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
      2b3p
      2bjd
      2bmy
      2bmz
      2bn0
      2bt7
      2bym
      2c1f
      2c3g
      2cmv
      2cn2
      2cu3
      2dm5
      2dvz
      2e0l
      2e0m
      2e74
      2e75
      2e76
      2eik
      2eil
      2enr
      2ev0
      2f5h
      2f91
      2fcm
      2fcn
      2fcq
      2fcs
      2ffh
      2ffx
      2fg4
      2fj4
      2fj5
      2fo7
      2fu4
      2g4h
      2gbr
      2gj2
      2gsm
      2gyd
      2hcr
      2ht0
      2hz1
      2hz2
      2hz3
      2igi
      2iy2
      2j4k
      2j6e
    PDB 2jdz-2x05
    PDB 2x09-3ccj
    PDB 3ccl-3ggf
    PDB 3h1u-3p5v
    PDB 3p5w-8ice

Cadmium in the structure of Crystal Structure Of the N-Terminal Dimer Domain of E.Coli Dsbg (pdb 2iy2)






The binding sites of Cadmium atom in the structure of Crystal Structure Of the N-Terminal Dimer Domain of E.Coli Dsbg (pdb code 2iy2). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 2iy2 structure was solved by S.-M.YEH, P.METCALF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)56.8-1.9
Space groupP41
a (A)56.842
b (A)56.842
c (A)42.049
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)19.6
Rfree (%)23.6


Cadmium Binding Sites:

Cadmium binding site 1 out of 4 in 2iy2


Cadmium binding site 1 out of 4 in 2iy2
Click to enlarge
stereopicture of Cadmium binding site 1 out of 4 in 2iy2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2iy2. 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: Lys48, A: His49, B: Pro24, B: Asn57, A: Hoh2023, A: Hoh2024,

conact list:


AtomAtomDistance (A)
CdO A:Lys484.96
CdNE2 A:His492.34
CdND1 A:His494.23
CdCD2 A:His493.47
CdCE1 A:His493.04
CdCG A:His494.46
CdCB B:Pro244.65
CdCB B:Asn574.27
CdO A:Hoh20232.30
CdO A:Hoh20242.08

interactive model:


Cadmium binding site 2 out of 4 in 2iy2


Cadmium binding site 2 out of 4 in 2iy2
Click to enlarge
stereopicture of Cadmium binding site 2 out of 4 in 2iy2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2iy2. 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: Asp46, A: Lys48, A: His49, B: Gly25,

conact list:


AtomAtomDistance (A)
CdCB A:Asp463.32
CdOD2 A:Asp464.28
CdOD1 A:Asp462.27
CdCG A:Asp463.13
CdCA A:Asp464.85
CdCD A:Lys484.53
CdND1 A:His494.90
CdCE1 A:His494.57
CdN B:Gly254.42
CdCA B:Gly254.39

interactive model:


Cadmium binding site 3 out of 4 in 2iy2


Cadmium binding site 3 out of 4 in 2iy2
Click to enlarge
stereopicture of Cadmium binding site 3 out of 4 in 2iy2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2iy2. 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: Pro24, A: Asn57, B: His49, A: Hoh2026, B: Hoh2022,

conact list:


AtomAtomDistance (A)
CdCB A:Pro244.39
CdCG A:Pro244.70
CdCB A:Asn574.31
CdND2 A:Asn574.86
CdNE2 B:His492.34
CdND1 B:His494.30
CdCD2 B:His493.45
CdCE1 B:His493.10
CdCG B:His494.49
CdO A:Hoh20262.34
CdO B:Hoh20222.27

interactive model:


Cadmium binding site 4 out of 4 in 2iy2


Cadmium binding site 4 out of 4 in 2iy2
Click to enlarge
stereopicture of Cadmium binding site 4 out of 4 in 2iy2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2iy2. 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: Gly25, B: Asp46, B: Lys48, B: His49, B: Hoh2019, B: Hoh2020,

conact list:


AtomAtomDistance (A)
CdN A:Gly254.41
CdCA A:Gly254.40
CdCB B:Asp463.38
CdOD2 B:Asp462.28
CdOD1 B:Asp464.35
CdCG B:Asp463.18
CdCA B:Asp464.93
CdCD B:Lys484.78
CdND1 B:His494.86
CdCE1 B:His494.49
CdO B:Hoh20194.69
CdO B:Hoh20202.41

interactive model:




© Copyright 2008-2012 by atomistry.com