Chemical elements
  Barium
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    Detection of Barrium
    PDB 1djh-3iqp
    PDB 3iqr-4e7y
      3iqr
      3lr4
      3nkv
      3ns4
      3oxj
      3p4b
      3s80
      3u38
      3v61
      3vg5
      3vg6
      439d
      4aeb
      4aob
      4e1u
      4e7y

Barium in the structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna (pdb 4e1u)






The binding sites of Barium atom in the structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna (pdb code 4e1u). This binding sites where shown with 5.0 Angstroms radius around Barium atom.
The 4e1u structure was solved by H.SONG, J.T.KAISER, J.K.BARTON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)23.3-0.9
Space groupP1
a (A)24.039
b (A)24.797
c (A)37.521
alpha (°)74.67
beta (°)84.42
gamma (°)76.21
Rfactor (%)14
Rfree (%)14.9


Barium Binding Sites:

Barium binding site 1 out of 2 in 4e1u


Barium binding site 1 out of 2 in 4e1u
Click to enlarge
stereopicture of Barium binding site 1 out of 2 in 4e1u
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 4e1u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Dg2, A: Dg3, B: Dc10, B: Dc11, A: R1z101, A: Hoh209, A: Hoh244, B: Hoh1085, B: Hoh1102,

conact list:


AtomAtomDistance (A)
BaN9 A:Dg24.89
BaC8 A:Dg23.92
BaC6 A:Dg23.44
BaC5 A:Dg23.41
BaC4 A:Dg24.64
BaH8 A:Dg24.25
BaN1 A:Dg24.78
BaN7 A:Dg22.83
BaO6 A:Dg22.93
BaC6 A:Dg33.73
BaC6 A:Dg34.04
BaC5 A:Dg34.41
BaC5 A:Dg34.64
BaH1 A:Dg34.75
BaN1 A:Dg34.73
BaN1 A:Dg34.99
BaN7 A:Dg34.44
BaN7 A:Dg34.66
BaO6 A:Dg32.78
BaO6 A:Dg33.20
BaH42 B:Dc103.80
BaH41 B:Dc104.64
BaN4 B:Dc104.44
BaH42 B:Dc114.27
BaH91 A:R1z1014.81
BaH101 A:R1z1014.87
BaO A:Hoh2093.12
BaO A:Hoh2442.67
BaO B:Hoh10853.02
BaO B:Hoh11022.81

interactive model:


Barium binding site 2 out of 2 in 4e1u


Barium binding site 2 out of 2 in 4e1u
Click to enlarge
stereopicture of Barium binding site 2 out of 2 in 4e1u
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 4e1u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Dc11, B: Dg2, B: Dg3, A: R1z105, B: Hoh1003, B: Hoh1004, B: Hoh1010, B: Hoh1024, B: Hoh1033, B: Hoh1054,

conact list:


AtomAtomDistance (A)
BaH42 A:Dc114.48
BaC8 B:Dg24.32
BaC8 B:Dg24.17
BaC6 B:Dg23.79
BaC6 B:Dg23.62
BaC5 B:Dg23.80
BaC5 B:Dg23.62
BaC4 B:Dg24.96
BaH8 B:Dg24.61
BaH8 B:Dg24.49
BaN1 B:Dg24.98
BaN7 B:Dg23.17
BaN7 B:Dg23.00
BaOP2 B:Dg24.91
BaOP2 B:Dg24.75
BaO6 B:Dg23.12
BaO6 B:Dg22.98
BaO6 B:Dg34.88
BaO6 B:Dg34.45
BaH131 A:R1z1054.61
BaH101 A:R1z1054.30
BaO B:Hoh10034.56
BaO B:Hoh10042.90
BaO B:Hoh10104.87
BaO B:Hoh10242.54
BaO B:Hoh10333.13
BaO B:Hoh10542.49

interactive model:




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