Chemical elements
  Palladium
    Isotopes
    Energy
    Production
    Application
    Physical Properties
    Chemical Properties
    Catalytic Activity
    Types
    PDB 1ks4-3np2
      1ks4
      2z5p
      2z5q
      2z5r
      2zg7
      2zg8
      2zg9
      3af7
      3af8
      3af9
      3bz4
      3c6s
      3esc
      3esd
      3fi6
      3noz
      3np0
      3np2

Palladium in the structure of Crystal Structure of Pd(Ally)/Apo-C126AFR (pdb 3af8)






The binding sites of Palladium atom in the structure of Crystal Structure of Pd(Ally)/Apo-C126AFR (pdb code 3af8). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 3af8 structure was solved by S.ABE, T.HIKAGE, Y.WATANABE, S.KITAGAWA, T.UENO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)27.8-1.7
Space groupF432
a (A)181.984
b (A)181.984
c (A)181.984
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18.1
Rfree (%)19.5


Palladium Binding Sites:

Palladium binding site 1 out of 2 in 3af8


Palladium binding site 1 out of 2 in 3af8
Click to enlarge
stereopicture of Palladium binding site 1 out of 2 in 3af8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 3af8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: X: Asp38, X: Glu45, X: Cys48, X: His49, X: Arg52, X: Pll179, X: Pll180,

conact list:


AtomAtomDistance (A)
PdCB X:Asp383.82
PdOD2 X:Asp384.57
PdOD1 X:Asp383.51
PdCG X:Asp383.78
PdCA X:Asp384.78
PdOE1 X:Glu452.22
PdOE2 X:Glu453.45
PdCD X:Glu453.17
PdCG X:Glu454.54
PdCB X:Cys483.55
PdSG X:Cys482.39
PdCA X:Cys484.92
PdND1 X:His494.09
PdCE1 X:His493.93
PdCZ X:Arg523.99
PdNE X:Arg523.94
PdNH1 X:Arg523.24
PdC20 X:Pll1792.29
PdPD X:Pll1790.00
PdC19 X:Pll1792.31
PdC21 X:Pll1792.29
PdC20 X:Pll1804.01
PdPD X:Pll1803.18
PdC21 X:Pll1804.87

interactive model:


Palladium binding site 2 out of 2 in 3af8


Palladium binding site 2 out of 2 in 3af8
Click to enlarge
stereopicture of Palladium binding site 2 out of 2 in 3af8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 3af8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: X: Glu45, X: Cys48, X: His49, X: Arg52, X: Pll179, X: Pll180, X: Hoh344,

conact list:


AtomAtomDistance (A)
PdO X:Glu454.65
PdOE1 X:Glu454.10
PdO X:Cys484.04
PdCB X:Cys483.99
PdSG X:Cys482.91
PdC X:Cys483.77
PdCA X:Cys484.54
PdNE2 X:His493.99
PdN X:His493.48
PdCB X:His493.79
PdND1 X:His492.10
PdCD2 X:His494.20
PdC X:His494.75
PdCE1 X:His492.82
PdCG X:His493.23
PdCA X:His493.39
PdCB X:Arg524.49
PdCB X:Arg524.54
PdCD X:Arg523.97
PdCZ X:Arg524.41
PdCG X:Arg524.14
PdCG X:Arg524.34
PdNE X:Arg523.54
PdNH1 X:Arg524.64
PdNH1 X:Arg524.80
PdC20 X:Pll1793.93
PdPD X:Pll1793.18
PdC19 X:Pll1794.37
PdC21 X:Pll1794.51
PdC20 X:Pll1802.32
PdPD X:Pll1800.00
PdC19 X:Pll1802.31
PdC21 X:Pll1802.30
PdO X:Hoh3444.60

interactive model:




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