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
    PDB 2x09-3ccj
    PDB 3ccl-3ggf
      3ccl
      3ccm
      3ccq
      3ccr
      3ccs
      3ccu
      3ccv
      3cd6
      3cel
      3cfk
      3cjk
      3cma
      3cme
      3cn6
      3cpw
      3cu7
      3cxc
      3d4c
      3die
      3dld
      3dtu
      3dze
      3eec
      3eig
      3f32
      3f33
      3f34
      3f35
      3f36
      3f37
      3f38
      3f39
      3fct
      3ffc
      3fgh
      3fi6
      3fqn
      3fqr
      3fqt
      3fqu
      3fqw
      3fqx
      3fye
      3fyi
      3g4s
      3g6e
      3g71
      3g7d
      3gbf
      3ggf
    PDB 3h1u-3p5v
    PDB 3p5w-8ice

Cadmium in the structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488C. Density For Anisomycin Is Visible But Not Included in the Model. (pdb 3ccr)






The binding sites of Cadmium atom in the structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488C. Density For Anisomycin Is Visible But Not Included in the Model. (pdb code 3ccr). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom.
The 3ccr structure was solved by G.BLAHA, G.GUREL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)49.8-3.0
Space groupC2221
a (A)212.411
b (A)299.520
c (A)574.897
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18
Rfree (%)24.7


Cadmium Binding Sites:

Cadmium binding site 1 out of 5 in 3ccr


Cadmium binding site 1 out of 5 in 3ccr
Click to enlarge
stereopicture of Cadmium binding site 1 out of 5 in 3ccr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3ccr. 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: O: Arg37, O: His40, 0: Hoh3101, O: Hoh3002, O: Hoh5322, O: Hoh5650,

conact list:


AtomAtomDistance (A)
CdCB O:Arg374.90
CdCZ O:Arg374.70
CdCG O:Arg374.66
CdNE O:Arg374.87
CdNH2 O:Arg374.92
CdNH1 O:Arg374.92
CdNE2 O:His404.88
CdCB O:His404.04
CdND1 O:His402.83
CdCD2 O:His404.96
CdCE1 O:His403.71
CdCG O:His403.83
CdO 0:Hoh31014.42
CdO O:Hoh30024.60
CdO O:Hoh53222.93
CdO O:Hoh56502.50

interactive model:


Cadmium binding site 2 out of 5 in 3ccr


Cadmium binding site 2 out of 5 in 3ccr
Click to enlarge
stereopicture of Cadmium binding site 2 out of 5 in 3ccr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3ccr. 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: U: Cys6, U: Tyr8, U: Cys9, U: His30, U: Phe31, U: Cys32, U: Ser33, U: Cys36, U: Glu37,

conact list:


AtomAtomDistance (A)
CdCB U:Cys64.53
CdSG U:Cys62.95
CdN U:Tyr84.96
CdCB U:Tyr83.91
CdCD1 U:Tyr84.36
CdCG U:Tyr84.51
CdCA U:Tyr84.85
CdN U:Cys94.17
CdCB U:Cys94.27
CdSG U:Cys93.91
CdCA U:Cys94.89
CdO U:His304.30
CdN U:Phe314.88
CdCB U:Phe314.11
CdCE2 U:Phe314.58
CdCD2 U:Phe313.65
CdC U:Phe314.32
CdCG U:Phe314.31
CdCA U:Phe313.77
CdN U:Cys323.88
CdSG U:Cys324.72
CdCA U:Cys324.98
CdO U:Ser334.65
CdN U:Ser334.81
CdO U:Cys364.72
CdCB U:Cys362.96
CdSG U:Cys363.89
CdC U:Cys364.27
CdCA U:Cys364.20
CdN U:Glu374.43

interactive model:


Cadmium binding site 3 out of 5 in 3ccr


Cadmium binding site 3 out of 5 in 3ccr
Click to enlarge
stereopicture of Cadmium binding site 3 out of 5 in 3ccr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3ccr. 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: Z: Cys63, Z: Asn65, Z: Cys66, Z: Cys81, Z: Tyr83, Z: Cys84, Z: Asp85, Z: Tyr86,

conact list:


