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-Fr (pdb 2zg7)






The binding sites of Palladium atom in the structure of Crystal Structure of Pd(Allyl)/Apo-Fr (pdb code 2zg7). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 2zg7 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)22.0-1.7
Space groupF432
a (A)181.450
b (A)181.450
c (A)181.450
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)17.6
Rfree (%)20.2


Palladium Binding Sites:

Palladium binding site 1 out of 4 in 2zg7


Palladium binding site 1 out of 4 in 2zg7
Click to enlarge
stereopicture of Palladium binding site 1 out of 4 in 2zg7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 2zg7. 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: Pll180, X: Pll181, X: Hoh404,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1142.14
PdND1 X:His1144.16
PdCD2 X:His1143.21
PdCE1 X:His1143.00
PdCG X:His1144.29
PdO X:Cys1263.23
PdCB X:Cys1263.31
PdSG X:Cys1262.47
PdC X:Cys1263.35
PdCA X:Cys1263.87
PdN X:Asp1273.84
PdCA X:Asp1274.28
PdOE1 X:Glu1304.99
PdCB X:Glu1304.54
PdC20 X:Pll1802.28
PdPD X:Pll1800.00
PdC19 X:Pll1802.25
PdC21 X:Pll1802.26
PdPD X:Pll1813.68
PdO X:Hoh4044.19

interactive model:


Palladium binding site 2 out of 4 in 2zg7


Palladium binding site 2 out of 4 in 2zg7
Click to enlarge
stereopicture of Palladium binding site 2 out of 4 in 2zg7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 2zg7. 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: Pro123, X: Cys126, X: Pll180, X: Pll181, X: Hoh404,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1144.30
PdCE1 X:His1144.06
PdCA X:Pro1234.66
PdCB X:Cys1263.29
PdSG X:Cys1262.38
PdCA X:Cys1264.75
PdPD X:Pll1803.68
PdC19 X:Pll1804.88
PdC20 X:Pll1812.32
PdPD X:Pll1810.00
PdC19 X:Pll1812.33
PdC21 X:Pll1812.32
PdO X:Hoh4042.34

interactive model:


Palladium binding site 3 out of 4 in 2zg7


Palladium binding site 3 out of 4 in 2zg7
Click to enlarge
stereopicture of Palladium binding site 3 out of 4 in 2zg7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Palladium in the PDB 2zg7. 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: Pll182, X: Pll183, X: Hoh266, X: Hoh396,

conact list:


AtomAtomDistance (A)
PdCB X:Asp383.85
PdOD2 X:Asp384.57
PdOD1 X:Asp383.63
PdCG X:Asp383.82
PdCA X:Asp384.82
PdOE1 X:Glu453.71
PdOE2 X:Glu452.30
PdCD X:Glu453.36
PdCG X:Glu454.70
PdCB X:Cys483.39
PdSG X:Cys482.31
PdCA X:Cys484.80
PdND1 X:His494.11
PdCE1 X:His493.99
PdC20 X:Pll1822.28
PdPD X:Pll1820.00
PdC19 X:Pll1822.30
PdC21 X:Pll1822.27
PdC20 X:Pll1834.02
PdPD X:Pll1833.12
PdC19 X:Pll1834.93
PdC21 X:Pll1834.81
PdO X:Hoh2663.66
PdO X:Hoh3964.11

interactive model:


Palladium binding site 4 out of 4 in 2zg7


Palladium binding site 4 out of 4 in 2zg7
Click to enlarge
stereopicture of Palladium binding site 4 out of 4 in 2zg7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Palladium in the PDB 2zg7. 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: Pll182, X: Pll183, X: Hoh261, X: Hoh266, X: Hoh396,

conact list:


AtomAtomDistance (A)
PdO X:Glu454.60
PdOE2 X:Glu454.34
PdO X:Cys483.97
PdCB X:Cys483.77
PdSG X:Cys482.57
PdC X:Cys483.67
PdCA X:Cys484.38
PdNE2 X:His494.19
PdN X:His493.41
PdCB X:His493.69
PdND1 X:His492.17
PdCD2 X:His494.32
PdC X:His494.73
PdCE1 X:His493.01
PdCG X:His493.26
PdCA X:His493.36
PdCB X:Arg524.55
PdCB X:Arg524.51
PdCG X:Arg524.33
PdCG X:Arg524.97
PdC20 X:Pll1824.35
PdPD X:Pll1823.12
PdC19 X:Pll1824.75
PdC21 X:Pll1824.37
PdC20 X:Pll1832.26
PdPD X:Pll1830.00
PdC19 X:Pll1832.32
PdC21 X:Pll1832.29
PdO X:Hoh2614.74
PdO X:Hoh2664.07
PdO X:Hoh3964.65

interactive model:




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