Chemical elements
  Nickel
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    PDB 1a5n-1g2a
    PDB 1g3v-1mn0
    PDB 1mro-1s9b
    PDB 1scr-1xmk
    PDB 1xu1-2cg5
    PDB 2cqz-2jih
    PDB 2jk8-2v4b
    PDB 2vbq-3c2q
    PDB 3c6c-3h85
    PDB 3hdp-3kvb
    PDB 3l1m-3o00
    PDB 3o01-4ubp
    PDB 8icl-9ant
      8icl
      9ant

Nickel in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Seven Base Pairs Of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) (pdb 8icl)






The binding sites of Nickel atom in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Seven Base Pairs Of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) (pdb code 8icl). This binding sites where shown with 5.0 Angstroms radius around Nickel atom.
The 8icl structure was solved by H.PELLETIER, M.R.SAWAYA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-3.1
Space groupP21212
a (A)178.721
b (A)57.784
c (A)48.382
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)16.4
Rfree (%)n/a


Nickel Binding Sites:

Nickel binding site 1 out of 2 in 8icl


Nickel binding site 1 out of 2 in 8icl
Click to enlarge
stereopicture of Nickel binding site 1 out of 2 in 8icl
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 8icl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp190, A: Asp192, A: Ni340, A: Dtp338, A: Hoh502, A: Hoh658,

conact list:


AtomAtomDistance (A)
NiO A:Asp1903.46
NiN A:Asp1904.30
NiCB A:Asp1904.68
NiOD2 A:Asp1904.38
NiC A:Asp1904.36
NiOD1 A:Asp1902.60
NiCG A:Asp1903.63
NiCA A:Asp1904.64
NiOD2 A:Asp1923.39
NiCG A:Asp1924.73
NiNI A:Ni3403.23
NiO1B A:Dtp3384.95
NiPG A:Dtp3383.16
NiPB A:Dtp3383.47
NiO3B A:Dtp3383.33
NiO2G A:Dtp3384.63
NiPA A:Dtp3382.79
NiO5' A:Dtp3383.74
NiO2B A:Dtp3383.05
NiO3G A:Dtp3383.10
NiO1G A:Dtp3382.47
NiO3A A:Dtp3383.37
NiO1A A:Dtp3381.36
NiO2A A:Dtp3383.81
NiO A:Hoh5024.59
NiO A:Hoh6583.41

interactive model:


Nickel binding site 2 out of 2 in 8icl


Nickel binding site 2 out of 2 in 8icl
Click to enlarge
stereopicture of Nickel binding site 2 out of 2 in 8icl
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 8icl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: P: Dg7, A: Asp190, A: Asp192, A: Asp256, A: Ni339, A: Dtp338, A: Hoh658,

conact list:


AtomAtomDistance (A)
NiC3' P:Dg73.28
NiO3' P:Dg72.23
NiC5' P:Dg74.49
NiC2' P:Dg74.59
NiC4' P:Dg73.96
NiO5' P:Dg74.70
NiO A:Asp1904.97
NiCB A:Asp1904.69
NiOD2 A:Asp1902.87
NiOD1 A:Asp1903.09
NiCG A:Asp1903.28
NiOD2 A:Asp1923.02
NiOD1 A:Asp1923.72
NiCG A:Asp1923.75
NiOD2 A:Asp2564.34
NiNI A:Ni3393.23
NiPA A:Dtp3383.69
NiO5' A:Dtp3384.19
NiO1A A:Dtp3382.90
NiO2A A:Dtp3383.80
NiO A:Hoh6583.49

interactive model:




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