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-H49AFR (pdb 2zg8)






The binding sites of Palladium atom in the structure of Crystal Structure of Pd(Allyl)/Apo-H49AFR (pdb code 2zg8). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 2zg8 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)25.1-1.6
Space groupF432
a (A)181.339
b (A)181.339
c (A)181.339
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18.8
Rfree (%)21.1


Palladium Binding Sites:

Palladium binding site 1 out of 4 in 2zg8


Palladium binding site 1 out of 4 in 2zg8
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stereopicture of Palladium binding site 1 out of 4 in 2zg8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 2zg8. 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: Pll182, X: Hoh302,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1144.28
PdCE1 X:His1144.07
PdOG X:Ser1184.27
PdCA X:Pro1234.67
PdCB X:Cys1263.30
PdSG X:Cys1262.31
PdCA X:Cys1264.75
PdPD X:Pll1823.63
PdC19 X:Pll1824.85
PdO X:Hoh3022.37

interactive model:


Palladium binding site 2 out of 4 in 2zg8


Palladium binding site 2 out of 4 in 2zg8
Click to enlarge
stereopicture of Palladium binding site 2 out of 4 in 2zg8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 2zg8. 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: Pll181, X: Pll183, X: Hoh249, X: Hoh345, X: Hoh382,

conact list:


AtomAtomDistance (A)
PdCB X:Asp383.85
PdOD2 X:Asp384.52
PdOD1 X:Asp383.68
PdCG X:Asp383.82
PdCA X:Asp384.86
PdOE1 X:Glu453.10
PdOE2 X:Glu452.29
PdCD X:Glu453.03
PdCG X:Glu454.51
PdCB X:Cys483.44
PdSG X:Cys482.36
PdCA X:Cys484.82
PdC20 X:Pll1812.32
PdPD X:Pll1810.00
PdC19 X:Pll1812.29
PdC21 X:Pll1812.29
PdC20 X:Pll1834.18
PdPD X:Pll1832.81
PdC19 X:Pll1834.88
PdC21 X:Pll1834.48
PdO X:Hoh2493.86
PdO X:Hoh3454.76
PdO X:Hoh3824.21

interactive model:


Palladium binding site 3 out of 4 in 2zg8


Palladium binding site 3 out of 4 in 2zg8
Click to enlarge
stereopicture of Palladium binding site 3 out of 4 in 2zg8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Palladium in the PDB 2zg8. 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: Pd175, X: Pll182, X: Hoh302,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1142.13
PdND1 X:His1144.17
PdCD2 X:His1143.20
PdCE1 X:His1143.01
PdCG X:His1144.29
PdO X:Cys1263.18
PdCB X:Cys1263.39
PdSG X:Cys1262.45
PdC X:Cys1263.38
PdCA X:Cys1263.92
PdN X:Asp1273.92
PdCA X:Asp1274.33
PdCB X:Glu1304.65
PdPD X:Pd1753.63
PdC20 X:Pll1822.27
PdPD X:Pll1820.00
PdC19 X:Pll1822.27
PdC21 X:Pll1822.24
PdO X:Hoh3024.13

interactive model:


Palladium binding site 4 out of 4 in 2zg8


Palladium binding site 4 out of 4 in 2zg8
Click to enlarge
stereopicture of Palladium binding site 4 out of 4 in 2zg8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Palladium in the PDB 2zg8. 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: Ala49, X: Arg52, X: Pll181, X: Pll183, X: Hoh237, X: Hoh352, X: Hoh382,

conact list:


AtomAtomDistance (A)
PdO X:Glu454.43
PdOE1 X:Glu452.32
PdOE2 X:Glu453.57
PdCD X:Glu453.29
PdCG X:Glu454.65
PdO X:Cys484.18
PdCB X:Cys483.76
PdSG X:Cys482.73
PdC X:Cys483.80
PdCA X:Cys484.44
PdN X:Ala493.53
PdC X:Ala495.00
PdCB X:Ala493.87
PdCA X:Ala493.59
PdCB X:Arg524.85
PdCB X:Arg524.87
PdCD X:Arg524.89
PdCG X:Arg524.58
PdNH2 X:Arg524.96
PdC20 X:Pll1814.23
PdPD X:Pll1812.81
PdC19 X:Pll1814.53
PdC21 X:Pll1814.26
PdC20 X:Pll1832.25
PdPD X:Pll1830.00
PdC19 X:Pll1832.29
PdC21 X:Pll1832.25
PdO X:Hoh2374.24
PdO X:Hoh3524.85
PdO X:Hoh3824.69

interactive model:




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