Chemical elements
  Barium
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    Detection of Barrium
    PDB 1djh-3iqp
      1djh
      1i0f
      1ihh
      1j6s
      1kd4
      1nta
      1qyk
      1sof
      1u9s
      1vbz
      1wro
      1xcs
      1xcu
      1y6s
      1y7f
      1zqb
      1zqn
      220d
      284d
      2adi
      2b5e
      2bou
      2cis
      2dns
      2dqo
      2drw
      2efu
      2efx
      2gpx
      2hol
      2itd
      2qde
      2v02
      2v2f
      2w2f
      2w54
      2w55
      2wsj
      2wtr
      2x6b
      3aa6
      3aa7
      3e8f
      3e8v
      3f2w
      3fqb
      3goj
      3gom
      3iqn
      3iqp
    PDB 3iqr-4e7y

Barium in the structure of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed With D-Phenylalanine (pdb 2dns)






The binding sites of Barium atom in the structure of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed With D-Phenylalanine (pdb code 2dns). This binding sites where shown with 5.0 Angstroms radius around Barium atom.
The 2dns structure was solved by S.OKAZAKI, A.SUZUKI, H.KOMEDA, Y.ASANO, T.YAMANE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.9-2.4
Space groupP1211
a (A)77.067
b (A)123.702
c (A)116.046
alpha (°)90.00
beta (°)104.44
gamma (°)90.00
Rfactor (%)19.5
Rfree (%)26.9


Barium Binding Sites:

Barium binding site 1 out of 20 in 2dns


Barium binding site 1 out of 20 in 2dns
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stereopicture of Barium binding site 1 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 2dns. 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: Ser121, A: Asp122, A: Glu232, A: Trp233, A: Phe234, A: Pro235, A: Hoh3023, A: Hoh3036, A: Hoh3071,

conact list:


AtomAtomDistance (A)
BaO A:Ser1212.67
BaN A:Ser1214.41
BaC A:Ser1213.65
BaCA A:Ser1214.63
BaN A:Asp1224.34
BaCB A:Asp1224.70
BaOD2 A:Asp1224.02
BaOD1 A:Asp1223.26
BaCG A:Asp1223.75
BaCA A:Asp1224.38
BaO A:Glu2322.77
BaC A:Glu2323.92
BaN A:Trp2334.53
BaC A:Trp2333.77
BaCA A:Trp2334.22
BaO A:Trp2333.08
BaN A:Phe2344.69
BaCD A:Pro2354.99
BaO A:Hoh30231.93
BaO A:Hoh30363.62
BaO A:Hoh30712.77

interactive model:


Barium binding site 2 out of 20 in 2dns


Barium binding site 2 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 2 out of 20 in 2dns
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 2dns. 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: Glu211, A: Asn212, A: Pro213, D: Asp53, A: Hoh3059, A: Hoh3116,

conact list:


AtomAtomDistance (A)
BaO A:Glu2112.94
BaC A:Glu2114.13
BaN A:Asn2124.99
BaND2 A:Asn2124.60
BaCA A:Asn2124.93
BaCD A:Pro2134.39
BaCB D:Asp534.97
BaOD2 D:Asp533.90
BaOD1 D:Asp534.29
BaCG D:Asp534.14
BaO A:Hoh30592.35
BaO A:Hoh31164.82

interactive model:


Barium binding site 3 out of 20 in 2dns


Barium binding site 3 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 3 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 2dns. 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: Glu303, A: Glu323, B: Glu323, F: Glu303, F: Glu323, A: Ba3020, B: Ba3019, F: Ba3008, B: Hoh3164,

conact list:


AtomAtomDistance (A)
BaOE1 A:Glu3034.85
BaOE2 A:Glu3234.11
BaOE2 B:Glu3234.59
BaOE1 F:Glu3034.37
BaOE2 F:Glu3234.32
BaBA A:Ba30204.05
BaBA B:Ba30193.97
BaBA F:Ba30083.00
BaO B:Hoh31644.82

interactive model:


Barium binding site 4 out of 20 in 2dns


Barium binding site 4 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 4 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 2dns. 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: Asn360, A: Ser361, A: Ser363,

conact list:


AtomAtomDistance (A)
BaO A:Asn3602.74
BaCB A:Asn3604.71
BaND2 A:Asn3604.98
BaC A:Asn3603.84
BaCA A:Asn3604.48
BaN A:Ser3614.87
BaN A:Ser3634.71
BaCB A:Ser3634.01
BaOG A:Ser3632.64
BaC A:Ser3634.24
BaCA A:Ser3634.53

interactive model:


Barium binding site 5 out of 20 in 2dns


Barium binding site 5 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 5 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 2dns. 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: Ser301, A: Glu323, B: Glu323, A: Ba3007, B: Ba3019, F: Ba3008,

conact list:


AtomAtomDistance (A)
BaO A:Ser3013.05
BaCB A:Ser3014.80
BaC A:Ser3014.11
BaCA A:Ser3014.64
BaOE1 A:Glu3233.05
BaOE2 A:Glu3233.32
BaCD A:Glu3233.54
BaCG A:Glu3234.96
BaOE1 B:Glu3233.77
BaOE2 B:Glu3232.86
BaCD B:Glu3233.68
BaBA A:Ba30074.05
BaBA B:Ba30193.13
BaBA F:Ba30083.56

interactive model:


Barium binding site 6 out of 20 in 2dns


Barium binding site 6 out of 20 in 2dns
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stereopicture of Barium binding site 6 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 2dns. 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: Ser121, B: Asp122, B: Glu232, B: Trp233, B: Phe234, B: Hoh3057, B: Hoh3059, B: Hoh3068, B: Hoh3095, B: Hoh3097, B: Hoh3103,

conact list:


AtomAtomDistance (A)
BaO B:Ser1212.91
BaN B:Ser1214.31
BaC B:Ser1213.81
BaCA B:Ser1214.71
BaN B:Asp1224.49
BaCB B:Asp1224.83
BaOD2 B:Asp1224.58
BaOD1 B:Asp1222.75
BaCG B:Asp1223.89
BaCA B:Asp1224.52
BaO B:Glu2322.74
BaCB B:Glu2325.00
BaC B:Glu2323.86
BaN B:Trp2334.45
BaC B:Trp2333.65
BaCA B:Trp2334.04
BaO B:Trp2332.87
BaN B:Phe2344.65
BaO B:Hoh30574.91
BaO B:Hoh30592.15
BaO B:Hoh30682.87
BaO B:Hoh30952.93
BaO B:Hoh30974.89
BaO B:Hoh31031.71

interactive model:


Barium binding site 7 out of 20 in 2dns


Barium binding site 7 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 7 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 2dns. 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: Ser301, B: Glu323, F: Glu323, A: Ba3007, A: Ba3020, F: Ba3008,

conact list:


AtomAtomDistance (A)
BaO B:Ser3013.03
BaCB B:Ser3014.66
BaC B:Ser3014.15
BaCA B:Ser3014.67
BaOE1 B:Glu3233.02
BaOE2 B:Glu3233.69
BaCD B:Glu3233.73
BaOE1 F:Glu3234.54
BaOE2 F:Glu3233.76
BaCD F:Glu3234.51
BaBA A:Ba30073.97
BaBA A:Ba30203.13
BaBA F:Ba30083.14

interactive model:


Barium binding site 8 out of 20 in 2dns


Barium binding site 8 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 8 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 2dns. 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: C: Ser121, C: Asp122, C: Glu232, C: Trp233, C: Phe234, C: Pro235, C: Hoh3107, C: Hoh3122, C: Hoh3145, C: Hoh3156, C: Hoh3161,

conact list:


AtomAtomDistance (A)
BaO C:Ser1212.88
BaN C:Ser1214.30
BaC C:Ser1213.82
BaCA C:Ser1214.69
BaN C:Asp1224.55
BaCB C:Asp1224.91
BaOD2 C:Asp1224.60
BaOD1 C:Asp1222.92
BaCG C:Asp1223.95
BaCA C:Asp1224.61
BaO C:Glu2322.78
BaC C:Glu2323.90
BaN C:Trp2334.45
BaC C:Trp2333.62
BaCA C:Trp2334.05
BaO C:Trp2332.90
BaN C:Phe2344.60
BaCD C:Pro2354.95
BaO C:Hoh31074.65
BaO C:Hoh31222.95
BaO C:Hoh31454.68
BaO C:Hoh31563.02
BaO C:Hoh31612.25

interactive model:


Barium binding site 9 out of 20 in 2dns


Barium binding site 9 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 9 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Barium in the PDB 2dns. 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: Leu36, C: Ala206, C: Ala207, C: Ala208, C: Asp209, C: Asp210, B: Hoh3137, C: Hoh3043, C: Hoh3046,

conact list:


AtomAtomDistance (A)
BaO B:Leu364.89
BaO C:Ala2062.88
BaC C:Ala2064.03
BaCA C:Ala2064.88
BaN C:Ala2074.93
BaCA C:Ala2074.88
BaO C:Ala2083.06
BaN C:Ala2084.73
BaC C:Ala2083.77
BaCA C:Ala2083.91
BaN C:Asp2094.92
BaN C:Asp2104.99
BaO B:Hoh31374.76
BaO C:Hoh30433.18
BaO C:Hoh30463.07

interactive model:


Barium binding site 10 out of 20 in 2dns


Barium binding site 10 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 10 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Barium in the PDB 2dns. 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: C: Ser301, C: Glu323, D: Glu323, C: Ba3011, D: Ba3012, E: Ba3010, D: Hoh3140,

conact list:


