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 Apo-Fr With High Content of Pd Ions (pdb 2z5r)






The binding sites of Palladium atom in the structure of Apo-Fr With High Content of Pd Ions (pdb code 2z5r). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 2z5r structure was solved by T.UENO, K.HIRATA, M.ABE, M.SUZUKI, S.ABE, N.SHIMIZU, M.YAMAMOTO, M.TAKATA, Y.WATANABE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)45.4-2.5
Space groupF432
a (A)181.594
b (A)181.594
c (A)181.594
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)21.9
Rfree (%)28.7


Palladium Binding Sites:

Palladium binding site 1 out of 10 in 2z5r


Palladium binding site 1 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 1 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 2z5r. 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: Ser2, A: Gln3, A: Ile4, A: Arg5, A: Gly73,

conact list:


AtomAtomDistance (A)
PdO A:Ser24.41
PdN A:Ser22.96
PdCB A:Ser24.27
PdOG A:Ser23.78
PdC A:Ser23.37
PdCA A:Ser23.55
PdN A:Gln32.71
PdCB A:Gln33.51
PdC A:Gln34.12
PdCA A:Gln33.51
PdN A:Ile43.69
PdCG1 A:Ile44.52
PdCA A:Ile44.89
PdN A:Arg54.64
PdCB A:Arg54.98
PdO A:Gly734.60
PdCA A:Gly734.82

interactive model:


Palladium binding site 2 out of 10 in 2z5r


Palladium binding site 2 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 2 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 2z5r. 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: Glu45, A: Gly46, A: Cys48, A: His49, A: Phe50, A: His173, A: Pd206, A: Pd207, A: Hoh1040,

conact list:


AtomAtomDistance (A)
PdO A:Glu453.62
PdOE1 A:Glu453.87
PdOE2 A:Glu452.74
PdCD A:Glu453.59
PdC A:Glu454.43
PdCG A:Glu454.90
PdO A:Gly464.10
PdN A:Gly464.76
PdC A:Gly464.48
PdCA A:Gly464.30
PdC A:Cys484.79
PdO A:His494.49
PdN A:His493.48
PdC A:His493.82
PdCB A:His491.82
PdCA A:His493.10
PdN A:Phe504.18
PdCB A:His1734.07
PdPD A:Pd2064.29
PdPD A:Pd2073.29
PdO A:Hoh10402.48

interactive model:


Palladium binding site 3 out of 10 in 2z5r


Palladium binding site 3 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 3 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Palladium in the PDB 2z5r. 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: Met68, A: Gln71, A: Arg72, A: His124, A: Phe128,

conact list:


AtomAtomDistance (A)
PdCB A:Met684.78
PdCG A:Met683.71
PdSD A:Met684.79
PdOE1 A:Gln714.69
PdCD A:Arg724.48
PdCG A:Arg724.76
PdO A:His1244.93
PdNE2 A:His1241.98
PdND1 A:His1243.94
PdCD2 A:His1243.09
PdCE1 A:His1242.78
PdCG A:His1244.11
PdCB A:Phe1284.22
PdCD1 A:Phe1284.32
PdCG A:Phe1284.29

interactive model:


Palladium binding site 4 out of 10 in 2z5r


Palladium binding site 4 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 4 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Palladium in the PDB 2z5r. 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: Gly34, A: Asp38, A: Glu45, A: Cys48, A: Pd206,

conact list:


AtomAtomDistance (A)
PdO A:Gly344.60
PdCB A:Asp383.79
PdOD2 A:Asp384.11
PdOD1 A:Asp383.84
PdCG A:Asp383.72
PdCA A:Asp384.78
PdOE2 A:Glu454.77
PdCG A:Glu454.57
PdO A:Cys484.93
PdCB A:Cys483.20
PdSG A:Cys481.87
PdC A:Cys484.67
PdCA A:Cys484.50
PdPD A:Pd2062.48

interactive model:


Palladium binding site 5 out of 10 in 2z5r


Palladium binding site 5 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 5 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Palladium in the PDB 2z5r. 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: His114, A: Cys126, A: Asp127, A: Glu130, A: Pd208,

conact list:


AtomAtomDistance (A)
PdNE2 A:His1141.83
PdND1 A:His1143.95
PdCD2 A:His1142.59
PdCE1 A:His1142.99
PdCG A:His1143.81
PdO A:Cys1263.42
PdC A:Cys1263.50
PdCB A:Cys1263.39
PdCA A:Cys1263.80
PdN A:Asp1273.92
PdCB A:Glu1304.84
PdPD A:Pd2083.60

interactive model:


Palladium binding site 6 out of 10 in 2z5r


Palladium binding site 6 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 6 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Palladium in the PDB 2z5r. 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: Glu45, A: Cys48, A: His49, A: Pd202, A: Pd204, A: Pd207,

conact list:


AtomAtomDistance (A)
PdO A:Glu453.77
PdOE1 A:Glu454.95
PdOE2 A:Glu452.83
PdCD A:Glu453.73
PdC A:Glu454.79
PdCG A:Glu453.83
PdO A:Cys483.79
PdN A:Cys484.85
PdCB A:Cys483.22
PdSG A:Cys482.40
PdC A:Cys483.33
PdCA A:Cys483.85
PdN A:His493.18
PdCB A:His493.52
PdCA A:His493.52
PdPD A:Pd2024.29
PdPD A:Pd2042.48
PdPD A:Pd2073.60

interactive model:


Palladium binding site 7 out of 10 in 2z5r


Palladium binding site 7 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 7 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Palladium in the PDB 2z5r. 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: Glu45, A: His49, A: Pd202, A: Pd206, A: Hoh1040,

conact list:


AtomAtomDistance (A)
PdOE1 A:Glu454.11
PdOE2 A:Glu452.60
PdCD A:Glu453.62
PdCG A:Glu454.80
PdCB A:His493.22
PdCA A:His494.44
PdPD A:Pd2023.29
PdPD A:Pd2063.60
PdO A:Hoh10404.54

interactive model:


Palladium binding site 8 out of 10 in 2z5r


Palladium binding site 8 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 8 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Palladium in the PDB 2z5r. 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: Cys126, A: Pd205,

conact list:


AtomAtomDistance (A)
PdCB A:Cys1264.64
PdPD A:Pd2053.60

interactive model:


Palladium binding site 9 out of 10 in 2z5r


Palladium binding site 9 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 9 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Palladium in the PDB 2z5r. 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:

conact list:


AtomAtomDistance (A)

interactive model:


Palladium binding site 10 out of 10 in 2z5r


Palladium binding site 10 out of 10 in 2z5r
Click to enlarge
stereopicture of Palladium binding site 10 out of 10 in 2z5r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Palladium in the PDB 2z5r. 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: Glu57, A: Arg64, A: His132, A: Glu136, A: Hoh1033,

conact list:


AtomAtomDistance (A)
PdCG A:Glu574.95
PdCD A:Arg644.72
PdCZ A:Arg642.51
PdNE A:Arg643.83
PdNH2 A:Arg642.48
PdNH1 A:Arg641.87
PdO A:His1324.01
PdOE1 A:Glu1362.17
PdCB A:Glu1364.38
PdOE2 A:Glu1361.58
PdCD A:Glu1362.10
PdCG A:Glu1363.65
PdO A:Hoh10333.39

interactive model:




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