Chemical elements
  Barium
    Isotopes
    Energy
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    Physical Properties
    Chemical Properties
    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 Crystal Structure of Glycine Riboswitch, Soaked in BA2+ (pdb 3oxj)






The binding sites of Barium atom in the structure of Crystal Structure of Glycine Riboswitch, Soaked in BA2+ (pdb code 3oxj). This binding sites where shown with 5.0 Angstroms radius around Barium atom.
The 3oxj structure was solved by L.HUANG, A.SERGANOV, D.J.PATEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-3.2
Space groupP3221
a (A)84.215
b (A)84.215
c (A)201.382
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)19.4
Rfree (%)22.4


Barium Binding Sites:

Barium binding site 1 out of 24 in 3oxj


Barium binding site 1 out of 24 in 3oxj
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stereopicture of Barium binding site 1 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 3oxj. 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: Gdp1,

conact list:


AtomAtomDistance (A)
BaC8 A:Gdp14.61
BaC6 A:Gdp14.12
BaC5 A:Gdp14.12
BaN7 A:Gdp13.50
BaO6 A:Gdp13.32

interactive model:


Barium binding site 2 out of 24 in 3oxj


Barium binding site 2 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 2 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 3oxj. 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: G8, A: A78, A: G79, A: G80, A: Ba203, A: Ba204, A: Ba222,

conact list:


AtomAtomDistance (A)
BaC6 A:G84.64
BaC5 A:G84.97
BaN7 A:G84.70
BaO6 A:G83.88
BaOP2 A:A784.71
BaN7 A:G794.38
BaOP2 A:G794.36
BaO6 A:G794.88
BaC6 A:G803.67
BaN1 A:G804.76
BaC5 A:G804.34
BaN7 A:G804.28
BaO6 A:G802.58
BaBA A:Ba2034.29
BaBA A:Ba2044.00
BaBA A:Ba2222.25

interactive model:


Barium binding site 3 out of 24 in 3oxj


Barium binding site 3 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 3 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 3oxj. 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: U6, A: G8, A: G80, A: Ba202, A: Ba222,

conact list:


AtomAtomDistance (A)
BaO4 A:U64.53
BaC6 A:G83.86
BaN1 A:G84.42
BaO6 A:G82.70
BaN7 A:G804.55
BaBA A:Ba2024.29
BaBA A:Ba2224.10

interactive model:


Barium binding site 4 out of 24 in 3oxj


Barium binding site 4 out of 24 in 3oxj
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stereopicture of Barium binding site 4 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 3oxj. 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: A77, A: A78, A: G79, A: G80, A: Ba202,

conact list:


AtomAtomDistance (A)
BaOP1 A:A774.79
BaOP2 A:A774.46
BaOP2 A:A784.24
BaC6 A:G793.77
BaN1 A:G794.88
BaC5 A:G794.45
BaN7 A:G794.36
BaO6 A:G792.62
BaC2 A:G804.81
BaC6 A:G803.92
BaN1 A:G803.85
BaC5 A:G804.97
BaO6 A:G803.55
BaBA A:Ba2024.00

interactive model:


Barium binding site 5 out of 24 in 3oxj


Barium binding site 5 out of 24 in 3oxj
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stereopicture of Barium binding site 5 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 3oxj. 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: A14, A: A21, A: A22, A: C74, A: A75,

conact list:


AtomAtomDistance (A)
BaOP1 A:A144.89
BaOP2 A:A144.99
BaO3' A:A214.06
BaOP1 A:A222.87
BaP A:A224.02
BaOP2 A:A224.87
BaC3' A:C744.79
BaO3' A:C744.83
BaOP2 A:C744.79
BaC8 A:A754.86
BaP A:A754.13
BaN7 A:A754.72
BaOP2 A:A752.68
BaO5' A:A754.68

interactive model:


Barium binding site 6 out of 24 in 3oxj


Barium binding site 6 out of 24 in 3oxj
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stereopicture of Barium binding site 6 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 3oxj. 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: C66, B: A33, B: C66,

conact list:


AtomAtomDistance (A)
BaOP1 A:A333.73
BaOP1 A:C664.36
BaOP1 B:A333.85
BaOP1 B:C664.36

interactive model:


Barium binding site 7 out of 24 in 3oxj


Barium binding site 7 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 7 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 3oxj. 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: B: G8, B: A78, B: G79, B: G80, B: Ba208, B: Ba223,

conact list:


AtomAtomDistance (A)
BaO6 B:G84.84
BaP B:A784.55
BaOP2 B:A783.67
BaO5' B:A784.54
BaC8 B:G794.29
BaC6 B:G794.56
BaC5 B:G794.30
BaN7 B:G793.37
BaOP2 B:G794.16
BaO6 B:G794.05
BaC6 B:G803.81
BaN1 B:G804.86
BaC5 B:G804.33
BaN7 B:G804.22
BaO6 B:G802.94
BaBA B:Ba2082.96
BaBA B:Ba2233.17

interactive model:


