Chemical elements
  Cadmium
    Isotopes
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    Physical Properties
    Chemical Properties
    PDB 1a4k-1exq
    PDB 1f48-1ihu
    PDB 1ii0-1mhu
    PDB 1mms-1qvg
    PDB 1qy0-1wb6
    PDB 1wje-2avp
    PDB 2b3p-2j6e
    PDB 2jdz-2x05
    PDB 2x09-3ccj
    PDB 3ccl-3ggf
    PDB 3h1u-3p5v
    PDB 3p5w-8ice
      3p5w
      3p5x
      3pk1
      3r52
      3r7c
      3sd6
      3stl
      3swb
      3tje
      3u90
      3uk8
      3vg3
      3vg4
      488d
      4aps
      4de6
      4dki
      4dzi
      4evc
      4evd
      4fdw
      4fmk
      4fvf
      4fvg
      4mt2
      7icf
      7icu
      8ice

Cadmium in the structure of Actinidin From Actinidia Arguta Planch (Sarusashi) (pdb 3p5x)






The binding sites of Cadmium atom in the structure of Actinidin From Actinidia Arguta Planch (Sarusashi) (pdb code 3p5x). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 3p5x structure was solved by Y.MANICKAM, N.NIRMAL, A.SUZUKI, Y.SUGIYAMA, T.YAMANE, V.DEVADASAN, A.SHARMA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)35.0-2.2
Space groupP212121
a (A)48.519
b (A)56.039
c (A)70.916
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)16.8
Rfree (%)22.2


Cadmium Binding Sites:

Cadmium binding site 1 out of 8 in 3p5x


Cadmium binding site 1 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 1 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Thr171, A: Gly174, A: Asp176, A: Asn199, A: Hoh261, A: Hoh286, A: Hoh287, A: Hoh302, A: Hoh335, A: Hoh346, A: Hoh348,

conact list:


AtomAtomDistance (A)
CdOG1 A:Thr1714.70
CdO A:Gly1744.90
CdCB A:Asp1764.33
CdOD2 A:Asp1762.69
CdOD1 A:Asp1762.29
CdCG A:Asp1762.83
CdND2 A:Asn1994.23
CdO A:Hoh2612.23
CdO A:Hoh2612.03
CdO A:Hoh2862.06
CdO A:Hoh2871.98
CdO A:Hoh3025.00
CdO A:Hoh3354.59
CdO A:Hoh3464.67
CdO A:Hoh3484.40

interactive model:


Cadmium binding site 2 out of 8 in 3p5x


Cadmium binding site 2 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 2 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gln19, A: Cso25, A: Asp161, A: His162, A: Trp184, A: Hoh290, A: Hoh354,

conact list:


AtomAtomDistance (A)
CdNE2 A:Gln194.04
CdOE1 A:Gln194.73
CdCD A:Gln194.78
CdCB A:Cso254.21
CdSG A:Cso253.47
CdOD A:Cso252.82
CdO A:Asp1614.16
CdNE2 A:His1624.42
CdCB A:His1623.72
CdND1 A:His1622.39
CdCD2 A:His1624.50
CdCE1 A:His1623.28
CdCG A:His1623.41
CdCA A:His1624.26
CdCZ2 A:Trp1844.82
CdNE1 A:Trp1844.70
CdO A:Hoh2902.21
CdO A:Hoh3544.19

interactive model:


Cadmium binding site 3 out of 8 in 3p5x


Cadmium binding site 3 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 3 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp101, A: Cd223, A: Hoh277,

conact list:


AtomAtomDistance (A)
CdCB A:Asp1014.46
CdOD2 A:Asp1013.95
CdOD1 A:Asp1012.83
CdCG A:Asp1013.51
CdCD A:Cd2230.00
CdCD A:Cd2232.16
CdO A:Hoh2774.67

interactive model:


Cadmium binding site 4 out of 8 in 3p5x


Cadmium binding site 4 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 4 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp101, A: Cd223, A: Hoh277,

conact list:


AtomAtomDistance (A)
CdCB A:Asp1014.40
CdOD2 A:Asp1012.85
CdOD1 A:Asp1012.46
CdCG A:Asp1012.96
CdCD A:Cd2232.16
CdCD A:Cd2230.00
CdO A:Hoh2774.21

interactive model:


Cadmium binding site 5 out of 8 in 3p5x


Cadmium binding site 5 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 5 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu191, A: Hoh285, A: Hoh288,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu1912.33
CdOE2 A:Glu1912.54
CdCD A:Glu1912.75
CdCG A:Glu1914.22
CdO A:Hoh2854.20
CdO A:Hoh2882.54

interactive model:


Cadmium binding site 6 out of 8 in 3p5x


Cadmium binding site 6 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 6 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp15, A: Hoh291, A: Hoh310, A: Hoh323, A: Hoh324,

conact list:


AtomAtomDistance (A)
CdCB A:Asp154.52
CdOD2 A:Asp152.53
CdOD1 A:Asp152.81
CdCG A:Asp153.03
CdO A:Hoh2912.76
CdO A:Hoh3104.52
CdO A:Hoh3234.60
CdO A:Hoh3244.38

interactive model:


Cadmium binding site 7 out of 8 in 3p5x


Cadmium binding site 7 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 7 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Thr59, A: Asn61, A: Thr71, A: Asp72, A: Gln75, A: Hoh236, A: Hoh298,

conact list:


AtomAtomDistance (A)
CdOG1 A:Thr594.56
CdCB A:Asn614.65
CdND2 A:Asn613.75
CdCG A:Asn614.65
CdOG1 A:Thr714.99
CdCB A:Asp724.66
CdOD2 A:Asp723.19
CdOD1 A:Asp722.46
CdCG A:Asp723.19
CdNE2 A:Gln754.68
CdO A:Hoh2362.09
CdO A:Hoh2982.39

interactive model:


Cadmium binding site 8 out of 8 in 3p5x


Cadmium binding site 8 out of 8 in 3p5x
Click to enlarge
stereopicture of Cadmium binding site 8 out of 8 in 3p5x
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 3p5x. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Ile16, A: Thr186, A: Hoh294, A: Hoh362, A: Hoh363, A: Hoh364, A: Hoh365,

conact list:


AtomAtomDistance (A)
CdO A:Ile164.19
CdN A:Thr1864.63
CdCB A:Thr1864.01
CdCG2 A:Thr1863.21
CdOG1 A:Thr1863.56
CdCA A:Thr1864.97
CdO A:Hoh2943.26
CdO A:Hoh3622.36
CdO A:Hoh3632.58
CdO A:Hoh3642.86
CdO A:Hoh3652.00

interactive model:




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