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Nickel in the structure of 3.0 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex With Nad (pdb 4egb)

The binding sites of Nickel atom in the structure of 3.0 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex With Nad (pdb code 4egb). This binding sites where shown with 5.0 Angstroms radius around Nickel atom.
The 4egb structure was solved by A.S.HALAVATY, M.KUHN, L.SHUVALOVA, G.MINASOV, W.F.ANDERSON, CENTER FORSTRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)30.0-3.0
Space groupI4
a (A)165.586
b (A)165.586
c (A)292.305
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)16.8
Rfree (%)22.8

Nickel Binding Sites:

Nickel binding site 1 out of 4 in 4egb


Nickel binding site 1 out of 4 in 4egb
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stereopicture of Nickel binding site 1 out of 4 in 4egb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 4egb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: His68, B: Glu72, G: His68, G: Val69, G: Glu72,

conact list:


AtomAtomDistance (A)
NiNE2 B:His681.97
NiND1 B:His684.11
NiCD2 B:His682.70
NiCE1 B:His683.14
NiCG B:His683.94
NiOE1 B:Glu722.50
NiCB B:Glu724.63
NiOE2 B:Glu722.68
NiCD B:Glu722.80
NiCG B:Glu724.16
NiNE2 G:His682.63
NiND1 G:His684.60
NiCD2 G:His682.86
NiCE1 G:His683.86
NiCG G:His684.14
NiCG2 G:Val694.65
NiCA G:Val694.91
NiOE1 G:Glu721.85
NiCB G:Glu724.58
NiOE2 G:Glu723.43
NiCD G:Glu722.94
NiCG G:Glu724.22

interactive model:


Nickel binding site 2 out of 4 in 4egb


Nickel binding site 2 out of 4 in 4egb
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stereopicture of Nickel binding site 2 out of 4 in 4egb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 4egb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: His68, C: Glu72, E: His68, E: Val69, E: Glu72,

conact list:


AtomAtomDistance (A)
NiNE2 C:His682.53
NiND1 C:His684.55
NiCD2 C:His682.77
NiCE1 C:His683.80
NiCG C:His684.09
NiOE1 C:Glu723.02
NiCB C:Glu724.36
NiOE2 C:Glu721.75
NiCD C:Glu722.60
NiCG C:Glu723.86
NiNE2 E:His682.52
NiND1 E:His684.54
NiCD2 E:His682.74
NiCE1 E:His683.80
NiCG E:His684.07
NiCG2 E:Val694.97
NiOE1 E:Glu721.80
NiCB E:Glu724.19
NiOE2 E:Glu722.71
NiCD E:Glu722.41
NiCG E:Glu723.69

interactive model:


Nickel binding site 3 out of 4 in 4egb


Nickel binding site 3 out of 4 in 4egb
Click to enlarge
stereopicture of Nickel binding site 3 out of 4 in 4egb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Nickel in the PDB 4egb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: His68, D: Glu72, F: His68, F: Glu72,

conact list:


AtomAtomDistance (A)
NiO D:His684.95
NiNE2 D:His682.34
NiND1 D:His684.35
NiCD2 D:His682.90
NiCE1 D:His683.46
NiCG D:His684.11
NiOE1 D:Glu721.94
NiCB D:Glu724.62
NiOE2 D:Glu723.31
NiCD D:Glu722.94
NiCG D:Glu724.28
NiNE2 F:His682.26
NiND1 F:His684.37
NiCD2 F:His682.89
NiCE1 F:His683.43
NiCG F:His684.15
NiOE1 F:Glu722.31
NiCB F:Glu724.52
NiOE2 F:Glu722.55
NiCD F:Glu722.65
NiCG F:Glu724.04

interactive model:


Nickel binding site 4 out of 4 in 4egb


Nickel binding site 4 out of 4 in 4egb
Click to enlarge
stereopicture of Nickel binding site 4 out of 4 in 4egb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Nickel in the PDB 4egb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His68, A: Val69, A: Glu72, H: His68, H: Glu72,

conact list:


AtomAtomDistance (A)
NiO A:His684.79
NiNE2 A:His682.49
NiND1 A:His684.44
NiCD2 A:His682.62
NiC A:His684.97
NiCE1 A:His683.75
NiCG A:His683.92
NiCG2 A:Val694.74
NiCA A:Val694.86
NiOE1 A:Glu721.79
NiCB A:Glu724.43
NiOE2 A:Glu723.47
NiCD A:Glu722.93
NiCG A:Glu724.18
NiNE2 H:His682.27
NiND1 H:His684.41
NiCD2 H:His682.98
NiCE1 H:His683.43
NiCG H:His684.23
NiOE1 H:Glu722.72
NiCB H:Glu724.91
NiOE2 H:Glu722.24
NiCD H:Glu722.78
NiCG H:Glu724.23

interactive model:




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