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
    PDB 1wje-2avp
    PDB 2b3p-2j6e
    PDB 2jdz-2x05
    PDB 2x09-3ccj
      2x09
      2x1z
      2x20
      2x21
      2x28
      2x7k
      2x7w
      2xdv
      2xgl
      2xo6
      2xq7
      2xvc
      2ydq
      2ydr
      2yds
      2z4q
      2z5p
      2z5q
      2z5r
      2za6
      2za8
      2zg7
      2zg8
      2zg9
      2zgd
      2zgg
      2znb
      2zqo
      2zur
      3a02
      3a04
      3a05
      3af7
      3af8
      3af9
      3afp
      3b40
      3bd4
      3bob
      3boe
      3boh
      3c4t
      3c7m
      3c99
      3c9c
      3cc2
      3cc4
      3cc7
      3cce
      3ccj
    PDB 3ccl-3ggf
    PDB 3h1u-3p5v
    PDB 3p5w-8ice

Cadmium in the structure of Cpoga D298N in Complex With TAB1-Derived O-Glcnac Peptide (pdb 2yds)






The binding sites of Cadmium atom in the structure of Cpoga D298N in Complex With TAB1-Derived O-Glcnac Peptide (pdb code 2yds). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 2yds structure was solved by M.SCHIMPL, V.S.BORODKIN, L.J.GRAY, D.M.F.VAN AALTEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)25.0-2.5
Space groupP61
a (A)118.090
b (A)118.090
c (A)148.260
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)20.007
Rfree (%)23.846


Cadmium Binding Sites:

Cadmium binding site 1 out of 19 in 2yds


Cadmium binding site 1 out of 19 in 2yds
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stereopicture of Cadmium binding site 1 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2yds. 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: Glu51, A: Thr178, A: Asn450, A: Met451, A: Asp452, A: Asn453, A: Hoh2004, A: Hoh2005, A: Hoh2034,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu513.40
CdOE2 A:Glu511.53
CdCD A:Glu512.73
CdCG A:Glu513.86
CdOG1 A:Thr1784.93
CdCB A:Asn4504.55
CdND2 A:Asn4504.00
CdC A:Asn4504.62
CdOD1 A:Asn4502.57
CdCG A:Asn4503.45
CdCA A:Asn4504.51
CdN A:Met4514.81
CdN A:Asp4524.48
CdCB A:Asp4524.64
CdOD2 A:Asp4523.58
CdOD1 A:Asp4522.33
CdCG A:Asp4523.30
CdCA A:Asp4524.92
CdN A:Asn4534.53
CdCB A:Asn4534.77
CdO A:Hoh20041.87
CdO A:Hoh20054.58
CdO A:Hoh20344.01

interactive model:


Cadmium binding site 2 out of 19 in 2yds


Cadmium binding site 2 out of 19 in 2yds
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stereopicture of Cadmium binding site 2 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2yds. 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: Glu54,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu543.06
CdOE2 A:Glu543.11
CdCD A:Glu543.37
CdCG A:Glu544.77

interactive model:


Cadmium binding site 3 out of 19 in 2yds


Cadmium binding site 3 out of 19 in 2yds
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stereopicture of Cadmium binding site 3 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2yds. 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: Asn39, A: Gln40, A: Asp58, A: Hoh2001, A: Hoh2007,

conact list:


AtomAtomDistance (A)
CdND2 A:Asn394.26
CdOD1 A:Asn394.39
CdCG A:Asn394.78
CdNE2 A:Gln404.61
CdCB A:Asp584.27
CdOD2 A:Asp582.13
CdOD1 A:Asp582.82
CdCG A:Asp582.79
CdO A:Hoh20012.21
CdO A:Hoh20074.90

interactive model:


Cadmium binding site 4 out of 19 in 2yds


Cadmium binding site 4 out of 19 in 2yds
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stereopicture of Cadmium binding site 4 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2yds. 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: Leu68, A: Val69, A: Gly70, A: Glu71, A: Glu72, A: Hoh2009, A: Hoh2016,

conact list:


AtomAtomDistance (A)
CdO A:Leu682.42
CdCB A:Leu684.81
CdC A:Leu683.53
CdCA A:Leu684.66
CdN A:Val694.16
CdC A:Val694.72
CdCA A:Val693.99
CdN A:Gly704.62
CdOE1 A:Glu712.39
CdOE2 A:Glu712.70
CdCD A:Glu712.90
CdCG A:Glu714.46
CdOE1 A:Glu724.11
CdOE2 A:Glu723.58
CdCD A:Glu724.19
CdO A:Hoh20092.46
CdO A:Hoh20164.21

interactive model:


Cadmium binding site 5 out of 19 in 2yds


Cadmium binding site 5 out of 19 in 2yds
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stereopicture of Cadmium binding site 5 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2yds. 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: Glu73, A: Ala74, A: Asp75, A: Glu108, A: Asp110, A: Asp111, A: Hoh2010, A: Hoh2019,

conact list:


AtomAtomDistance (A)
CdO A:Glu732.28
CdCB A:Glu734.56
CdC A:Glu733.43
CdCA A:Glu734.45
CdO A:Ala744.82
CdN A:Ala744.22
CdC A:Ala744.28
CdCA A:Ala744.14
CdN A:Asp754.39
CdN A:Glu1084.95
CdOE1 A:Glu1082.42
CdCB A:Glu1084.55
CdOE2 A:Glu1084.33
CdCD A:Glu1083.57
CdCG A:Glu1084.50
CdOD1 A:Asp1104.13
CdCB A:Asp1114.52
CdOD2 A:Asp1112.78
CdOD1 A:Asp1112.58
CdCG A:Asp1113.03
CdO A:Hoh20104.37
CdO A:Hoh20192.02

interactive model:


Cadmium binding site 6 out of 19 in 2yds


Cadmium binding site 6 out of 19 in 2yds
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stereopicture of Cadmium binding site 6 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2yds. 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: Asp112, A: Hoh2020, A: Hoh2021,

conact list:


AtomAtomDistance (A)
CdCB A:Asp1124.67
CdOD2 A:Asp1122.24
CdOD1 A:Asp1123.88
CdCG A:Asp1123.40
CdO A:Hoh20202.57
CdO A:Hoh20211.87

interactive model:


Cadmium binding site 7 out of 19 in 2yds


Cadmium binding site 7 out of 19 in 2yds
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stereopicture of Cadmium binding site 7 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2yds. 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: Val109, A: Asp117, A: Leu120, A: Thr124, A: Glu145,

conact list:


AtomAtomDistance (A)
CdCA A:Val1094.92
CdCB A:Asp1174.29
CdOD2 A:Asp1172.78
CdOD1 A:Asp1172.07
CdCG A:Asp1172.78
CdCA A:Asp1174.86
CdCD1 A:Leu1204.78
CdCB A:Thr1244.75
CdOG1 A:Thr1243.73
CdOE1 A:Glu1453.39
CdOE2 A:Glu1452.53
CdCD A:Glu1453.34
CdCG A:Glu1454.77

interactive model:


Cadmium binding site 8 out of 19 in 2yds


Cadmium binding site 8 out of 19 in 2yds
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stereopicture of Cadmium binding site 8 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 2yds. 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: Asn138, A: Asp139, A: Hoh2026, A: Hoh2027,

conact list:


AtomAtomDistance (A)
CdND2 A:Asn1383.22
CdOD1 A:Asn1384.92
CdCG A:Asn1384.45
CdCB A:Asp1394.22
CdOD2 A:Asp1392.52
CdOD1 A:Asp1392.49
CdCG A:Asp1392.79
CdO A:Hoh20264.56
CdO A:Hoh20274.91

interactive model:


Cadmium binding site 9 out of 19 in 2yds


Cadmium binding site 9 out of 19 in 2yds
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stereopicture of Cadmium binding site 9 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 2yds. 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: Asp150, A: Lys250, A: Asp252, A: Lys326,

conact list:


AtomAtomDistance (A)
CdOD2 A:Asp1503.76
CdOD1 A:Asp1503.91
CdCG A:Asp1504.21
CdO A:Lys2504.57
CdCB A:Asp2524.81
CdOD2 A:Asp2523.44
CdOD1 A:Asp2522.55
CdCG A:Asp2523.38
CdNZ A:Lys3264.24

interactive model:


