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
    PDB 3p5w-8ice
      3p5w
      3p5x
      3pk1
      3r52
      3r7c
      3sd6
      3stl
      3swb
      3tje
      3u90
      3uk8
      3vg3
      3vg4
      488d
      4aps
      4de6
      4dki
      4dzi
      4evc
      4evd
      4fdw
      4fmk
      4fvf
      4fvg
      4mt2
      7icf
      7icu
      8ice

Cadmium in the structure of Crystal Structure of A Leucine Rich Hypothetical Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 At 2.05 A Resolution (pdb 4fdw)






The binding sites of Cadmium atom in the structure of Crystal Structure of A Leucine Rich Hypothetical Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 At 2.05 A Resolution (pdb code 4fdw). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 4fdw structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)45.8-2.0
Space groupP21212
a (A)79.140
b (A)112.320
c (A)55.990
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18.1
Rfree (%)22


Cadmium Binding Sites:

Cadmium binding site 1 out of 15 in 4fdw


Cadmium binding site 1 out of 15 in 4fdw
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stereopicture of Cadmium binding site 1 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 4fdw. 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: Asp82, A: Hoh609, A: Hoh615, A: Hoh781, A: Hoh801,

conact list:


AtomAtomDistance (A)
CdOE2 A:Glu514.57
CdO A:Asp824.84
CdCB A:Asp824.20
CdOD2 A:Asp822.36
CdOD1 A:Asp822.36
CdCG A:Asp822.68
CdO A:Hoh6092.14
CdO A:Hoh6152.11
CdO A:Hoh7812.54
CdO A:Hoh8014.00

interactive model:


Cadmium binding site 2 out of 15 in 4fdw


Cadmium binding site 2 out of 15 in 4fdw
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stereopicture of Cadmium binding site 2 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 4fdw. 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: Asp52, A: Lys119, A: Hoh676, A: Hoh693, A: Hoh797, A: Hoh851, A: Hoh852,

conact list:


AtomAtomDistance (A)
CdCB A:Asp524.63
CdOD2 A:Asp522.33
CdOD1 A:Asp523.38
CdCG A:Asp523.21
CdCE A:Lys1194.26
CdNZ A:Lys1193.59
CdO A:Hoh6762.42
CdO A:Hoh6934.29
CdO A:Hoh7974.48
CdO A:Hoh8514.45
CdO A:Hoh8524.95

interactive model:


Cadmium binding site 3 out of 15 in 4fdw


Cadmium binding site 3 out of 15 in 4fdw
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stereopicture of Cadmium binding site 3 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 4fdw. 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: Ser54, A: Glu56, A: Cd511, A: Hoh601, A: Hoh721,

conact list:


AtomAtomDistance (A)
CdCB A:Ser544.84
CdOG A:Ser543.82
CdOE1 A:Glu562.47
CdOE2 A:Glu562.56
CdCD A:Glu562.85
CdCG A:Glu564.36
CdCA A:Glu564.95
CdCD A:Cd5114.06
CdO A:Hoh6012.02
CdO A:Hoh7214.03

interactive model:


Cadmium binding site 4 out of 15 in 4fdw


Cadmium binding site 4 out of 15 in 4fdw
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stereopicture of Cadmium binding site 4 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 4fdw. 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: Gln343, A: Gly344, A: Ser367, A: Ala368, A: Asn370, A: Asn371, A: Cd514, A: Cl518, A: Hoh603, A: Hoh605, A: Hoh706, A: Hoh735,

conact list:


AtomAtomDistance (A)
CdCG A:Gln3434.90
CdN A:Gly3444.28
CdCA A:Gly3444.15
CdO A:Ser3672.43
CdCB A:Ser3673.01
CdCB A:Ser3673.08
CdOG A:Ser3673.35
CdOG A:Ser3672.38
CdC A:Ser3673.27
CdCA A:Ser3673.63
CdCA A:Ser3673.59
CdN A:Ala3684.45
CdC A:Ala3684.85
CdN A:Asn3704.49
CdCB A:Asn3704.68
CdND2 A:Asn3703.94
CdOD1 A:Asn3702.29
CdCG A:Asn3703.42
CdCA A:Asn3704.96
CdN A:Asn3714.31
CdCB A:Asn3714.51
CdCD A:Cd5143.89
CdCL A:Cl5182.55
CdO A:Hoh6032.42
CdO A:Hoh6052.65
CdO A:Hoh7064.49
CdO A:Hoh7354.41

interactive model:


Cadmium binding site 5 out of 15 in 4fdw


Cadmium binding site 5 out of 15 in 4fdw
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stereopicture of Cadmium binding site 5 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 4fdw. 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: Glu315, A: Cd506, A: Hoh677, A: Hoh700, A: Hoh772,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu3152.45
CdCB A:Glu3154.80
CdOE2 A:Glu3152.29
CdCD A:Glu3152.69
CdCG A:Glu3154.20
CdCD A:Cd5064.53
CdO A:Hoh6774.76
CdO A:Hoh7002.63
CdO A:Hoh7724.63

interactive model:


Cadmium binding site 6 out of 15 in 4fdw


Cadmium binding site 6 out of 15 in 4fdw
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stereopicture of Cadmium binding site 6 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 4fdw. 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: Asp313, A: Glu315, A: Cd505, A: Hoh604, A: Hoh700, A: Hoh772, A: Hoh785,

conact list:


AtomAtomDistance (A)
CdCB A:Asp3134.44
CdOD2 A:Asp3132.74
CdOD1 A:Asp3132.44
CdCG A:Asp3132.93
CdN A:Glu3154.83
CdOE1 A:Glu3152.41
CdCB A:Glu3154.00
CdOE2 A:Glu3154.55
CdCD A:Glu3153.40
CdCG A:Glu3153.69
CdCD A:Cd5054.53
CdO A:Hoh6042.51
CdO A:Hoh7004.89
CdO A:Hoh7723.11
CdO A:Hoh7854.40

interactive model:


Cadmium binding site 7 out of 15 in 4fdw


Cadmium binding site 7 out of 15 in 4fdw
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stereopicture of Cadmium binding site 7 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 4fdw. 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: Glu336, A: Pro358, A: Ala359, A: Glu380, A: Cd508, A: Hoh660, A: Hoh668, A: Hoh686, A: Hoh795,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu3362.56
CdOE2 A:Glu3362.30
CdCD A:Glu3362.76
CdCG A:Glu3364.26
CdCB A:Pro3584.18
CdCG A:Pro3584.93
CdCA A:Pro3584.29
CdN A:Ala3594.64
CdOE1 A:Glu3802.57
CdOE2 A:Glu3804.45
CdCD A:Glu3803.80
CdCG A:Glu3804.89
CdCD A:Cd5083.71
CdO A:Hoh6604.64
CdO A:Hoh6682.19
CdO A:Hoh6862.13
CdO A:Hoh7954.78

interactive model:


Cadmium binding site 8 out of 15 in 4fdw


Cadmium binding site 8 out of 15 in 4fdw
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stereopicture of Cadmium binding site 8 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 4fdw. 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: Lys378, A: Glu380, A: Cd507, A: Hoh668, A: Hoh686, A: Hoh800,

conact list:


AtomAtomDistance (A)
CdNZ A:Lys3784.00
CdOE1 A:Glu3802.91
CdOE2 A:Glu3802.36
CdCD A:Glu3802.96
CdCG A:Glu3804.43
CdCD A:Cd5073.71
CdO A:Hoh6683.99
CdO A:Hoh6864.68
CdO A:Hoh8003.46

interactive model:


Cadmium binding site 9 out of 15 in 4fdw


Cadmium binding site 9 out of 15 in 4fdw
Click to enlarge
stereopicture of Cadmium binding site 9 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 4fdw. 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: Asp178, A: Lys199, A: Glu200, A: Hoh650, A: Hoh687, A: Hoh719, A: Hoh779,

conact list:


AtomAtomDistance (A)
CdCB A:Asp1784.24
CdOD2 A:Asp1782.16
CdOD1 A:Asp1782.69
CdCG A:Asp1782.76
CdCB A:Lys1994.53
CdCD A:Lys1994.75
CdCG A:Lys1994.92
CdN A:Glu2004.80
CdOE1 A:Glu2004.65
CdOE1 A:Glu2004.73
CdCD A:Glu2004.81
CdCD A:Glu2005.00
CdCG A:Glu2004.51
CdO A:Hoh6502.18
CdO A:Hoh6872.53
CdO A:Hoh7192.23
CdO A:Hoh7792.66

interactive model:


