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

Protein crystallography data

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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with 3- Nitrotoluene, PDB code: 2bmr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2bmr

Go back to Nickel Binding Sites List in 2bmr
Nickel binding site 1 out of 2 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with 3- Nitrotoluene


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 3- Nitrotoluene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1195

b:14.6
occ:0.75
OE2 B:GLU18 1.7 24.2 1.0
O B:HOH2259 2.0 29.8 1.0
OE1 B:GLU160 2.0 13.4 1.0
NE2 B:HIS14 2.1 15.8 1.0
O B:HOH2047 2.1 27.0 1.0
O B:HOH2048 2.3 27.1 1.0
CD B:GLU18 2.6 21.6 1.0
CD B:GLU160 3.0 13.4 1.0
CE1 B:HIS14 3.0 18.1 1.0
OE1 B:GLU18 3.0 25.5 1.0
CD2 B:HIS14 3.1 15.6 1.0
OE2 B:GLU160 3.3 14.7 1.0
CG B:GLU18 4.0 19.9 1.0
O B:HOH2260 4.1 24.8 1.0
ND1 B:HIS14 4.1 17.3 1.0
CG B:HIS14 4.2 13.8 1.0
O B:HOH2038 4.2 21.4 1.0
CG B:GLU160 4.3 10.3 1.0
OD2 B:ASP15 4.8 15.0 1.0
CB B:GLU160 4.8 8.9 1.0

Nickel binding site 2 out of 2 in 2bmr

Go back to Nickel Binding Sites List in 2bmr
Nickel binding site 2 out of 2 in the The Crystal Structure of Nitrobenzene Dioxygenase in Complex with 3- Nitrotoluene


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 3- Nitrotoluene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1196

b:9.8
occ:0.50
O2 B:EDO1198 2.0 15.8 1.0
O1 B:EDO1198 2.1 23.7 1.0
O B:HOH2013 2.1 23.9 1.0
O B:HOH2002 2.2 21.7 1.0
C2 B:EDO1198 2.8 20.0 1.0
C1 B:EDO1198 2.9 22.3 1.0
O B:MET2 3.9 19.9 0.5
O B:MET2 3.9 20.1 0.5
OE2 B:GLU7 4.1 21.3 1.0
O B:HOH2016 4.3 13.3 1.0
O B:HOH2299 4.3 24.7 1.0
O B:HOH2298 4.4 35.0 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 08:06:57 2020
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