Chemical elements
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    PDB 131d-1bli
    PDB 1bph-1d10
    PDB 1d11-1ej2
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    PDB 3v72-4ag2
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    PDB 4ecn-4g8t
    PDB 4gdt-8icw
      4gdt
      4gdu
      4gdv
      4gdw
      4gib
      4mat
      4mt2
      4znb
      7gep
      7ice
      7icf
      7icg
      7ich
      7ici
      7icj
      7ick
      7icl
      7icm
      7icn
      7ico
      7icp
      7icq
      7icr
      7ics
      7ict
      7icu
      7icv
      7kme
      8ica
      8icb
      8icc
      8ice
      8icf
      8icg
      8ich
      8ici
      8icj
      8ick
      8icl
      8icm
      8icn
      8ico
      8icp
      8icq
      8icr
      8ics
      8ict
      8icu
      8icv
      8icw
    PDB 8icx-9icy

Sodium in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of MGCL2 (pdb 7ick)






The binding sites of Sodium atom in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of MGCL2 (pdb code 7ick). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 7ick 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)20.0-2.9
Space groupP21212
a (A)178.561
b (A)57.740
c (A)48.469
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)15.2
Rfree (%)n/a


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 7ick


Sodium binding site 1 out of 2 in 7ick
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 7ick
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 7ick. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: P: Dt5, P: Dg6, A: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, A: Hoh601,

conact list:


AtomAtomDistance (A)
NaO3' P:Dt54.72
NaOP1 P:Dg62.35
NaP P:Dg63.54
NaOP2 P:Dg63.86
NaO5' P:Dg64.50
NaO A:Leu1004.89
NaO A:Thr1012.27
NaCG2 A:Thr1014.86
NaC A:Thr1013.36
NaCA A:Thr1014.20
NaO A:Arg1024.24
NaN A:Arg1024.26
NaC A:Arg1023.90
NaCA A:Arg1024.32
NaO A:Val1032.41
NaN A:Val1033.81
NaC A:Val1033.19
NaCA A:Val1034.12
NaN A:Ser1043.86
NaC A:Ser1044.29
NaCA A:Ser1043.93
NaN A:Gly1053.93
NaC A:Gly1054.72
NaCA A:Gly1054.95
NaO A:Ile1062.49
NaN A:Ile1063.78
NaCB A:Ile1064.65
NaC A:Ile1063.57
NaCA A:Ile1064.20
NaN A:Gly1074.62
NaCA A:Gly1074.92
NaO A:Hoh6013.30

interactive model:


Sodium binding site 2 out of 2 in 7ick


Sodium binding site 2 out of 2 in 7ick
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 7ick
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 7ick. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: P: Dg3, P: Hoh615,

conact list:


AtomAtomDistance (A)
NaOP1 P:Dg33.50
NaP P:Dg34.24
NaOP2 P:Dg34.04
NaO P:Hoh6154.50

interactive model:




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