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
      1qy0
      1qy1
      1qy2
      1r0i
      1rj4
      1rk6
      1rlw
      1rp4
      1rq1
      1rtx
      1rwi
      1rwl
      1rzm
      1s24
      1s72
      1sm3
      1t8x
      1t96
      1t99
      1tq5
      1ue5
      1ur5
      1uvo
      1uvp
      1uxj
      1uxk
      1vcf
      1vel
      1vq4
      1vq5
      1vq6
      1vq7
      1vq8
      1vq9
      1vqk
      1vql
      1vqm
      1vqn
      1vqo
      1vqp
      1vqq
      1vsj
      1w1a
      1w1b
      1w2b
      1w77
      1w9h
      1wb4
      1wb5
      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 The Structure Of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb 1vqn)






The binding sites of Cadmium atom in the structure of The Structure Of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqn). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 1vqn structure was solved by T.M.SCHMEING, T.A.STEITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)50.0-2.4
Space groupC2221
a (A)211.721
b (A)298.782
c (A)575.272
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)21.2
Rfree (%)24.8


Cadmium Binding Sites:

Cadmium binding site 1 out of 5 in 1vqn


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

conact list:


AtomAtomDistance (A)
CdCB O:Arg374.88
CdCZ O:Arg374.75
CdCG O:Arg374.36
CdNE O:Arg374.92
CdNH1 O:Arg374.73
CdCA O:Arg374.96
CdNE2 O:His404.74
CdCB O:His403.93
CdND1 O:His402.77
CdCD2 O:His404.79
CdCE1 O:His403.63
CdCG O:His403.70
CdO O:Hoh30024.69
CdO O:Hoh56502.59

interactive model:


Cadmium binding site 2 out of 5 in 1vqn


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

conact list:


AtomAtomDistance (A)
CdCB U:Cys63.24
CdSG U:Cys62.48
CdCA U:Cys64.73
CdCB U:Tyr84.69
CdC U:Tyr84.94
CdN U:Cys93.82
CdCB U:Cys93.43
CdSG U:Cys92.48
CdC U:Cys95.00
CdCA U:Cys94.21
CdN U:Gly104.88
CdOG1 U:Thr114.25
CdN U:Cys324.14
CdCB U:Cys323.68
CdSG U:Cys322.55
CdC U:Cys324.97
CdCA U:Cys324.46
CdN U:Ser334.84
CdOG U:Ser334.48
CdCB U:Cys363.54
CdSG U:Cys362.42
CdCA U:Cys364.96

interactive model:


Cadmium binding site 3 out of 5 in 1vqn


Cadmium binding site 3 out of 5 in 1vqn
Click to enlarge
stereopicture of Cadmium binding site 3 out of 5 in 1vqn
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1vqn. 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: Z: Cys39, Z: Asn41, Z: Cys42, Z: Glu44, Z: Cys57, Z: Tyr59, Z: Cys60,

conact list:


AtomAtomDistance (A)
CdCB Z:Cys392.96
CdSG Z:Cys392.37
CdC Z:Cys394.92
CdCA Z:Cys394.45
CdCB Z:Asn414.30
CdND2 Z:Asn414.24
CdC Z:Asn414.66
CdCG Z:Asn414.79
CdCA Z:Asn414.91
CdN Z:Cys424.20
CdCB Z:Cys423.81
CdSG Z:Cys422.70
CdCA Z:Cys424.61
CdCB Z:Glu444.83
CdCB Z:Cys573.42
CdSG Z:Cys572.51
CdCA Z:Cys574.85
CdCB Z:Tyr594.03
CdCE2 Z:Tyr594.81
CdCD2 Z:Tyr593.79
CdC Z:Tyr594.78
CdCG Z:Tyr594.37
CdCA Z:Tyr594.88
CdN Z:Cys603.77
CdCB Z:Cys603.60
CdSG Z:Cys602.37
CdCA Z:Cys604.31

interactive model:


Cadmium binding site 4 out of 5 in 1vqn


Cadmium binding site 4 out of 5 in 1vqn
Click to enlarge
stereopicture of Cadmium binding site 4 out of 5 in 1vqn
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1vqn. 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: Cys19, 1: Arg21, 1: Cys22, 1: Gly23, 1: Cys34, 1: Ser36, 1: Cys37, 1: Gly38, 1: Phe39, 1: Hoh9480,

conact list:


AtomAtomDistance (A)
CdCB 1:Cys193.08
CdSG 1:Cys192.54
CdCA 1:Cys194.56
CdCB 1:Arg214.53
CdCD 1:Arg214.96
CdC 1:Arg214.71
CdCA 1:Arg214.97
CdN 1:Cys223.69
CdCB 1:Cys223.30
CdSG 1:Cys222.39
CdC 1:Cys224.87
CdCA 1:Cys224.08
CdN 1:Gly234.93
CdCB 1:Cys343.17
CdSG 1:Cys342.43
CdCA 1:Cys344.62
CdCB 1:Ser364.74
CdC 1:Ser364.85
CdN 1:Cys373.77
CdCB 1:Cys373.31
CdSG 1:Cys372.46
CdC 1:Cys374.76
CdCA 1:Cys374.09
CdN 1:Gly384.91
CdN 1:Phe394.88
CdCB 1:Phe394.36
CdO 1:Hoh94804.74

interactive model:


Cadmium binding site 5 out of 5 in 1vqn


Cadmium binding site 5 out of 5 in 1vqn
Click to enlarge
stereopicture of Cadmium binding site 5 out of 5 in 1vqn
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1vqn. 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: 3: Cys11, 3: His13, 3: Cys14, 3: Gln18, 3: Cys71, 3: Cys74, 3: Hoh9497,

conact list:


AtomAtomDistance (A)
CdCB 3:Cys113.45
CdSG 3:Cys112.39
CdCA 3:Cys114.88
CdCB 3:His134.39
CdC 3:His134.66
CdCA 3:His134.94
CdN 3:Cys143.63
CdCB 3:Cys143.38
CdSG 3:Cys142.42
CdCA 3:Cys144.06
CdOE1 3:Gln184.15
CdCD 3:Gln184.82
CdCB 3:Cys712.97
CdSG 3:Cys712.25
CdCA 3:Cys714.44
CdN 3:Cys744.00
CdCB 3:Cys743.43
CdSG 3:Cys742.42
CdCA 3:Cys744.31
CdO 3:Hoh94974.68

interactive model:




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