Chemical elements
  Cadmium
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    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
      3h1u
      3h7g
      3h7p
      3haf
      3heq
      3her
      3hes
      3hjx
      3hmw
      3hrt
      3i55
      3i56
      3iis
      3iiu
      3inz
      3ip1
      3ivk
      3jqx
      3kbm
      3kbs
      3kcl
      3kd0
      3kls
      3km9
      3ktr
      3kxd
      3kxu
      3l3v
      3l6p
      3le1
      3liz
      3lkw
      3m31
      3mmu
      3mmw
      3ng1
      3noz
      3np0
      3np2
      3nqi
      3nvj
      3o39
      3oeo
      3om3
      3oma
      3omi
      3omn
      3ow2
      3p5u
      3p5v
    PDB 3p5w-8ice

Cadmium in the structure of Crystal Structure Of the Catalytic Core of An Rna Polymerase Ribozyme Complexed With An Antigen Binding Antibody Fragment (pdb 3ivk)






The binding sites of Cadmium atom in the structure of Crystal Structure Of the Catalytic Core of An Rna Polymerase Ribozyme Complexed With An Antigen Binding Antibody Fragment (pdb code 3ivk). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 3ivk structure was solved by Y.KOLDOBSKAYA, E.M.DUGUID, D.M.SHECHNER, S.KOIDE, A.A.KOSSIAKOFF, D.P.BARTEL, J.A.PICCIRILLI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)50.0-3.1
Space groupC2221
a (A)207.499
b (A)206.452
c (A)135.926
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)20.7
Rfree (%)22.5


Cadmium Binding Sites:

Cadmium binding site 1 out of 2 in 3ivk


Cadmium binding site 1 out of 2 in 3ivk
Click to enlarge
stereopicture of Cadmium binding site 1 out of 2 in 3ivk
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3ivk. 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: L: Ser1, L: Asp2, L: Pro96, H: Asp65,

conact list:


AtomAtomDistance (A)
CdOG L:Ser14.20
CdCB L:Asp24.35
CdOD2 L:Asp22.19
CdOD1 L:Asp22.89
CdCG L:Asp22.88
CdCD L:Pro964.68
CdCG L:Pro964.65
CdCB H:Asp654.19
CdOD2 H:Asp652.42
CdOD1 H:Asp652.29
CdCG H:Asp652.69
CdCA H:Asp654.99

interactive model:


Cadmium binding site 2 out of 2 in 3ivk


Cadmium binding site 2 out of 2 in 3ivk
Click to enlarge
stereopicture of Cadmium binding site 2 out of 2 in 3ivk
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3ivk. 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: B: Ser1, B: Asp2, B: Pro96, A: Asp65,

conact list:


AtomAtomDistance (A)
CdOG B:Ser14.15
CdCB B:Asp24.41
CdOD2 B:Asp22.27
CdOD1 B:Asp22.89
CdCG B:Asp22.93
CdCD B:Pro964.68
CdCG B:Pro964.69
CdCB A:Asp654.25
CdOD2 A:Asp652.48
CdOD1 A:Asp652.34
CdCG A:Asp652.74

interactive model:




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