Nickel in PDB 2bmo: The Crystal Structure of Nitrobenzene Dioxygenase

The structure of The Crystal Structure of Nitrobenzene Dioxygenase, PDB code: 2bmo 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)	52.00 / 1.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	121.586, 121.586, 84.356, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.2

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

Iron

(Fe)

3 atoms

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

Nickel binding site 1 out of 2 in the The Crystal Structure of Nitrobenzene Dioxygenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Nitrobenzene Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1195 b:16.7 occ:0.75 OE2 B:GLU18 1.9 24.8 0.8 OE1 B:GLU160 2.0 13.7 1.0 O B:HOH2056 2.0 24.0 1.0 O B:HOH2269 2.0 36.4 1.0 NE2 B:HIS14 2.0 17.1 1.0 O B:HOH2055 2.2 32.5 1.0 CD B:GLU18 2.5 21.5 0.8 OE1 B:GLU18 2.6 24.9 0.8 CE1 B:HIS14 3.0 16.4 1.0 CD B:GLU160 3.0 12.6 1.0 CD2 B:HIS14 3.1 14.3 1.0 OE2 B:GLU160 3.4 14.2 1.0 CG B:GLU18 3.9 17.9 0.8 O B:HOH2023 4.0 39.8 1.0 O B:HOH2268 4.0 27.0 1.0 ND1 B:HIS14 4.1 16.7 1.0 CG B:HIS14 4.2 13.6 1.0 O B:HOH2045 4.2 22.1 1.0 CG B:GLU160 4.3 10.9 1.0 O B:HOH2020 4.3 33.6 1.0 CG B:GLU18 4.3 14.8 0.2 CD B:GLU18 4.5 15.6 0.2 O B:HOH2022 4.6 45.1 1.0 CB B:GLU160 4.7 9.5 1.0 CB B:GLU18 4.8 14.4 0.2 OD2 B:ASP15 4.8 14.8 1.0 OE2 B:GLU18 4.8 16.4 0.2 OE1 B:GLU18 4.9 16.1 0.2 CB B:GLU18 4.9 16.0 0.8

Nickel binding site 2 out of 2 in the The Crystal Structure of Nitrobenzene Dioxygenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Nitrobenzene Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1196 b:10.2 occ:0.50 O B:HOH2140 2.1 18.1 1.0 NE2 B:HIS56 2.1 14.6 1.0 CE1 B:HIS56 3.1 15.9 1.0 CD2 B:HIS56 3.1 13.2 1.0 OE1 B:GLU55 4.0 15.2 0.5 CD B:GLU55 4.1 15.1 0.5 OE2 B:GLU55 4.2 17.4 0.5 ND1 B:HIS56 4.2 16.0 1.0 CG B:HIS56 4.3 13.0 1.0 CG B:GLU55 4.8 15.5 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