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

Protein crystallography data

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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene, PDB code: 2bmq:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2bmq

Go back to Nickel Binding Sites List in 2bmq
Nickel binding site 1 out of 2 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene


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 in Complex with Nitrobenzene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1195

b:17.8
occ:0.90
OE1 B:GLU160 2.0 13.8 1.0
O B:HOH2256 2.0 29.6 1.0
NE2 B:HIS14 2.0 17.1 1.0
OE2 B:GLU18 2.1 23.6 1.0
O B:HOH2061 2.1 29.0 1.0
O B:HOH2060 2.3 30.5 1.0
CE1 B:HIS14 2.9 20.2 1.0
CD B:GLU18 2.9 23.1 1.0
CD B:GLU160 3.0 13.8 1.0
CD2 B:HIS14 3.1 17.1 1.0
OE1 B:GLU18 3.2 25.9 1.0
O B:HOH2043 3.3 26.8 1.0
OE2 B:GLU160 3.4 14.7 1.0
ND1 B:HIS14 4.1 19.8 1.0
O B:HOH2254 4.1 24.9 1.0
CG B:HIS14 4.2 15.2 1.0
O B:HOH2049 4.2 22.3 1.0
CG B:GLU160 4.3 11.8 1.0
CG B:GLU18 4.3 18.0 1.0
O B:HOH2020 4.3 40.6 1.0
OD2 B:ASP15 4.7 15.8 1.0
CB B:GLU160 4.8 9.5 1.0
O B:HOH2232 4.9 33.2 1.0
CB B:GLU18 4.9 16.0 1.0
NH1 B:ARG138 5.0 13.3 0.5

Nickel binding site 2 out of 2 in 2bmq

Go back to Nickel Binding Sites List in 2bmq
Nickel binding site 2 out of 2 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with Nitrobenzene


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 in Complex with Nitrobenzene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1196

b:17.1
occ:0.75
NE2 B:HIS56 2.1 20.9 1.0
CE1 B:HIS56 3.0 21.1 1.0
CD2 B:HIS56 3.1 20.6 1.0
OE1 B:GLU55 3.9 18.4 0.5
ND1 B:HIS56 4.1 21.8 1.0
CD B:GLU55 4.2 16.0 0.5
CG B:HIS56 4.2 16.8 1.0
O B:HOH2132 4.4 41.2 1.0
OE2 B:GLU55 4.5 19.9 0.5
CG B:GLU55 4.8 17.4 1.0
CB B:GLU55 5.0 14.2 1.0

Reference:

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
Page generated: Fri Sep 25 08:06:54 2020
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