Cadmium binding site 10 out of 15 in 4fdw


Cadmium binding site 10 out of 15 in 4fdw
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stereopicture of Cadmium binding site 10 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 4fdw. 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: Glu233, A: Lys256, A: Hoh812,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu2332.57
CdOE2 A:Glu2332.85
CdCD A:Glu2333.04
CdCG A:Glu2334.50
CdCE A:Lys2564.60
CdNZ A:Lys2564.33
CdO A:Hoh8123.27

interactive model:


Cadmium binding site 11 out of 15 in 4fdw


Cadmium binding site 11 out of 15 in 4fdw
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stereopicture of Cadmium binding site 11 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 4fdw. 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: Ser54, A: Ile55, A: Glu56, A: Cd503, A: Hoh601, A: Hoh634, A: Hoh693, A: Hoh721, A: Hoh816,

conact list:


AtomAtomDistance (A)
CdCB A:Ser543.44
CdOG A:Ser542.18
CdC A:Ser544.56
CdCA A:Ser544.10
CdO A:Ile554.34
CdN A:Ile554.31
CdC A:Ile554.82
CdOE2 A:Glu564.14
CdCD A:Cd5034.06
CdO A:Hoh6012.59
CdO A:Hoh6343.02
CdO A:Hoh6932.66
CdO A:Hoh7212.59
CdO A:Hoh8163.05

interactive model:


Cadmium binding site 12 out of 15 in 4fdw


Cadmium binding site 12 out of 15 in 4fdw
Click to enlarge
stereopicture of Cadmium binding site 12 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 4fdw. 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: Lys166, A: Glu188,

conact list:


AtomAtomDistance (A)
CdNZ A:Lys1664.79
CdOE1 A:Glu1882.51
CdOE2 A:Glu1883.39
CdCD A:Glu1883.30
CdCG A:Glu1884.70

interactive model:


Cadmium binding site 13 out of 15 in 4fdw


Cadmium binding site 13 out of 15 in 4fdw
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stereopicture of Cadmium binding site 13 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cadmium in the PDB 4fdw. 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: Asp106, A: His124, A: Glu144, A: Cl516, A: Cl517, A: Hoh683, A: Hoh827, A: Hoh853,

conact list:


AtomAtomDistance (A)
CdCB A:Asp1064.62
CdOD2 A:Asp1063.45
CdOD1 A:Asp1062.44
CdCG A:Asp1063.27
CdCE1 A:His1244.57
CdO A:Glu1444.17
CdCL A:Cl5164.37
CdCL A:Cl5173.69
CdO A:Hoh6832.64
CdO A:Hoh8273.59
CdO A:Hoh8532.92

interactive model:


Cadmium binding site 14 out of 15 in 4fdw


Cadmium binding site 14 out of 15 in 4fdw
Click to enlarge
stereopicture of Cadmium binding site 14 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Cadmium in the PDB 4fdw. 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: Tyr321, A: Gln343, A: Ser367, A: Cd504, A: Hoh603, A: Hoh605, A: Hoh706, A: Hoh735, A: Hoh755,

conact list:


AtomAtomDistance (A)
CdOH A:Tyr3214.81
CdNE2 A:Gln3434.32
CdCB A:Ser3674.96
CdCB A:Ser3674.87
CdOG A:Ser3674.44
CdOG A:Ser3674.13
CdCD A:Cd5043.89
CdO A:Hoh6032.86
CdO A:Hoh6053.06
CdO A:Hoh7064.20
CdO A:Hoh7352.45
CdO A:Hoh7554.84

interactive model:


Cadmium binding site 15 out of 15 in 4fdw


Cadmium binding site 15 out of 15 in 4fdw
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stereopicture of Cadmium binding site 15 out of 15 in 4fdw
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Cadmium in the PDB 4fdw. 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: Glu410, A: Lys413, A: Asn414, A: Hoh805, A: Hoh838,

conact list:


AtomAtomDistance (A)
CdOE1 A:Glu4102.96
CdOE2 A:Glu4102.37
CdCD A:Glu4102.95
CdCG A:Glu4104.36
CdCB A:Lys4134.90
CdCD A:Lys4134.54
CdOD1 A:Asn4144.68
CdO A:Hoh8052.99
CdO A:Hoh8382.70

interactive model:




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