Chemical elements
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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 Containing the T. Solenopsae Kt-23 in Complex With S-Adenosyl Methionine (pdb 4aob)






The binding sites of Barium atom in the structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex With S-Adenosyl Methionine (pdb code 4aob). This binding sites where shown with 5.0 Angstroms radius around Barium atom.
The 4aob structure was solved by K.T.SCHROEDER, P.DALDROP, S.A.MCPHEE, D.M.J.LILLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)50.0-3.0
Space groupP43212
a (A)61.300
b (A)61.300
c (A)157.538
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18.906
Rfree (%)23.943


Barium Binding Sites:

Barium binding site 1 out of 15 in 4aob


Barium binding site 1 out of 15 in 4aob
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stereopicture of Barium binding site 1 out of 15 in 4aob
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 4aob. 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:A854.38
BaC6 A:A854.68
BaC5 A:A854.31
BaN6 A:A854.53
BaN7 A:A853.77
BaOP2 A:A854.66
BaN9 A:G864.99
BaC8 A:G863.79
BaC6 A:G864.06
BaC5 A:G863.75
BaN7 A:G862.79
BaC4 A:G864.98
BaO6 A:G863.63
BaN6 A:A874.47
BaN7 A:A874.97

interactive model:


Barium binding site 2 out of 15 in 4aob


Barium binding site 2 out of 15 in 4aob
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stereopicture of Barium binding site 2 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 4aob. 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: U67, A: C69, A: A70, A: U81, A: G82, A: A83, A: Hoh2007, A: Hoh2008,

conact list:


AtomAtomDistance (A)
BaOP1 A:U674.30
BaN4 A:C694.30
BaN6 A:A704.60
BaN3 A:U814.82
BaC5 A:U814.30
BaC4 A:U813.77
BaO4 A:U812.90
BaC6 A:G824.04
BaC5 A:G824.59
BaN7 A:G824.37
BaO6 A:G822.97
BaN6 A:A834.21
BaO A:Hoh20074.68
BaO A:Hoh20084.27

interactive model:


Barium binding site 3 out of 15 in 4aob


Barium binding site 3 out of 15 in 4aob
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stereopicture of Barium binding site 3 out of 15 in 4aob
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 4aob. 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: A24, A: C25, A: U64, A: C66, A: U67, A: G68,

conact list:


AtomAtomDistance (A)
BaN6 A:A244.31
BaN7 A:A244.80
BaN4 A:C254.54
BaN3 A:U644.72
BaC2 A:U643.71
BaN1 A:U644.39
BaC1' A:U644.11
BaO2 A:U642.62
BaO3' A:U644.83
BaC2' A:U644.22
BaO2' A:U643.13
BaOP2 A:C664.45
BaC5 A:U674.42
BaC4 A:U674.14
BaO4 A:U673.20
BaO6 A:G684.81

interactive model:


Barium binding site 4 out of 15 in 4aob


Barium binding site 4 out of 15 in 4aob
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stereopicture of Barium binding site 4 out of 15 in 4aob
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 4aob. 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: G23, A: U26, A: G27, A: G28, A: C66, A: Hoh2003,

conact list:


AtomAtomDistance (A)
BaO6 A:G234.87
BaN3 A:U264.86
BaC6 A:U264.40
BaC5 A:U263.63
BaC4 A:U263.91
BaOP2 A:U264.69
BaO4 A:U263.86
BaC8 A:G274.31
BaC6 A:G273.96
BaC5 A:G273.91
BaN7 A:G273.21
BaO6 A:G273.34
BaC6 A:G284.26
BaC5 A:G284.47
BaN7 A:G284.07
BaO6 A:G283.60
BaN4 A:C664.99
BaO A:Hoh20033.63

interactive model:


Barium binding site 5 out of 15 in 4aob


Barium binding site 5 out of 15 in 4aob
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stereopicture of Barium binding site 5 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 4aob. 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: G15, A: G16, A: G17, A: Hoh2002,

conact list:


AtomAtomDistance (A)
BaC8 A:G154.83
BaC6 A:G153.98
BaN1 A:G154.78
BaC5 A:G154.08
BaN7 A:G154.08
BaC4 A:G154.91
BaO6 A:G153.83
BaC8 A:G164.22
BaC6 A:G163.68
BaC5 A:G163.70
BaN7 A:G163.05
BaO6 A:G163.02
BaN7 A:G174.71
BaO6 A:G174.58
BaO A:Hoh20024.99

interactive model:


Barium binding site 6 out of 15 in 4aob


Barium binding site 6 out of 15 in 4aob
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stereopicture of Barium binding site 6 out of 15 in 4aob
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 4aob. 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: G13, A: C60, A: A61,

conact list:


AtomAtomDistance (A)
BaC8 A:G134.25
BaC6 A:G134.25
BaC5 A:G134.07
BaN7 A:G133.24
BaOP2 A:G134.95
BaO6 A:G133.72
BaO2 A:C604.60
BaC2' A:C604.53
BaO2' A:C604.34
BaOP2 A:A614.05

interactive model:


Barium binding site 7 out of 15 in 4aob


Barium binding site 7 out of 15 in 4aob
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stereopicture of Barium binding site 7 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 4aob. 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: K1108, A: Ba1121, A: Hoh2010,

conact list:


AtomAtomDistance (A)
BaC8 A:G13.89
BaC6 A:G14.23
BaC5 A:G13.90
BaN7 A:G12.95
BaO6 A:G13.81
BaK A:K11084.96
BaBA A:Ba11214.51
BaO A:Hoh20104.64

interactive model:


Barium binding site 8 out of 15 in 4aob


Barium binding site 8 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 8 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 4aob. 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: U54, A: G55,

conact list:


AtomAtomDistance (A)
BaN1 A:A454.55
BaN6 A:A454.71
BaN3 A:A464.75
BaC2 A:A463.42
BaC6 A:A464.12
BaN1 A:A462.95
BaN6 A:A464.39
BaC5 A:U544.65
BaC4 A:U544.57
BaO4 A:U544.55
BaC8 A:G553.95
BaC6 A:G554.76
BaC5 A:G554.29
BaN7 A:G553.20
BaOP2 A:G554.15
BaO6 A:G554.45

interactive model:


Barium binding site 9 out of 15 in 4aob


Barium binding site 9 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 9 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Barium in the PDB 4aob. 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: G74, A: Ba1104,

conact list:


AtomAtomDistance (A)
BaC6 A:G743.88
BaN1 A:G744.36
BaO6 A:G742.81
BaBA A:Ba11044.58

interactive model:


Barium binding site 10 out of 15 in 4aob


Barium binding site 10 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 10 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Barium in the PDB 4aob. 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: Ba1103,

conact list:


AtomAtomDistance (A)
BaN7 A:G734.91
BaOP2 A:G734.95
BaC8 A:G744.04
BaC6 A:G743.95
BaC5 A:G743.77
BaN7 A:G743.10
BaC4 A:G744.89
BaO6 A:G743.58
BaOP2 A:A764.54
BaBA A:Ba11034.58

interactive model:


Barium binding site 11 out of 15 in 4aob


Barium binding site 11 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 11 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Barium in the PDB 4aob. 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: A50, A: A52, A: Ba1106,

conact list:


AtomAtomDistance (A)
BaC5 A:A494.99
BaN6 A:A494.87
BaN7 A:A494.40
BaN9 A:A504.65
BaC8 A:A503.38
BaC6 A:A504.28
BaC5 A:A503.69
BaN6 A:A503.99
BaN7 A:A502.56
BaC4 A:A504.80
BaOP1 A:A523.44
BaP A:A524.75
BaBA A:Ba11064.82

interactive model:


Barium binding site 12 out of 15 in 4aob


Barium binding site 12 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 12 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Barium in the PDB 4aob. 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: A50, A: A52, A: Ba1105,

conact list:


AtomAtomDistance (A)
BaN6 A:A494.94
BaC6 A:A503.61
BaN1 A:A504.25
BaC5 A:A504.65
BaN6 A:A502.39
BaOP1 A:A523.92
BaC5' A:A524.70
BaBA A:Ba11054.82

interactive model:


Barium binding site 13 out of 15 in 4aob


Barium binding site 13 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 13 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Barium in the PDB 4aob. 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: C8, A: A10, A: G11, A: U64, A: K1112, A: Sam1116, A: Hoh2006,

conact list:


AtomAtomDistance (A)
BaO2' A:C84.53
BaC6 A:A104.99
BaC5 A:A104.96
BaN6 A:A104.17
BaN7 A:A104.23
BaC6 A:G113.94
BaN1 A:G114.82
BaC5 A:G114.89
BaO6 A:G112.74
BaOP1 A:U643.09
BaP A:U643.87
BaOP2 A:U644.04
BaC5' A:U644.77
BaO5' A:U644.27
BaK A:K11123.72
BaOXT A:Sam11164.59
BaO A:Hoh20064.98

interactive model:


Barium binding site 14 out of 15 in 4aob


Barium binding site 14 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 14 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Barium in the PDB 4aob. 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: A33, A: Hoh2009,

conact list:


AtomAtomDistance (A)
BaOP2 A:A334.24
BaO A:Hoh20093.14

interactive model:


Barium binding site 15 out of 15 in 4aob


Barium binding site 15 out of 15 in 4aob
Click to enlarge
stereopicture of Barium binding site 15 out of 15 in 4aob
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Barium in the PDB 4aob. 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: Ba1101, A: Hoh2010,

conact list:


AtomAtomDistance (A)
BaP A:G14.23
BaN7 A:G14.97
BaOP2 A:G12.82
BaO5' A:G14.74
BaBA A:Ba11014.51
BaO A:Hoh20103.14

interactive model:




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