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(Allyl)/Apo-C48AFR (pdb 3af9)






The binding sites of Palladium atom in the structure of Crystal Structure of Pd(Allyl)/Apo-C48AFR (pdb code 3af9). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 3af9 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)25.6-1.9
Space groupF432
a (A)182.433
b (A)182.433
c (A)182.433
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)17.7
Rfree (%)20.3


Palladium Binding Sites:

Palladium binding site 1 out of 2 in 3af9


Palladium binding site 1 out of 2 in 3af9
Click to enlarge
stereopicture of Palladium binding site 1 out of 2 in 3af9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 3af9. 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: His114, X: Cys126, X: Asp127, X: Glu130, X: Pll179, X: Pd180, X: Hoh293,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1142.14
PdND1 X:His1144.15
PdCD2 X:His1143.21
PdCE1 X:His1142.99
PdCG X:His1144.29
PdO X:Cys1263.31
PdCB X:Cys1263.29
PdSG X:Cys1262.45
PdC X:Cys1263.40
PdCA X:Cys1263.89
PdN X:Asp1273.86
PdCA X:Asp1274.28
PdCB X:Glu1304.56
PdC20 X:Pll1792.37
PdPD X:Pll1790.00
PdC19 X:Pll1792.25
PdC21 X:Pll1792.31
PdPD X:Pd1803.56
PdO X:Hoh2933.00

interactive model:


Palladium binding site 2 out of 2 in 3af9


Palladium binding site 2 out of 2 in 3af9
Click to enlarge
stereopicture of Palladium binding site 2 out of 2 in 3af9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 3af9. 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: His114, X: Ser118, X: Pro123, X: Cys126, X: Pll179, X: Hoh293,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1144.21
PdND1 X:His1144.91
PdCE1 X:His1143.94
PdCB X:Ser1184.94
PdCA X:Ser1184.99
PdCA X:Pro1234.73
PdCB X:Cys1263.28
PdSG X:Cys1262.39
PdCA X:Cys1264.74
PdPD X:Pll1793.56
PdC19 X:Pll1794.68
PdO X:Hoh2933.11

interactive model:




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