Barium binding site 8 out of 24 in 3oxj


Barium binding site 8 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 8 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 3oxj. 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: B: A77, B: A78, B: G79, B: G80, B: Ba207, B: Ba223,

conact list:


AtomAtomDistance (A)
BaOP1 B:A774.68
BaP B:A774.85
BaOP2 B:A774.06
BaOP2 B:A784.58
BaC6 B:G793.88
BaC5 B:G794.51
BaN7 B:G794.36
BaO6 B:G792.75
BaC6 B:G803.83
BaN1 B:G804.01
BaC5 B:G804.85
BaO6 B:G803.29
BaBA B:Ba2072.96
BaBA B:Ba2234.69

interactive model:


Barium binding site 9 out of 24 in 3oxj


Barium binding site 9 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 9 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Barium in the PDB 3oxj. 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: B: U6, B: G7, B: G8, B: G80, B: Ba223,

conact list:


AtomAtomDistance (A)
BaC4 B:U64.92
BaO4 B:U64.39
BaO6 B:G74.62
BaC6 B:G83.77
BaN1 B:G84.16
BaO6 B:G82.77
BaN7 B:G804.89
BaBA B:Ba2234.29

interactive model:


Barium binding site 10 out of 24 in 3oxj


Barium binding site 10 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 10 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Barium in the PDB 3oxj. 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: B: G25, B: G26,

conact list:


AtomAtomDistance (A)
BaC8 B:G254.62
BaC6 B:G254.58
BaC5 B:G254.43
BaN7 B:G253.72
BaO6 B:G254.10
BaC8 B:G264.61
BaC6 B:G264.99
BaC5 B:G264.72
BaN7 B:G263.75
BaO6 B:G264.49

interactive model:


Barium binding site 11 out of 24 in 3oxj


Barium binding site 11 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 11 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Barium in the PDB 3oxj. 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: G17, A: U18, A: U19,

conact list:


AtomAtomDistance (A)
BaC3' A:G174.90
BaO3' A:G174.54
BaC2' A:G174.50
BaO2' A:G174.72
BaOP1 A:U182.88
BaP A:U184.19
BaOP2 A:U184.97
BaC5 A:U194.28
BaC4 A:U194.00
BaO4 A:U193.31

interactive model:


Barium binding site 12 out of 24 in 3oxj


Barium binding site 12 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 12 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Barium in the PDB 3oxj. 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: G72, A: G73, A: Ba214,

conact list:


AtomAtomDistance (A)
BaC8 A:G724.55
BaC6 A:G724.42
BaC5 A:G724.28
BaN7 A:G723.73
BaO6 A:G724.07
BaC8 A:G734.52
BaC6 A:G734.24
BaC5 A:G734.19
BaN7 A:G733.43
BaO6 A:G733.57
BaBA A:Ba2144.19

interactive model:


Barium binding site 13 out of 24 in 3oxj


Barium binding site 13 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 13 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Barium in the PDB 3oxj. 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: A37, A: A64,

conact list:


AtomAtomDistance (A)
BaC8 A:A374.26
BaC5 A:A374.61
BaN6 A:A374.85
BaN7 A:A373.67
BaOP2 A:A374.29
BaOP1 A:A644.59
BaOP2 A:A644.30

interactive model:


Barium binding site 14 out of 24 in 3oxj


Barium binding site 14 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 14 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Barium in the PDB 3oxj. 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: U69, A: C70, A: A71, A: G72, A: Ba212,

conact list:


AtomAtomDistance (A)
BaC3' A:U694.63
BaO3' A:U693.58
BaC2' A:U694.89
BaO2' A:U693.94
BaC3' A:C704.94
BaP A:C703.57
BaO3' A:C704.95
BaOP2 A:C702.79
BaC5' A:C704.83
BaO5' A:C703.63
BaOP1 A:A714.82
BaC8 A:A714.65
BaP A:A714.01
BaN7 A:A714.19
BaOP2 A:A712.57
BaO5' A:A714.65
BaC6 A:G724.74
BaC5 A:G724.88
BaN7 A:G724.25
BaO6 A:G723.90
BaBA A:Ba2124.19

interactive model:


Barium binding site 15 out of 24 in 3oxj


Barium binding site 15 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 15 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Barium in the PDB 3oxj. 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: B: Gdp1,

conact list:


AtomAtomDistance (A)
BaC8 B:Gdp14.59
BaC6 B:Gdp14.10
BaC5 B:Gdp14.10
BaN7 B:Gdp13.49
BaO6 B:Gdp13.30

interactive model:


Barium binding site 16 out of 24 in 3oxj


Barium binding site 16 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 16 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Barium in the PDB 3oxj. 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: B: C16, B: G17, B: U20, B: A21,

conact list:


AtomAtomDistance (A)
BaN4 B:C164.65
BaC8 B:G174.86
BaC6 B:G174.30
BaC5 B:G174.36
BaN7 B:G173.77
BaO6 B:G173.62
BaC3' B:U204.44
BaO3' B:U204.17
BaC2' B:U204.08
BaO2' B:U203.16
BaC3' B:A215.00
BaP B:A214.79
BaO3' B:A214.71
BaO4' B:A214.78
BaC5' B:A214.74
BaC4' B:A214.15
BaO5' B:A214.06

interactive model:


Barium binding site 17 out of 24 in 3oxj


Barium binding site 17 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 17 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Barium in the PDB 3oxj. 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: B: A37, B: A64,

conact list:


AtomAtomDistance (A)
BaC8 B:A374.52
BaC6 B:A374.84
BaC5 B:A374.52
BaN6 B:A374.38
BaN7 B:A373.72
BaOP2 B:A374.22
BaOP2 B:A644.38

interactive model:


Barium binding site 18 out of 24 in 3oxj


Barium binding site 18 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 18 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Barium in the PDB 3oxj. 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: B: A40, B: G42, B: A59, B: G60, B: U61, B: G62,

conact list:


AtomAtomDistance (A)
BaOP2 B:A404.93
BaO6 B:G424.77
BaC6 B:A594.88
BaC5 B:A594.76
BaN6 B:A594.44
BaN7 B:A594.28
BaC8 B:G604.42
BaC6 B:G604.09
BaC5 B:G604.06
BaN7 B:G603.31
BaO6 B:G603.41
BaN3 B:U614.95
BaC5 B:U614.94
BaC4 B:U614.12
BaO4 B:U613.11
BaC6 B:G624.87
BaN1 B:G624.61
BaO6 B:G624.82

interactive model:


Barium binding site 19 out of 24 in 3oxj


Barium binding site 19 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 19 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Barium in the PDB 3oxj. 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: B: G42,

conact list:


AtomAtomDistance (A)
BaOP2 B:G424.79

interactive model:


Barium binding site 20 out of 24 in 3oxj


Barium binding site 20 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 20 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Barium in the PDB 3oxj. 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: B: G50,

conact list:


AtomAtomDistance (A)
BaC8 B:G504.60
BaC6 B:G504.22
BaC5 B:G504.22
BaN7 B:G503.52
BaO6 B:G503.56

interactive model:


Barium binding site 21 out of 24 in 3oxj


Barium binding site 21 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 21 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 21 of Barium in the PDB 3oxj. 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: C39, A: A40, A: G62,

conact list:


AtomAtomDistance (A)
BaC3' A:C394.74
BaP A:C394.76
BaOP2 A:C394.17
BaC5' A:C394.37
BaO5' A:C394.56
BaOP2 A:A404.40
BaC6 A:G624.38
BaN1 A:G624.37
BaO6 A:G623.52

interactive model:


Barium binding site 22 out of 24 in 3oxj


Barium binding site 22 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 22 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 22 of Barium in the PDB 3oxj. 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: G7, A: G8, A: G80, A: Ba202, A: Ba203,

conact list:


AtomAtomDistance (A)
BaC8 A:G74.99
BaN7 A:G74.54
BaOP2 A:G74.28
BaC8 A:G84.29
BaC6 A:G83.76
BaC5 A:G83.78
BaN7 A:G83.14
BaO6 A:G83.09
BaC6 A:G804.17
BaO6 A:G803.01
BaBA A:Ba2022.25
BaBA A:Ba2034.10

interactive model:


Barium binding site 23 out of 24 in 3oxj


Barium binding site 23 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 23 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 23 of Barium in the PDB 3oxj. 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: B: G7, B: G8, B: G80, B: Ba207, B: Ba208, B: Ba209,

conact list:


AtomAtomDistance (A)
BaOP2 B:G74.81
BaC8 B:G84.64
BaC6 B:G83.69
BaN1 B:G84.98
BaC5 B:G83.91
BaN7 B:G83.45
BaO6 B:G82.86
BaC6 B:G803.93
BaN1 B:G804.91
BaC5 B:G804.71
BaN7 B:G804.74
BaO6 B:G802.79
BaBA B:Ba2073.17
BaBA B:Ba2084.69
BaBA B:Ba2094.29

interactive model:


Barium binding site 24 out of 24 in 3oxj


Barium binding site 24 out of 24 in 3oxj
Click to enlarge
stereopicture of Barium binding site 24 out of 24 in 3oxj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 24 of Barium in the PDB 3oxj. 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: A40, A: A41, A: G42, A: C43, A: G60, A: U61, A: G62,

conact list:


AtomAtomDistance (A)
BaOP2 A:A404.54
BaOP2 A:A414.12
BaC6 A:G424.89
BaO6 A:G423.70
BaN4 A:C434.72
BaC6 A:G604.14
BaC5 A:G604.92
BaN7 A:G604.93
BaO6 A:G603.00
BaN3 A:U614.61
BaC4 A:U614.27
BaO4 A:U613.29
BaN2 A:G624.07
BaC2 A:G624.69
BaN1 A:G624.87

interactive model:




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