Chemical elements
  Cadmium
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    PDB 1a4k-1exq
    PDB 1f48-1ihu
    PDB 1ii0-1mhu
    PDB 1mms-1qvg
      1mms
      1mnu
      1mox
      1mpa
      1mqo
      1mrb
      1mrt
      1mup
      1mwr
      1mws
      1mwt
      1mwu
      1n0i
      1n2z
      1n8r
      1ncx
      1ng1
      1nji
      1np8
      1npe
      1nz4
      1oeb
      1oee
      1on3
      1on9
      1oo2
      1orq
      1oyr
      1p8z
      1p9e
      1pck
      1pcw
      1pe1
      1pew
      1pl3
      1psc
      1pw3
      1q7y
      1q7z
      1q81
      1q82
      1q85
      1q86
      1q8a
      1q8j
      1qjk
      1qjl
      1qjw
      1qvf
      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

Cadmium in the structure of Crystal Structure Of Ccdap-Puromycin Bound At The Peptidyl Transferase Center of the 50S Ribosomal Subunit (pdb 1q7y)






The binding sites of Cadmium atom in the structure of Crystal Structure Of Ccdap-Puromycin Bound At The Peptidyl Transferase Center of the 50S Ribosomal Subunit (pdb code 1q7y). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 1q7y structure was solved by J.L.HANSEN, T.M.SCHMEING, P.B.MOORE, T.A.STEITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-3.2
Space groupC2221
a (A)212.902
b (A)300.474
c (A)575.176
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)22.5
Rfree (%)28


Cadmium Binding Sites:

Cadmium binding site 1 out of 5 in 1q7y


Cadmium binding site 1 out of 5 in 1q7y
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stereopicture of Cadmium binding site 1 out of 5 in 1q7y
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1q7y. 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: P: Arg37, P: His40, P: Hoh3002, P: Hoh5322, P: Hoh5650,

conact list:


AtomAtomDistance (A)
CdO P:Arg374.21
CdCB P:Arg374.55
CdCZ P:Arg374.74
CdC P:Arg374.71
CdCG P:Arg374.06
CdNE P:Arg374.78
CdNH1 P:Arg374.88
CdCA P:Arg374.22
CdNE2 P:His404.23
CdCB P:His403.43
CdND1 P:His402.45
CdCD2 P:His404.16
CdCE1 P:His403.32
CdCG P:His403.14
CdCA P:His404.91
CdO P:Hoh30024.45
CdO P:Hoh53223.79
CdO P:Hoh56503.65

interactive model:


Cadmium binding site 2 out of 5 in 1q7y


Cadmium binding site 2 out of 5 in 1q7y
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stereopicture of Cadmium binding site 2 out of 5 in 1q7y
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1q7y. 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: V: Cys6, V: Tyr8, V: Cys9, V: Gly10, V: Thr11, V: Cys32, V: Ser33, V: Cys36,

conact list:


AtomAtomDistance (A)
CdCB V:Cys63.33
CdSG V:Cys62.57
CdCA V:Cys64.83
CdCB V:Tyr84.55
CdCD2 V:Tyr84.89
CdN V:Cys93.94
CdCB V:Cys93.49
CdSG V:Cys92.53
CdCA V:Cys94.32
CdN V:Gly104.94
CdOG1 V:Thr114.46
CdN V:Cys323.94
CdCB V:Cys323.44
CdSG V:Cys322.18
CdC V:Cys324.73
CdCA V:Cys324.21
CdN V:Ser334.49
CdOG V:Ser334.36
CdCB V:Cys363.26
CdSG V:Cys362.28
CdCA V:Cys364.65

interactive model:


Cadmium binding site 3 out of 5 in 1q7y


Cadmium binding site 3 out of 5 in 1q7y
Click to enlarge
stereopicture of Cadmium binding site 3 out of 5 in 1q7y
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1q7y. 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: 1: Cys39, 1: Val41, 1: Cys42, 1: Cys57, 1: His59, 1: Cys60, 1: Gly61, 1: Tyr62,

conact list:


AtomAtomDistance (A)
CdCB 1:Cys393.80
CdSG 1:Cys393.16
CdCB 1:Val414.59
CdCG1 1:Val414.68
CdN 1:Cys423.94
CdCB 1:Cys423.32
CdSG 1:Cys422.98
CdCA 1:Cys424.25
CdCB 1:Cys573.18
CdSG 1:Cys572.36
CdCA 1:Cys574.68
CdCB 1:His594.59
CdCD2 1:His594.64
CdC 1:His594.77
CdCG 1:His594.99
CdN 1:Cys603.62
CdCB 1:Cys602.96
CdSG 1:Cys602.48
CdC 1:Cys604.51
CdCA 1:Cys603.82
CdN 1:Gly614.88
CdN 1:Tyr624.96
CdCB 1:Tyr624.58

interactive model:


Cadmium binding site 4 out of 5 in 1q7y


Cadmium binding site 4 out of 5 in 1q7y
Click to enlarge
stereopicture of Cadmium binding site 4 out of 5 in 1q7y
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1q7y. 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: 2: Cys19, 2: Arg21, 2: Cys22, 2: Gly23, 2: Glu24, 2: Cys34, 2: Ser36, 2: Cys37, 2: Phe39, 2: Hoh1020,

conact list:


AtomAtomDistance (A)
CdO 2:Cys194.87
CdCB 2:Cys192.87
CdSG 2:Cys192.50
CdC 2:Cys194.87
CdCA 2:Cys194.39
CdCB 2:Arg214.41
CdC 2:Arg214.48
CdCA 2:Arg214.86
CdN 2:Cys223.32
CdCB 2:Cys223.11
CdSG 2:Cys222.13
CdC 2:Cys224.43
CdCA 2:Cys223.72
CdN 2:Gly234.50
CdO 2:Glu244.85
CdN 2:Glu244.77
CdCB 2:Glu244.84
CdCB 2:Cys343.46
CdSG 2:Cys342.68
CdCA 2:Cys344.88
CdCB 2:Ser364.71
CdC 2:Ser364.89
CdN 2:Cys373.87
CdCB 2:Cys373.22
CdSG 2:Cys372.50
CdC 2:Cys374.92
CdCA 2:Cys374.13
CdCB 2:Phe394.72
CdO 2:Hoh10204.39

interactive model:


Cadmium binding site 5 out of 5 in 1q7y


Cadmium binding site 5 out of 5 in 1q7y
Click to enlarge
stereopicture of Cadmium binding site 5 out of 5 in 1q7y
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1q7y. 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: 4: Cys11, 4: His13, 4: Cys14, 4: Cys71, 4: Cys74, 4: Gly75, 4: Hoh8536, 4: Hoh8561,

conact list:


AtomAtomDistance (A)
CdCB 4:Cys113.60
CdSG 4:Cys112.66
CdCB 4:His134.22
CdC 4:His134.62
CdCA 4:His134.92
CdN 4:Cys143.54
CdCB 4:Cys143.24
CdSG 4:Cys142.95
CdCA 4:Cys143.94
CdCB 4:Cys713.00
CdSG 4:Cys712.09
CdC 4:Cys714.93
CdCA 4:Cys714.41
CdN 4:Cys744.18
CdCB 4:Cys743.13
CdSG 4:Cys742.29
CdC 4:Cys744.86
CdCA 4:Cys744.22
CdN 4:Gly754.97
CdO 4:Hoh85364.79
CdO 4:Hoh85613.44

interactive model:




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