Cadmium binding site 10 out of 19 in 2yds


Cadmium binding site 10 out of 19 in 2yds
Click to enlarge
stereopicture of Cadmium binding site 10 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 2yds. 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: Gly57, A: Asp58, A: Gly59, A: Asn138, A: Asp139, A: Glu170, A: Hoh2007, A: Hoh2026, A: Hoh2027, A: Hoh2033,

conact list:


AtomAtomDistance (A)
CdC A:Gly574.78
CdCA A:Gly574.45
CdN A:Asp584.18
CdO A:Gly594.69
CdN A:Gly594.77
CdOD1 A:Asn1384.34
CdCG A:Asn1384.95
CdN A:Asp1394.66
CdOD1 A:Asp1394.18
CdOE1 A:Glu1702.33
CdOE2 A:Glu1702.47
CdCD A:Glu1702.76
CdCG A:Glu1704.29
CdO A:Hoh20073.07
CdO A:Hoh20262.12
CdO A:Hoh20272.32
CdO A:Hoh20332.05

interactive model:


Cadmium binding site 11 out of 19 in 2yds


Cadmium binding site 11 out of 19 in 2yds
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stereopicture of Cadmium binding site 11 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 2yds. 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: Arg228, A: Arg264, A: Glu272, A: His276, A: Hoh2058, A: Hoh2060,

conact list:


AtomAtomDistance (A)
CdCD A:Arg2284.70
CdNH2 A:Arg2644.97
CdOE1 A:Glu2723.00
CdOE2 A:Glu2723.85
CdCD A:Glu2723.46
CdCG A:Glu2724.29
CdNE2 A:His2762.54
CdND1 A:His2764.57
CdCD2 A:His2763.62
CdCE1 A:His2763.38
CdCG A:His2764.71
CdO A:Hoh20581.85
CdO A:Hoh20604.79

interactive model:


Cadmium binding site 12 out of 19 in 2yds


Cadmium binding site 12 out of 19 in 2yds
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stereopicture of Cadmium binding site 12 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 2yds. 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: Glu282, A: Asp286, A: Lys322, A: Hoh2062, A: Hoh2063, A: Hoh2064,

conact list:


AtomAtomDistance (A)
CdO A:Glu2824.50
CdOE1 A:Glu2822.14
CdCB A:Glu2824.93
CdOE2 A:Glu2823.27
CdCD A:Glu2823.05
CdCG A:Glu2824.45
CdCB A:Asp2864.37
CdOD2 A:Asp2862.48
CdOD1 A:Asp2862.55
CdCG A:Asp2862.86
CdNZ A:Lys3224.73
CdO A:Hoh20622.26
CdO A:Hoh20631.95
CdO A:Hoh20644.56

interactive model:


Cadmium binding site 13 out of 19 in 2yds


Cadmium binding site 13 out of 19 in 2yds
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stereopicture of Cadmium binding site 13 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cadmium in the PDB 2yds. 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: Glu362, A: Asn390, A: Asp424, A: Hoh2074,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu3622.40
CdOE2 A:Glu3622.14
CdCD A:Glu3622.58
CdCG A:Glu3624.10
CdO A:Asn3904.46
CdCB A:Asn3904.88
CdCB A:Asp4244.39
CdOD2 A:Asp4242.34
CdOD1 A:Asp4242.72
CdCG A:Asp4242.89
CdO A:Hoh20744.23

interactive model:


Cadmium binding site 14 out of 19 in 2yds


Cadmium binding site 14 out of 19 in 2yds
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stereopicture of Cadmium binding site 14 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Cadmium in the PDB 2yds. 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: Asp388, A: Hoh2080, A: Hoh2081,

conact list:


AtomAtomDistance (A)
CdCB A:Asp3884.71
CdOD2 A:Asp3883.37
CdOD1 A:Asp3882.52
CdCG A:Asp3883.29
CdO A:Hoh20803.31
CdO A:Hoh20813.60

interactive model:


Cadmium binding site 15 out of 19 in 2yds


Cadmium binding site 15 out of 19 in 2yds
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stereopicture of Cadmium binding site 15 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Cadmium in the PDB 2yds. 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: Thr400, A: Lys404, A: Gly405, A: Lys406, A: Leu407, A: Glu432, A: His433, A: Phe601, A: Hoh2083, A: Hoh2091, A: Hoh2117,

conact list:


