Chemical elements
  Manganese
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    PDB 117e-1cs0
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    PDB 2dvd-2g38
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    PDB 2iie-2mnr
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    PDB 3py5-3tmy
    PDB 3twz-4e5f
    PDB 4e5g-8icv
    PDB 8icw-9xim
      8icw
      8icx
      8icy
      8prk
      8xia
      9ica
      9icl
      9icq
      9icr
      9ics
      9ict
      9icu
      9xia
      9xim

Manganese in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs Of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb 9icq)






The binding sites of Manganese atom in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs Of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 9icq). This binding sites where shown with 5.0 Angstroms radius around Manganese atom.
The 9icq 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)178.676
b (A)57.705
c (A)48.482
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)16.5
Rfree (%)n/a


Manganese Binding Sites:

Manganese binding site 1 out of 2 in 9icq


Manganese binding site 1 out of 2 in 9icq
Click to enlarge
stereopicture of Manganese binding site 1 out of 2 in 9icq
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 9icq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gly179, A: Ser188, A: Gly189, A: Asp190, A: Asp192, A: Dtp338, A: Hoh502, A: Hoh660,

conact list:


AtomAtomDistance (A)
MnCA A:Gly1794.77
MnCB A:Ser1884.99
MnN A:Gly1894.73
MnC A:Gly1894.90
MnCA A:Gly1894.97
MnO A:Asp1903.53
MnN A:Asp1903.95
MnCB A:Asp1904.47
MnOD2 A:Asp1903.85
MnC A:Asp1904.33
MnOD1 A:Asp1902.74
MnCG A:Asp1903.38
MnCA A:Asp1904.49
MnCB A:Asp1924.89
MnOD2 A:Asp1922.94
MnCG A:Asp1924.21
MnO1B A:Dtp3384.76
MnPG A:Dtp3383.17
MnPB A:Dtp3383.28
MnO3B A:Dtp3383.33
MnO2G A:Dtp3384.65
MnPA A:Dtp3383.09
MnO5' A:Dtp3383.82
MnO2B A:Dtp3382.75
MnO3G A:Dtp3382.87
MnO1G A:Dtp3382.70
MnO3A A:Dtp3383.19
MnO1A A:Dtp3382.01
MnO2A A:Dtp3384.37
MnO A:Hoh5023.99
MnO A:Hoh6604.79

interactive model:


Manganese binding site 2 out of 2 in 9icq


Manganese binding site 2 out of 2 in 9icq
Click to enlarge
stereopicture of Manganese binding site 2 out of 2 in 9icq
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 9icq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp190, A: Asp192, A: Arg254, A: Asp256, A: Dtp338, A: Hoh660,

conact list:


AtomAtomDistance (A)
MnCB A:Asp1903.75
MnOD2 A:Asp1903.70
MnOD1 A:Asp1903.17
MnCG A:Asp1903.30
MnOD2 A:Asp1924.70
MnOD1 A:Asp1924.01
MnCG A:Asp1924.66
MnCZ A:Arg2544.58
MnNH2 A:Arg2543.98
MnCB A:Asp2564.56
MnOD2 A:Asp2562.95
MnOD1 A:Asp2563.65
MnCG A:Asp2563.48
MnO1A A:Dtp3384.87
MnO A:Hoh6603.40

interactive model:




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