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-H114AFR (pdb 2zg9)






The binding sites of Palladium atom in the structure of Crystal Structure of Pd(Allyl)/Apo-H114AFR (pdb code 2zg9). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 2zg9 structure was solved by S.ABE, J.NIEMEYER, M.ABE, T.UENO, T.HIKAGE, G.ERKER, Y.WATANABE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)25.1-1.8
Space groupF432
a (A)181.176
b (A)181.176
c (A)181.176
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)17.7
Rfree (%)21.1


Palladium Binding Sites:

Palladium binding site 1 out of 3 in 2zg9


Palladium binding site 1 out of 3 in 2zg9
Click to enlarge
stereopicture of Palladium binding site 1 out of 3 in 2zg9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 2zg9. 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: Cys126, X: Pll180, X: Hoh291,

conact list:


AtomAtomDistance (A)
PdCB X:Cys1263.29
PdSG X:Cys1262.35
PdCA X:Cys1264.75
PdC20 X:Pll1802.30
PdPD X:Pll1800.00
PdC19 X:Pll1802.31
PdC21 X:Pll1802.29
PdO X:Hoh2914.30

interactive model:


Palladium binding site 2 out of 3 in 2zg9


Palladium binding site 2 out of 3 in 2zg9
Click to enlarge
stereopicture of Palladium binding site 2 out of 3 in 2zg9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 2zg9. 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: Pll181, X: Pll182, X: Hoh323, X: Hoh335, X: Hoh359,

conact list:


AtomAtomDistance (A)
PdCB X:Asp383.82
PdOD2 X:Asp384.55
PdOD1 X:Asp383.53
PdCG X:Asp383.78
PdCA X:Asp384.83
PdOE1 X:Glu452.28
PdOE2 X:Glu453.51
PdCD X:Glu453.25
PdCG X:Glu454.65
PdCB X:Cys483.39
PdSG X:Cys482.28
PdCA X:Cys484.80
PdND1 X:His494.04
PdCE1 X:His493.88
PdC20 X:Pll1812.27
PdPD X:Pll1810.00
PdC19 X:Pll1812.29
PdC21 X:Pll1812.29
PdC20 X:Pll1824.08
PdPD X:Pll1823.13
PdC19 X:Pll1824.99
PdC21 X:Pll1824.44
PdO X:Hoh3234.24
PdO X:Hoh3354.88
PdO X:Hoh3594.64

interactive model:


Palladium binding site 3 out of 3 in 2zg9


Palladium binding site 3 out of 3 in 2zg9
Click to enlarge
stereopicture of Palladium binding site 3 out of 3 in 2zg9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Palladium in the PDB 2zg9. 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: Pll181, X: Pll182, X: Hoh316, X: Hoh323,

conact list:


AtomAtomDistance (A)
PdO X:Glu454.56
PdOE1 X:Glu454.23
PdO X:Cys483.93
PdCB X:Cys483.79
PdSG X:Cys482.56
PdC X:Cys483.66
PdCA X:Cys484.38
PdNE2 X:His494.15
PdN X:His493.45
PdCB X:His493.68
PdND1 X:His492.12
PdCD2 X:His494.29
PdC X:His494.74
PdCE1 X:His492.97
PdCG X:His493.23
PdCA X:His493.37
PdCB X:Arg524.59
PdC20 X:Pll1813.82
PdPD X:Pll1813.13
PdC19 X:Pll1814.62
PdC21 X:Pll1814.56
PdC20 X:Pll1822.27
PdPD X:Pll1820.00
PdC19 X:Pll1822.28
PdC21 X:Pll1822.28
PdO X:Hoh3164.70
PdO X:Hoh3234.46

interactive model:




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