Iron in PDB 2bmq: The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene

The structure of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene, PDB code: 2bmq was solved by R.Friemann, M.M.Ivkovic-Jensen, D.J.Lessner, C.Yu, D.T.Gibson, R.E.Parales, H.Eklund, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.00 / 1.55
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	121.533, 121.533, 84.179, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19.2

The structure of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

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

Iron binding site 1 out of 3 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1440 b:14.3 occ:1.00 FE1 A:FES1440 0.0 14.3 1.0 S2 A:FES1440 2.2 15.6 1.0 S1 A:FES1440 2.2 14.7 1.0 SG A:CYS99 2.3 14.4 1.0 SG A:CYS79 2.4 13.6 1.0 FE2 A:FES1440 2.7 14.5 1.0 CB A:CYS99 3.1 13.9 1.0 CB A:CYS79 3.2 13.4 1.0 CB A:HIS81 4.1 15.3 1.0 CB A:TYR101 4.2 14.2 1.0 ND1 A:HIS81 4.4 13.3 1.0 ND1 A:HIS102 4.5 15.1 1.0 CA A:CYS99 4.6 13.9 1.0 N A:HIS102 4.6 14.6 1.0 CA A:CYS79 4.6 13.3 1.0 CB A:LYS84 4.7 15.2 1.0 N A:ARG82 4.7 14.8 1.0 CG A:HIS81 4.8 14.9 1.0 CB A:TRP104 4.8 14.0 1.0 N A:TYR101 4.9 14.2 1.0 N A:HIS81 4.9 15.4 1.0 C A:CYS99 5.0 14.3 1.0

Iron binding site 2 out of 3 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1440 b:14.5 occ:1.00 FE2 A:FES1440 0.0 14.5 1.0 ND1 A:HIS102 2.1 15.1 1.0 ND1 A:HIS81 2.2 13.3 1.0 S2 A:FES1440 2.2 15.6 1.0 S1 A:FES1440 2.2 14.7 1.0 FE1 A:FES1440 2.7 14.3 1.0 CE1 A:HIS102 3.0 15.6 1.0 CG A:HIS102 3.1 14.6 1.0 CG A:HIS81 3.1 14.9 1.0 CE1 A:HIS81 3.2 14.4 1.0 CB A:HIS81 3.4 15.3 1.0 CB A:HIS102 3.4 14.1 1.0 N A:HIS102 3.8 14.6 1.0 CB A:TYR101 4.0 14.2 1.0 NE2 A:HIS102 4.1 15.1 1.0 CD2 A:HIS102 4.2 15.1 1.0 N A:ARG82 4.2 14.8 1.0 CA A:HIS102 4.2 14.8 1.0 NE2 A:HIS81 4.3 14.7 1.0 CD2 A:HIS81 4.3 15.5 1.0 CG A:ARG82 4.3 16.9 1.0 CG A:TYR101 4.3 15.5 1.0 SG A:CYS79 4.4 13.6 1.0 CD1 A:TYR101 4.4 13.5 1.0 SG A:CYS99 4.6 14.4 1.0 CB A:ARG82 4.6 15.4 1.0 CA A:HIS81 4.6 15.0 1.0 C A:TYR101 4.7 14.9 1.0 C A:HIS81 4.8 15.6 1.0 CA A:TYR101 4.9 14.6 1.0

Iron binding site 3 out of 3 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1441 b:17.3 occ:1.00 NE2 A:HIS211 2.1 13.9 1.0 NE2 A:HIS206 2.1 17.3 1.0 O A:HOH2227 2.2 26.1 1.0 OD2 A:ASP360 2.2 20.4 1.0 O A:HOH2401 2.4 28.4 1.0 OD1 A:ASP360 2.4 23.9 1.0 CG A:ASP360 2.6 19.3 1.0 CE1 A:HIS211 3.1 15.0 1.0 CD2 A:HIS206 3.1 17.4 1.0 CD2 A:HIS211 3.1 15.7 1.0 CE1 A:HIS206 3.2 15.3 1.0 O A:HOH2334 3.8 39.1 1.0 CB A:ASP360 4.1 17.6 1.0 ND1 A:HIS211 4.2 14.0 1.0 OD1 A:ASN199 4.2 20.0 1.0 CG A:HIS211 4.3 13.3 1.0 CG A:HIS206 4.3 14.9 1.0 ND1 A:HIS206 4.3 15.9 1.0 O A:HOH2339 4.3 28.2 1.0 C5 A:NBZ1442 4.4 28.8 1.0 ND2 A:ASN199 4.6 18.1 1.0 CG2 A:THR210 4.7 14.4 1.0 O1 A:NBZ1442 4.7 32.6 1.0 CG A:ASN199 4.9 17.1 1.0 C6 A:NBZ1442 4.9 30.0 1.0 C4 A:NBZ1442 4.9 28.6 1.0

R.Friemann, M.M.Ivkovic-Jensen, D.J.Lessner, C.L.Yu, D.T.Gibson, R.E.Parales, H.Eklund, S.Ramaswamy. Structural Insight Into the Dioxygenation of Nitroarene Compounds: the Crystal Structure of Nitrobenzene Dioxygenase. J. Mol. Biol. V. 348 1139 2005.
ISSN: ISSN 0022-2836
PubMed: 15854650
DOI: 10.1016/J.JMB.2005.03.052