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 Sam-I Riboswitch From T. Tencongensis Variant A94G Bound With Sam (pdb 3iqr)






The binding sites of Barium atom in the structure of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound With Sam (pdb code 3iqr). This binding sites where shown with 5.0 Angstroms radius around Barium atom.
The 3iqr structure was solved by R.K.MONTANGE, R.T.BATEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.9-2.5
Space groupP43212
a (A)61.804
b (A)61.804
c (A)157.568
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)24.9
Rfree (%)29.3


Barium Binding Sites:

Barium binding site 1 out of 9 in 3iqr


Barium binding site 1 out of 9 in 3iqr
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stereopicture of Barium binding site 1 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 3iqr. 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: A49, A: G50, A: A52, A: Hoh440,

conact list:


AtomAtomDistance (A)
BaN7 A:A494.62
BaN9 A:G504.99
BaC8 A:G503.97
BaC6 A:G503.58
BaN1 A:G504.91
BaC5 A:G503.50
BaN7 A:G502.87
BaC4 A:G504.77
BaO6 A:G503.07
BaOP1 A:A524.13
BaP A:A524.65
BaOP2 A:A524.22
BaO A:Hoh4403.50

interactive model:


Barium binding site 2 out of 9 in 3iqr


Barium binding site 2 out of 9 in 3iqr
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stereopicture of Barium binding site 2 out of 9 in 3iqr
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 3iqr. 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: G16, A: U17, A: G18, A: G19,

conact list:


AtomAtomDistance (A)
BaOP2 A:G164.99
BaC5 A:U174.92
BaOP2 A:U174.75
BaO4 A:U174.77
BaC6 A:G183.75
BaN1 A:G184.78
BaC5 A:G184.51
BaN7 A:G184.54
BaO6 A:G182.66
BaO6 A:G194.81

interactive model:


Barium binding site 3 out of 9 in 3iqr


Barium binding site 3 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 3 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 3iqr. 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: G73, A: G74, A: A76, A: Hoh405,

conact list:


AtomAtomDistance (A)
BaN7 A:G734.88
BaC8 A:G744.25
BaC6 A:G743.37
BaN1 A:G744.64
BaC5 A:G743.54
BaN7 A:G743.11
BaC4 A:G744.80
BaO6 A:G742.72
BaOP1 A:A764.35
BaOP2 A:A764.84
BaO A:Hoh4054.23

interactive model:


Barium binding site 4 out of 9 in 3iqr


Barium binding site 4 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 4 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 3iqr. 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: C25, A: U64, A: C66, A: U67, A: G68, A: Hoh419,

conact list:


AtomAtomDistance (A)
BaN4 A:C254.57
BaC2 A:U644.11
BaN1 A:U644.73
BaC1' A:U644.32
BaO2 A:U643.06
BaC2' A:U643.66
BaO2' A:U642.87
BaOP2 A:C664.32
BaC5 A:U674.29
BaC4 A:U673.98
BaO4 A:U673.04
BaO6 A:G684.71
BaO A:Hoh4194.74

interactive model:


Barium binding site 5 out of 9 in 3iqr


Barium binding site 5 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 5 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 3iqr. 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: C31, A: G32,

conact list:


AtomAtomDistance (A)
BaOP2 A:C314.74
BaC8 A:G324.57
BaC5 A:G324.68
BaN7 A:G323.87
BaOP2 A:G324.62
BaO6 A:G324.71

interactive model:


Barium binding site 6 out of 9 in 3iqr


Barium binding site 6 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 6 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 3iqr. 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: A9, A: A10, A: G11, A: A62, A: U63, A: U64,

conact list:


AtomAtomDistance (A)
BaC3' A:A94.91
BaO3' A:A93.64
BaC8 A:A104.77
BaP A:A103.78
BaN7 A:A104.65
BaOP2 A:A102.90
BaO5' A:A104.17
BaC8 A:G115.00
BaC6 A:G114.97
BaC5 A:G114.86
BaN7 A:G114.00
BaOP2 A:G114.70
BaO6 A:G114.30
BaOP1 A:A623.93
BaC3' A:U634.27
BaO3' A:U633.43
BaC5' A:U634.69
BaC4' A:U634.11
BaOP1 A:U644.39
BaP A:U643.84
BaOP2 A:U643.20

interactive model:


Barium binding site 7 out of 9 in 3iqr


Barium binding site 7 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 7 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 3iqr. 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: A85, A: G86, A: A87,

conact list:


AtomAtomDistance (A)
BaC8 A:A854.69
BaC6 A:A854.70
BaC5 A:A854.47
BaN6 A:A854.39
BaN7 A:A853.95
BaOP2 A:A854.92
BaC8 A:G864.22
BaC6 A:G863.90
BaC5 A:G863.83
BaN7 A:G863.11
BaO6 A:G863.29
BaN6 A:A874.72

interactive model:


Barium binding site 8 out of 9 in 3iqr


Barium binding site 8 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 8 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 3iqr. 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: A45, A: A46, A: G55, A: G56,

conact list:


AtomAtomDistance (A)
BaC6 A:A454.88
BaN1 A:A454.30
BaN6 A:A454.62
BaN3 A:A464.65
BaC2 A:A463.37
BaC6 A:A464.36
BaN1 A:A463.12
BaN6 A:A464.75
BaC8 A:G554.25
BaC6 A:G554.23
BaC5 A:G554.03
BaN7 A:G553.31
BaOP2 A:G554.79
BaO6 A:G553.80
BaO6 A:G564.99

interactive model:


Barium binding site 9 out of 9 in 3iqr


Barium binding site 9 out of 9 in 3iqr
Click to enlarge
stereopicture of Barium binding site 9 out of 9 in 3iqr
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Barium in the PDB 3iqr. 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: G1, A: G2, A: Hoh402, A: Hoh403,

conact list:


AtomAtomDistance (A)
BaC8 A:G13.95
BaC6 A:G14.00
BaC5 A:G13.79
BaN7 A:G12.91
BaOP3 A:G14.54
BaO6 A:G13.48
BaO6 A:G25.00
BaO A:Hoh4024.89
BaO A:Hoh4034.22

interactive model:




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