Chemical elements
  Cadmium
    Isotopes
    Energy
    Production
    Application
    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
      2jdz
      2jf5
      2jhf
      2jih
      2jsc
      2mhu
      2mpa
      2mrb
      2mrt
      2nnd
      2nne
      2oa9
      2otj
      2otl
      2ozq
      2p5q
      2p64
      2pzi
      2q88
      2q89
      2qa4
      2qex
      2qp9
      2qtf
      2qth
      2r1f
      2v2i
      2v2j
      2v2l
      2v2m
      2v2n
      2v2o
      2v2p
      2v2r
      2v2s
      2v4b
      2vg9
      2vli
      2vzo
      2vzs
      2vzt
      2vzu
      2w0o
      2w2c
      2w5e
      2w5f
      2wxt
      2wxu
      2wy6
      2x05
    PDB 2x09-3ccj
    PDB 3ccl-3ggf
    PDB 3h1u-3p5v
    PDB 3p5w-8ice

Cadmium in the structure of The Structural Identification Of the Interaction Site and Functional State of Rbp For Its Membrane Receptor (pdb 2nnd)






The binding sites of Cadmium atom in the structure of The Structural Identification Of the Interaction Site and Functional State of Rbp For Its Membrane Receptor (pdb code 2nnd). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 2nnd structure was solved by C.REDONDO, R.J.BINGHAM, M.VOUROPOULOU, S.W.HOMANS, J.B.FINDLAY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)42.3-1.6
Space groupP43212
a (A)53.636
b (A)53.636
c (A)137.347
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)19
Rfree (%)22.7


Cadmium Binding Sites:

Cadmium binding site 1 out of 4 in 2nnd


Cadmium binding site 1 out of 4 in 2nnd
Click to enlarge
stereopicture of Cadmium binding site 1 out of 4 in 2nnd
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2nnd. 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: Gln140, A: Glu143, A: Hoh381, A: Hoh419, A: Hoh446, A: Hoh485, A: Hoh563, A: Hoh567, A: Hoh594,

conact list:


AtomAtomDistance (A)
CdNE2 A:Gln1404.17
CdOE1 A:Gln1404.51
CdCD A:Gln1404.80
CdOE1 A:Glu1432.26
CdOE2 A:Glu1432.48
CdCD A:Glu1432.69
CdCG A:Glu1434.21
CdO A:Hoh3812.42
CdO A:Hoh4194.52
CdO A:Hoh4464.29
CdO A:Hoh4854.94
CdO A:Hoh5634.14
CdO A:Hoh5673.93
CdO A:Hoh5942.36

interactive model:


Cadmium binding site 2 out of 4 in 2nnd


Cadmium binding site 2 out of 4 in 2nnd
Click to enlarge
stereopicture of Cadmium binding site 2 out of 4 in 2nnd
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2nnd. 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: Glu13, A: Hoh410, A: Hoh431, A: Hoh433, A: Hoh448, A: Hoh552,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu132.27
CdOE2 A:Glu132.62
CdCD A:Glu132.78
CdCG A:Glu134.30
CdO A:Hoh4105.00
CdO A:Hoh4312.42
CdO A:Hoh4332.30
CdO A:Hoh4482.16
CdO A:Hoh5524.52

interactive model:


Cadmium binding site 3 out of 4 in 2nnd


Cadmium binding site 3 out of 4 in 2nnd
Click to enlarge
stereopicture of Cadmium binding site 3 out of 4 in 2nnd
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2nnd. 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: Thr95, A: His108, A: His145, A: Cd373, A: Hoh400, A: Hoh430, A: Hoh487, A: Hoh534, A: Hoh547, A: Hoh554,

conact list:


AtomAtomDistance (A)
CdCB A:Thr954.90
CdCG2 A:Thr954.90
CdOG1 A:Thr953.70
CdO A:His1084.73
CdNE2 A:His1084.12
CdCB A:His1083.86
CdND1 A:His1082.51
CdCD2 A:His1084.25
CdCE1 A:His1083.14
CdCG A:His1083.37
CdCE1 A:His1454.46
CdCD A:Cd3733.63
CdO A:Hoh4004.39
CdO A:Hoh4302.30
CdO A:Hoh4872.32
CdO A:Hoh5344.33
CdO A:Hoh5472.57
CdO A:Hoh5543.67

interactive model:


Cadmium binding site 4 out of 4 in 2nnd


Cadmium binding site 4 out of 4 in 2nnd
Click to enlarge
stereopicture of Cadmium binding site 4 out of 4 in 2nnd
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2nnd. 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: His145, A: Cd202, A: Hoh383, A: Hoh480, A: Hoh505, A: Hoh523, A: Hoh547, A: Hoh554,

conact list:


AtomAtomDistance (A)
CdNE2 A:His1452.97
CdND1 A:His1453.63
CdCD2 A:His1454.29
CdCE1 A:His1452.43
CdCG A:His1454.61
CdCD A:Cd2023.63
CdO A:Hoh3833.81
CdO A:Hoh4802.44
CdO A:Hoh5054.39
CdO A:Hoh5234.62
CdO A:Hoh5472.49
CdO A:Hoh5543.86

interactive model:




© Copyright 2008-2012 by atomistry.com