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 Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid (pdb 3esc)






The binding sites of Palladium atom in the structure of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid (pdb code 3esc). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 3esc structure was solved by L.RUTTEN, J.P.B.A.MANNIE, M.LUTZ, P.GROS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)44.0-1.2
Space groupP63
a (A)83.949
b (A)83.949
c (A)55.771
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)16.6
Rfree (%)19.4


Palladium Binding Sites:

Palladium binding site 1 out of 2 in 3esc


Palladium binding site 1 out of 2 in 3esc
Click to enlarge
stereopicture of Palladium binding site 1 out of 2 in 3esc
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 3esc. 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: A: Leu81, A: Sxc215,

conact list:


AtomAtomDistance (A)
PdCB A:Leu814.54
PdCD2 A:Leu814.29
PdCG A:Leu813.99
PdS1 A:Sxc2152.30
PdS1 A:Sxc2153.04
PdC9 A:Sxc2153.28
PdC9 A:Sxc2153.28
PdC12 A:Sxc2153.17
PdC12 A:Sxc2152.60
PdPD1 A:Sxc2150.00
PdPD1 A:Sxc2151.53
PdC1 A:Sxc2152.02
PdC1 A:Sxc2152.05
PdBR1 A:Sxc2152.44
PdBR1 A:Sxc2153.37
PdS2 A:Sxc2152.26
PdS2 A:Sxc2152.42
PdC2 A:Sxc2152.99
PdC2 A:Sxc2153.10
PdC6 A:Sxc2153.04
PdC6 A:Sxc2152.91
PdC5 A:Sxc2154.37
PdC5 A:Sxc2154.17
PdC7 A:Sxc2153.17
PdC7 A:Sxc2153.43
PdC4 A:Sxc2154.85
PdC4 A:Sxc2154.74
PdC10 A:Sxc2153.26
PdC10 A:Sxc2152.97
PdC3 A:Sxc2154.31
PdC3 A:Sxc2154.36

interactive model:


Palladium binding site 2 out of 2 in 3esc


Palladium binding site 2 out of 2 in 3esc
Click to enlarge
stereopicture of Palladium binding site 2 out of 2 in 3esc
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 3esc. 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: A: Sxc215, A: Hoh565,

conact list:


AtomAtomDistance (A)
PdS1 A:Sxc2152.90
PdS1 A:Sxc2152.33
PdC9 A:Sxc2153.32
PdC9 A:Sxc2153.24
PdC12 A:Sxc2153.99
PdC12 A:Sxc2153.27
PdPD1 A:Sxc2151.53
PdPD1 A:Sxc2150.00
PdC1 A:Sxc2152.12
PdC1 A:Sxc2151.96
PdBR1 A:Sxc2153.25
PdBR1 A:Sxc2152.43
PdS2 A:Sxc2152.48
PdS2 A:Sxc2152.26
PdC2 A:Sxc2152.95
PdC2 A:Sxc2152.98
PdC6 A:Sxc2153.00
PdC6 A:Sxc2152.97
PdC5 A:Sxc2154.24
PdC5 A:Sxc2154.23
PdC7 A:Sxc2153.18
PdC7 A:Sxc2153.19
PdC4 A:Sxc2154.68
PdC4 A:Sxc2154.78
PdC10 A:Sxc2153.22
PdC10 A:Sxc2153.20
PdC3 A:Sxc2154.16
PdC3 A:Sxc2154.32
PdO A:Hoh5654.85

interactive model:




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