AtomAtomDistance (A)
CdOG1 A:Thr4004.28
CdO A:Lys4042.48
CdCB A:Lys4043.90
CdC A:Lys4043.46
CdCG A:Lys4044.74
CdCA A:Lys4043.81
CdN A:Gly4054.65
CdO A:Lys4064.67
CdCD2 A:Leu4074.99
CdCD A:Glu4324.93
CdNE2 A:His4332.70
CdND1 A:His4334.74
CdCD2 A:His4333.65
CdCE1 A:His4333.62
CdCG A:His4334.79
CdCE2 A:Phe6014.95
CdO A:Hoh20832.69
CdO A:Hoh20913.10
CdO A:Hoh21173.42

interactive model:


Cadmium binding site 16 out of 19 in 2yds


Cadmium binding site 16 out of 19 in 2yds
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stereopicture of Cadmium binding site 16 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Cadmium in the PDB 2yds. 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: His413, A: Gly494, A: Arg495, A: Glu496, A: Hoh2077,

conact list:


AtomAtomDistance (A)
CdNE2 A:His4132.37
CdND1 A:His4134.38
CdCD2 A:His4133.45
CdCE1 A:His4133.20
CdCG A:His4134.52
CdO A:Gly4944.71
CdCA A:Arg4954.62
CdN A:Glu4964.77
CdCD A:Glu4964.97
CdCG A:Glu4964.99
CdO A:Hoh20774.79

interactive model:


Cadmium binding site 17 out of 19 in 2yds


Cadmium binding site 17 out of 19 in 2yds
Click to enlarge
stereopicture of Cadmium binding site 17 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Cadmium in the PDB 2yds. 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: Asp474, A: Arg531, A: Glu534, A: Ala535, A: Asn538, A: Hoh2042, A: Hoh2105, A: Hoh2106, A: Hoh2115,

conact list:


AtomAtomDistance (A)
CdCB A:Asp4744.46
CdOD2 A:Asp4742.52
CdOD1 A:Asp4742.69
CdCG A:Asp4742.95
CdCZ A:Arg5314.05
CdNH2 A:Arg5314.07
CdNH1 A:Arg5313.29
CdO A:Glu5344.80
CdOE1 A:Glu5342.82
CdOE2 A:Glu5342.64
CdCD A:Glu5343.11
CdCG A:Glu5344.64
CdN A:Ala5354.96
CdCA A:Ala5354.64
CdCB A:Asn5384.42
CdOD1 A:Asn5384.15
CdCG A:Asn5384.44
CdO A:Hoh20423.09
CdO A:Hoh21054.81
CdO A:Hoh21062.88
CdO A:Hoh21153.20

interactive model:


Cadmium binding site 18 out of 19 in 2yds


Cadmium binding site 18 out of 19 in 2yds
Click to enlarge
stereopicture of Cadmium binding site 18 out of 19 in 2yds
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Cadmium in the PDB 2yds. 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: Asp457, A: Asn461, A: Glu500, A: Hoh2099, A: Hoh2100, A: Hoh2111, A: Hoh2112,

conact list:


AtomAtomDistance (A)
CdCB A:Asp4574.91
CdOD2 A:Asp4572.85
CdOD1 A:Asp4573.36
CdCG A:Asp4573.46
CdND2 A:Asn4614.08
CdOE2 A:Glu5004.60
CdO A:Hoh20993.21
CdO A:Hoh21002.94
CdO A:Hoh21113.44
CdO A:Hoh21124.75

interactive model:


Cadmium binding site 19 out of 19 in 2yds


Cadmium binding site 19 out of 19 in 2yds
Click to enlarge
stereopicture of Cadmium binding site 19 out of 19 in 2yds
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Cadmium in the PDB 2yds. 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: Asp112, A: Ile113, A: Asp117,

conact list:


AtomAtomDistance (A)
CdOD1 A:Asp1124.84
CdO A:Ile1134.84
CdCB A:Asp1174.76
CdOD2 A:Asp1173.68
CdOD1 A:Asp1174.77
CdCG A:Asp1174.19

interactive model:




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