AtomAtomDistance (A)
CdCB Z:Cys634.71
CdSG Z:Cys633.96
CdCB Z:Asn654.12
CdND2 Z:Asn654.63
CdCG Z:Asn654.96
CdN Z:Cys664.71
CdCB Z:Cys664.50
CdSG Z:Cys664.15
CdO Z:Cys813.88
CdCB Z:Cys813.42
CdSG Z:Cys813.75
CdC Z:Cys814.27
CdCA Z:Cys814.44
CdN Z:Tyr834.32
CdCB Z:Tyr833.84
CdCD2 Z:Tyr834.36
CdC Z:Tyr834.15
CdCG Z:Tyr834.62
CdCA Z:Tyr834.29
CdO Z:Cys844.56
CdN Z:Cys843.11
CdCB Z:Cys843.86
CdSG Z:Cys843.02
CdC Z:Cys843.78
CdCA Z:Cys843.73
CdO Z:Asp854.95
CdN Z:Asp853.58
CdC Z:Asp854.21
CdCA Z:Asp854.36
CdN Z:Tyr863.81
CdCB Z:Tyr863.69
CdCG Z:Tyr864.95
CdCA Z:Tyr864.37

interactive model:


Cadmium binding site 4 out of 5 in 3ccr


Cadmium binding site 4 out of 5 in 3ccr
Click to enlarge
stereopicture of Cadmium binding site 4 out of 5 in 3ccr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3ccr. 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: 1: Cys19, 1: Arg21, 1: Cys22, 1: Gly23, 1: Glu24, 1: Cys34, 1: Ser36, 1: Cys37, 1: Gly38, 1: Phe39,

conact list:


AtomAtomDistance (A)
CdCB 1:Cys193.11
CdSG 1:Cys192.58
CdCA 1:Cys194.60
CdCB 1:Arg214.60
CdCD 1:Arg214.98
CdC 1:Arg214.79
CdN 1:Cys223.72
CdCB 1:Cys223.30
CdSG 1:Cys222.22
CdC 1:Cys224.91
CdCA 1:Cys224.10
CdN 1:Gly234.97
CdO 1:Glu244.97
CdCB 1:Cys343.10
CdSG 1:Cys342.44
CdCA 1:Cys344.57
CdCB 1:Ser364.81
CdC 1:Ser364.83
CdN 1:Cys373.70
CdCB 1:Cys373.30
CdSG 1:Cys372.37
CdC 1:Cys374.61
CdCA 1:Cys373.99
CdN 1:Gly384.84
CdN 1:Phe394.73
CdCB 1:Phe394.07

interactive model:


Cadmium binding site 5 out of 5 in 3ccr


Cadmium binding site 5 out of 5 in 3ccr
Click to enlarge
stereopicture of Cadmium binding site 5 out of 5 in 3ccr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3ccr. 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: 3: Cys11, 3: Cys14, 3: Glu16, 3: His17, 3: Gln18, 3: Cys71, 3: Cys74, 3: Hoh9063,

conact list:


AtomAtomDistance (A)
CdO 3:Cys114.32
CdN 3:Cys114.47
CdCB 3:Cys113.17
CdSG 3:Cys114.10
CdC 3:Cys114.79
CdCA 3:Cys114.32
CdCB 3:Cys143.26
CdSG 3:Cys143.71
CdCA 3:Cys144.64
CdO 3:Glu164.21
CdC 3:Glu164.65
CdCG 3:Glu164.54
CdC 3:His174.90
CdNE2 3:Gln183.90
CdN 3:Gln184.42
CdCB 3:Gln184.05
CdCD 3:Gln184.58
CdCG 3:Gln184.51
CdCA 3:Gln184.82
CdCB 3:Cys713.95
CdSG 3:Cys713.26
CdSG 3:Cys744.97
CdO 3:Hoh90634.77

interactive model:




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