Chemical elements
  Cadmium
    Isotopes
    Energy
    Production
    Application
    Physical Properties
    Chemical Properties
    PDB 1a4k-1exq
    PDB 1f48-1ihu
      1f48
      1fa7
      1fe0
      1fe1
      1feu
      1ffk
      1fnu
      1fnv
      1fnw
      1fws
      1fwt
      1fww
      1fxp
      1fy2
      1fy6
      1fye
      1g01
      1g0c
      1g3w
      1g8f
      1g8g
      1g8h
      1gkk
      1gkl
      1gl0
      1gl1
      1gm6
      1guy
      1gwg
      1gyn
      1h96
      1h9p
      1hb6
      1heu
      1hf3
      1hk7
      1hq4
      1hrs
      1hsl
      1i05
      1i06
      1i0d
      1i4m
      1i6w
      1ib4
      1ibs
      1ier
      1ies
      1ihf
      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
    PDB 3p5w-8ice

Cadmium in the structure of Aquifex Aeolicus KDO8P Synthase in Complex With Pep, A5P and Cadmium (pdb 1fww)






The binding sites of Cadmium atom in the structure of Aquifex Aeolicus KDO8P Synthase in Complex With Pep, A5P and Cadmium (pdb code 1fww). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 1fww structure was solved by H.S.DUEWEL, S.RADAEV, J.WANG, R.W.WOODARD, D.L.GATTI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)27.1-1.9
Space groupP3121
a (A)84.108
b (A)84.108
c (A)159.780
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)20.5
Rfree (%)23.8


Cadmium Binding Sites:

Cadmium binding site 1 out of 2 in 1fww


Cadmium binding site 1 out of 2 in 1fww
Click to enlarge
stereopicture of Cadmium binding site 1 out of 2 in 1fww
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1fww. 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: Cys1011, A: Lys1041, A: Lys1046, A: His1185, A: Glu1222, A: Asp1233, A: Pep1268, A: A5p1269, A: Hoh3189, A: Hoh3211,

conact list:


AtomAtomDistance (A)
CdCB A:Cys10113.54
CdSG A:Cys10112.55
CdCA A:Cys10114.34
CdNZ A:Lys10414.65
CdCE A:Lys10464.72
CdNZ A:Lys10463.95
CdNE2 A:His11852.52
CdND1 A:His11854.37
CdCD2 A:His11853.60
CdCE1 A:His11853.20
CdCG A:His11854.59
CdOE1 A:Glu12222.37
CdOE2 A:Glu12222.45
CdCD A:Glu12222.69
CdCG A:Glu12224.14
CdCB A:Asp12334.04
CdOD2 A:Asp12332.25
CdOD1 A:Asp12334.42
CdCG A:Asp12333.41
CdC1 A:Pep12684.29
CdO1 A:Pep12684.12
CdO2' A:Pep12684.63
CdC2 A:Pep12684.72
CdC2 A:A5p12694.85
CdO2 A:A5p12694.01
CdO4 A:A5p12694.92
CdO A:Hoh31893.79
CdO A:Hoh32112.34

interactive model:


Cadmium binding site 2 out of 2 in 1fww


Cadmium binding site 2 out of 2 in 1fww
Click to enlarge
stereopicture of Cadmium binding site 2 out of 2 in 1fww
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1fww. 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: Cys2011, B: Lys2041, B: Lys2046, B: His2185, B: Glu2222, B: Ser2232, B: Asp2233, B: Pep2268, B: Hoh3194,

conact list:


AtomAtomDistance (A)
CdCB B:Cys20113.62
CdSG B:Cys20112.67
CdCA B:Cys20114.39
CdNZ B:Lys20414.76
CdCE B:Lys20464.77
CdNZ B:Lys20464.12
CdNE2 B:His21852.32
CdND1 B:His21854.17
CdCD2 B:His21853.45
CdCE1 B:His21852.99
CdCG B:His21854.42
CdOE1 B:Glu22222.29
CdOE2 B:Glu22222.45
CdCD B:Glu22222.66
CdCG B:Glu22224.14
CdOG B:Ser22324.82
CdCB B:Asp22333.94
CdOD2 B:Asp22332.16
CdOD1 B:Asp22334.28
CdCG B:Asp22333.29
CdC1 B:Pep22684.28
CdO1 B:Pep22684.10
CdO2' B:Pep22684.63
CdC2 B:Pep22684.64
CdO B:Hoh31942.52

interactive model:




© Copyright 2008-2012 by atomistry.com