Iron in PDB 2bmr: The Crystal Structure of Nitrobenzene Dioxygenase in Complex with 3- Nitrotoluene

The structure of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with 3- Nitrotoluene, PDB code: 2bmr 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)	52.55 / 1.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	121.625, 121.625, 84.002, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.1

The structure of The Crystal Structure of Nitrobenzene Dioxygenase in Complex with 3- Nitrotoluene 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 3- Nitrotoluene (pdb code 2bmr). 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 3- Nitrotoluene, PDB code: 2bmr:
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 3- Nitrotoluene


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 3- Nitrotoluene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1440 b:12.2 occ:1.00 FE1 A:FES1440 0.0 12.2 1.0 S1 A:FES1440 2.2 12.8 1.0 S2 A:FES1440 2.2 14.0 1.0 SG A:CYS99 2.3 12.7 1.0 SG A:CYS79 2.4 11.9 1.0 FE2 A:FES1440 2.7 13.0 1.0 CB A:CYS99 3.1 12.8 1.0 CB A:CYS79 3.2 12.7 1.0 CB A:HIS81 4.1 13.2 1.0 CB A:TYR101 4.2 12.2 1.0 ND1 A:HIS81 4.5 11.9 1.0 ND1 A:HIS102 4.5 11.8 1.0 CA A:CYS99 4.5 12.5 1.0 N A:HIS102 4.6 12.4 1.0 CB A:LYS84 4.6 14.4 1.0 CA A:CYS79 4.6 11.8 1.0 N A:ARG82 4.7 13.4 1.0 CG A:HIS81 4.8 12.9 1.0 CB A:TRP104 4.8 12.7 1.0 N A:TYR101 4.9 12.7 1.0 N A:HIS81 4.9 13.3 1.0 C A:CYS99 4.9 12.7 1.0 CA A:TYR101 5.0 12.2 1.0

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


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 3- Nitrotoluene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1440 b:13.0 occ:1.00 FE2 A:FES1440 0.0 13.0 1.0 ND1 A:HIS102 2.1 11.8 1.0 ND1 A:HIS81 2.2 11.9 1.0 S2 A:FES1440 2.2 14.0 1.0 S1 A:FES1440 2.2 12.8 1.0 FE1 A:FES1440 2.7 12.2 1.0 CE1 A:HIS102 3.0 14.1 1.0 CG A:HIS81 3.1 12.9 1.0 CG A:HIS102 3.1 13.0 1.0 CE1 A:HIS81 3.2 13.4 1.0 CB A:HIS81 3.3 13.2 1.0 CB A:HIS102 3.5 12.7 1.0 N A:HIS102 3.8 12.4 1.0 CB A:TYR101 4.0 12.2 1.0 NE2 A:HIS102 4.2 12.5 1.0 N A:ARG82 4.2 13.4 1.0 CD2 A:HIS102 4.2 13.9 1.0 CD2 A:HIS81 4.3 14.1 1.0 CA A:HIS102 4.3 12.4 1.0 NE2 A:HIS81 4.3 13.8 1.0 CG A:ARG82 4.3 15.1 1.0 CG A:TYR101 4.3 12.6 1.0 SG A:CYS79 4.4 11.9 1.0 CD1 A:TYR101 4.5 11.0 1.0 SG A:CYS99 4.6 12.7 1.0 CA A:HIS81 4.6 13.1 1.0 CB A:ARG82 4.6 13.8 1.0 C A:TYR101 4.7 12.8 1.0 C A:HIS81 4.8 13.2 1.0 CA A:TYR101 4.9 12.2 1.0

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


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 3- Nitrotoluene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1441 b:18.5 occ:1.00 O A:HOH2230 2.1 21.4 1.0 NE2 A:HIS211 2.1 13.8 1.0 NE2 A:HIS206 2.1 15.1 1.0 OD2 A:ASP360 2.3 22.6 1.0 O A:HOH2422 2.3 25.4 1.0 OD1 A:ASP360 2.4 23.4 1.0 CG A:ASP360 2.7 19.9 1.0 CE1 A:HIS211 3.0 14.5 1.0 CD2 A:HIS206 3.1 15.0 1.0 CE1 A:HIS206 3.1 14.4 1.0 CD2 A:HIS211 3.1 14.5 1.0 CB A:ASP360 4.1 17.9 1.0 ND1 A:HIS211 4.2 13.4 1.0 ND1 A:HIS206 4.2 14.7 1.0 CG A:HIS206 4.2 13.2 1.0 CG A:HIS211 4.2 13.3 1.0 OD1 A:ASN199 4.2 19.2 1.0 O A:HOH2352 4.3 24.2 1.0 C4 A:3NT1442 4.4 29.6 1.0 O2N A:3NT1442 4.5 32.9 1.0 ND2 A:ASN199 4.7 15.9 1.0 CG2 A:THR210 4.7 13.6 1.0 C3 A:3NT1442 4.8 30.1 1.0 C5 A:3NT1442 4.9 28.7 1.0 CG A:ASN199 4.9 15.0 1.0 N3 A:3NT1442 4.9 31.2 1.0 O A:TRP356 5.0 14.5 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