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Nickel in PDB 3bem: Crystal Structure of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis at 1.65 A Resolution

Protein crystallography data

The structure of Crystal Structure of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis at 1.65 A Resolution, PDB code: 3bem was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.58 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.620, 69.200, 61.850, 90.00, 100.54, 90.00
R / Rfree (%) 15.1 / 17.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis at 1.65 A Resolution (pdb code 3bem). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis at 1.65 A Resolution, PDB code: 3bem:

Nickel binding site 1 out of 1 in 3bem

Go back to Nickel Binding Sites List in 3bem
Nickel binding site 1 out of 1 in the Crystal Structure of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni400

b:54.7
occ:1.00
NE2 A:HIS6 2.1 24.5 1.0
O B:HOH450 2.2 43.0 1.0
OE1 A:GLU10 2.4 21.3 0.5
OE2 A:GLU10 2.5 18.0 0.5
CD A:GLU10 2.6 18.8 0.5
NE2 B:HIS0 2.6 34.2 1.0
CD2 B:HIS0 3.0 40.8 1.0
CD2 A:HIS6 3.0 22.7 1.0
CE1 A:HIS6 3.1 24.7 1.0
CE1 B:HIS0 3.8 36.2 1.0
CG A:GLU10 3.9 29.0 0.5
CG A:HIS6 4.2 21.9 1.0
ND1 A:HIS6 4.2 24.8 1.0
CG B:HIS0 4.2 25.8 1.0
CG A:GLU10 4.4 23.4 0.5
ND1 B:HIS0 4.6 24.2 1.0
CB A:GLU10 4.8 21.0 0.5
CB A:GLU10 4.8 15.8 0.5

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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