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 25PD(Allyl)/Apo-Fr (pdb 3af7)






The binding sites of Palladium atom in the structure of Crystal Structure of 25PD(Allyl)/Apo-Fr (pdb code 3af7). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 3af7 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)25.2-1.6
Space groupF432
a (A)181.520
b (A)181.520
c (A)181.520
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)19.2
Rfree (%)21.2


Palladium Binding Sites:

Palladium binding site 1 out of 5 in 3af7


Palladium binding site 1 out of 5 in 3af7
Click to enlarge
stereopicture of Palladium binding site 1 out of 5 in 3af7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 3af7. 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: Phe37, X: Asp38, X: Glu45, X: Cys48, X: His49, X: Pd178, X: Pll179, X: Hoh326, X: Hoh333, X: Hoh352,

conact list:


AtomAtomDistance (A)
PdO X:Phe374.73
PdN X:Asp384.85
PdCB X:Asp383.96
PdOD2 X:Asp384.99
PdOD1 X:Asp383.00
PdCG X:Asp383.85
PdCA X:Asp384.07
PdO X:Glu454.63
PdN X:Glu454.48
PdCB X:Glu453.82
PdCD X:Glu454.75
PdC X:Glu454.70
PdCG X:Glu453.69
PdCA X:Glu453.70
PdCB X:Cys483.80
PdSG X:Cys483.76
PdND1 X:His494.85
PdCE1 X:His494.55
PdPD X:Pd1784.89
PdC20 X:Pll1794.19
PdPD X:Pll1792.37
PdC19 X:Pll1794.65
PdC21 X:Pll1794.24
PdO X:Hoh3264.34
PdO X:Hoh3332.23
PdO X:Hoh3524.06

interactive model:


Palladium binding site 2 out of 5 in 3af7


Palladium binding site 2 out of 5 in 3af7
Click to enlarge
stereopicture of Palladium binding site 2 out of 5 in 3af7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 3af7. 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: Pd177, X: Pll179, X: Hoh352,

conact list:


AtomAtomDistance (A)
PdO X:Glu454.66
PdO X:Cys484.03
PdCB X:Cys484.11
PdSG X:Cys483.18
PdC X:Cys483.80
PdCA X:Cys484.62
PdNE2 X:His493.58
PdN X:His493.49
PdCB X:His493.77
PdCB X:His493.72
PdND1 X:His491.90
PdND1 X:His494.08
PdCD2 X:His493.89
PdC X:His494.71
PdCE1 X:His492.44
PdCG X:His493.05
PdCG X:His494.38
PdCA X:His493.38
PdCA X:His493.37
PdCB X:Arg524.46
PdCD X:Arg523.70
PdCG X:Arg524.27
PdNE X:Arg524.74
PdNH1 X:Arg524.47
PdPD X:Pd1774.89
PdC20 X:Pll1794.93
PdPD X:Pll1793.23
PdC19 X:Pll1792.95
PdC21 X:Pll1793.97
PdO X:Hoh3524.14

interactive model:


Palladium binding site 3 out of 5 in 3af7


Palladium binding site 3 out of 5 in 3af7
Click to enlarge
stereopicture of Palladium binding site 3 out of 5 in 3af7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Palladium in the PDB 3af7. 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: Pd177, X: Pd178, X: Pll179, X: Hoh333, X: Hoh352,

conact list:


AtomAtomDistance (A)
PdCB X:Asp383.79
PdOD2 X:Asp384.51
PdOD1 X:Asp383.34
PdCG X:Asp383.69
PdCA X:Asp384.66
PdCG X:Glu454.96
PdCB X:Cys483.57
PdSG X:Cys482.45
PdCA X:Cys484.91
PdND1 X:His494.07
PdCE1 X:His493.92
PdCD X:Arg524.85
PdPD X:Pd1772.37
PdPD X:Pd1783.23
PdC20 X:Pll1792.55
PdPD X:Pll1790.00
PdC19 X:Pll1792.37
PdC21 X:Pll1792.29
PdO X:Hoh3334.35
PdO X:Hoh3523.84

interactive model:


Palladium binding site 4 out of 5 in 3af7


Palladium binding site 4 out of 5 in 3af7
Click to enlarge
stereopicture of Palladium binding site 4 out of 5 in 3af7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Palladium in the PDB 3af7. 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: Pll180, X: Pll181, X: Hoh304,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1142.20
PdND1 X:His1144.30
PdCD2 X:His1143.16
PdCE1 X:His1143.20
PdCG X:His1144.32
PdO X:Cys1263.24
PdCB X:Cys1263.38
PdCB X:Cys1263.26
PdSG X:Cys1262.27
PdSG X:Cys1264.21
PdC X:Cys1263.55
PdCA X:Cys1263.71
PdCA X:Cys1263.73
PdN X:Asp1274.41
PdC20 X:Pll1802.29
PdPD X:Pll1800.00
PdC19 X:Pll1802.43
PdC21 X:Pll1802.29
PdPD X:Pll1813.77
PdC19 X:Pll1814.96
PdC21 X:Pll1814.89
PdO X:Hoh3043.80

interactive model:


Palladium binding site 5 out of 5 in 3af7


Palladium binding site 5 out of 5 in 3af7
Click to enlarge
stereopicture of Palladium binding site 5 out of 5 in 3af7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Palladium in the PDB 3af7. 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: Cys126, X: Pll180, X: Pll181, X: Hoh304,

conact list:


AtomAtomDistance (A)
PdNE2 X:His1144.34
PdCE1 X:His1144.30
PdOG X:Ser1184.83
PdCB X:Cys1263.41
PdCB X:Cys1263.46
PdSG X:Cys1262.40
PdSG X:Cys1263.68
PdCA X:Cys1264.87
PdCA X:Cys1264.93
PdPD X:Pll1803.77
PdC19 X:Pll1804.95
PdC20 X:Pll1812.31
PdPD X:Pll1810.00
PdC19 X:Pll1812.29
PdC21 X:Pll1812.28
PdO X:Hoh3042.27

interactive model:




© Copyright 2008-2012 by atomistry.com