP362 5.0 19.9 1.0

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


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 Anthracene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe829 b:17.2 occ:1.00 FE1 A:FES829 0.0 17.2 1.0 ND1 A:HIS104 2.1 15.5 1.0 S1 A:FES829 2.2 18.2 1.0 ND1 A:HIS83 2.2 18.0 1.0 S2 A:FES829 2.2 16.3 1.0 FE2 A:FES829 2.7 15.9 1.0 CG A:HIS104 3.1 15.6 1.0 CE1 A:HIS104 3.1 15.9 1.0 CG A:HIS83 3.1 17.8 1.0 CE1 A:HIS83 3.2 17.4 1.0 CB A:HIS83 3.3 17.5 1.0 CB A:HIS104 3.4 16.8 1.0 N A:HIS104 3.7 17.8 1.0 N A:ARG84 4.0 17.5 1.0 CB A:TYR103 4.1 17.4 1.0 CA A:HIS104 4.1 17.4 1.0 NE2 A:HIS104 4.2 16.7 1.0 CD2 A:HIS104 4.2 16.0 1.0 CD2 A:HIS83 4.3 18.7 1.0 NE2 A:HIS83 4.3 16.1 1.0 CG A:ARG84 4.3 20.7 1.0 SG A:CYS81 4.3 15.4 1.0 CG A:TYR103 4.4 16.0 1.0 SG A:CYS101 4.5 17.2 1.0 CA A:HIS83 4.6 17.6 1.0 CB A:ARG84 4.6 18.3 1.0 CD2 A:TYR103 4.6 16.4 1.0 C A:TYR103 4.6 17.8 1.0 C A:HIS83 4.8 17.6 1.0 CA A:ARG84 4.9 17.6 1.0 C A:HIS104 4.9 18.2 1.0 CA A:TYR103 4.9 17.1 1.0 CD1 A:TRP106 5.0 18.9 1.0

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


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 Anthracene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe829 b:15.9 occ:1.00 FE2 A:FES829 0.0 15.9 1.0 S1 A:FES829 2.2 18.2 1.0 S2 A:FES829 2.2 16.3 1.0 SG A:CYS81 2.3 15.4 1.0 SG A:CYS101 2.3 17.2 1.0 FE1 A:FES829 2.7 17.2 1.0 CB A:CYS101 3.1 17.1 1.0 CB A:CYS81 3.1 15.8 1.0 CB A:HIS83 4.1 17.5 1.0 CB A:TYR103 4.2 17.4 1.0 N A:HIS104 4.5 17.8 1.0 ND1 A:HIS83 4.5 18.0 1.0 ND1 A:HIS104 4.5 15.5 1.0 CB A:LYS86 4.5 18.6 1.0 CA A:CYS101 4.6 17.4 1.0 CA A:CYS81 4.6 15.9 1.0 N A:ARG84 4.7 17.5 1.0 CG A:HIS83 4.8 17.8 1.0 CB A:TRP106 4.8 18.1 1.0 N A:TYR103 4.9 16.7 1.0 N A:HIS83 4.9 18.2 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