AtomAtomDistance (A)
BaO C:Ser3013.56
BaC C:Ser3014.55
BaCA C:Ser3015.00
BaOE1 C:Glu3234.17
BaOE2 C:Glu3233.09
BaCD C:Glu3234.00
BaOE1 D:Glu3234.32
BaOE2 D:Glu3233.05
BaCD D:Glu3233.99
BaBA C:Ba30113.16
BaBA D:Ba30123.38
BaBA E:Ba30104.13
BaO D:Hoh31403.86

interactive model:


Barium binding site 11 out of 20 in 2dns


Barium binding site 11 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 11 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Barium in the PDB 2dns. 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: C: Glu323, D: Glu323, E: Glu303, C: Ba3009, D: Ba3012, E: Ba3010, D: Hoh3140, E: Hoh3070,

conact list:


AtomAtomDistance (A)
BaOE2 C:Glu3234.48
BaOE2 D:Glu3234.53
BaOE2 E:Glu3034.84
BaBA C:Ba30093.16
BaBA D:Ba30124.52
BaBA E:Ba30102.66
BaO D:Hoh31404.75
BaO E:Hoh30704.35

interactive model:


Barium binding site 12 out of 20 in 2dns


Barium binding site 12 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 12 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Barium in the PDB 2dns. 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: D: Ser301, D: Glu323, D: Lys359, E: Glu323, C: Ba3009, C: Ba3011, E: Ba3010,

conact list:


AtomAtomDistance (A)
BaO D:Ser3013.10
BaCB D:Ser3014.45
BaOG D:Ser3014.62
BaC D:Ser3014.20
BaCA D:Ser3014.67
BaOE1 D:Glu3233.34
BaOE2 D:Glu3233.47
BaCD D:Glu3233.82
BaNZ D:Lys3594.16
BaOE2 E:Glu3233.75
BaCD E:Glu3234.78
BaBA C:Ba30093.38
BaBA C:Ba30114.52
BaBA E:Ba30103.09

interactive model:


Barium binding site 13 out of 20 in 2dns


Barium binding site 13 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 13 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Barium in the PDB 2dns. 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: D: Ser285, D: Asn286, D: Hoh3033,

conact list:


AtomAtomDistance (A)
BaO D:Ser2854.57
BaCB D:Asn2864.66
BaND2 D:Asn2864.24
BaOD1 D:Asn2863.45
BaCG D:Asn2863.86
BaCA D:Asn2864.59
BaO D:Hoh30334.05

interactive model:


Barium binding site 14 out of 20 in 2dns


Barium binding site 14 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 14 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Barium in the PDB 2dns. 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: D: Ile120, D: Ser121, D: Asp122, D: Glu232, D: Trp233, D: Phe234, D: Hoh3124, D: Hoh3137,

conact list:


AtomAtomDistance (A)
BaCG2 D:Ile1204.93
BaO D:Ser1212.74
BaN D:Ser1214.24
BaC D:Ser1213.72
BaCA D:Ser1214.65
BaN D:Asp1224.42
BaCB D:Asp1224.70
BaOD2 D:Asp1224.52
BaOD1 D:Asp1222.70
BaCG D:Asp1223.79
BaCA D:Asp1224.46
BaO D:Glu2322.68
BaC D:Glu2323.84
BaN D:Trp2334.43
BaC D:Trp2333.85
BaCA D:Trp2334.09
BaO D:Trp2333.20
BaN D:Phe2344.88
BaO D:Hoh31243.23
BaO D:Hoh31371.49

interactive model:


Barium binding site 15 out of 20 in 2dns


Barium binding site 15 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 15 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Barium in the PDB 2dns. 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: D: Asn360, D: Ser361, D: Arg362,

conact list:


AtomAtomDistance (A)
BaO D:Asn3602.71
BaC D:Asn3603.82
BaCA D:Asn3604.54
BaO D:Ser3614.44
BaN D:Ser3614.80
BaC D:Ser3614.58
BaCA D:Ser3614.93
BaO D:Arg3623.47
BaC D:Arg3624.26

interactive model:


Barium binding site 16 out of 20 in 2dns


Barium binding site 16 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 16 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Barium in the PDB 2dns. 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: D: Ser301, D: Glu323, E: Ser301, E: Glu323, C: Ba3009, C: Ba3011, D: Ba3012, D: Hoh3128,

conact list:


AtomAtomDistance (A)
BaO D:Ser3013.97
BaC D:Ser3014.68
BaCA D:Ser3014.86
BaOE2 D:Glu3234.64
BaO E:Ser3014.70
BaOE2 E:Glu3233.04
BaCD E:Glu3234.19
BaCG E:Glu3234.68
BaBA C:Ba30094.13
BaBA C:Ba30112.66
BaBA D:Ba30123.09
BaO D:Hoh31283.37

interactive model:


Barium binding site 17 out of 20 in 2dns


Barium binding site 17 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 17 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Barium in the PDB 2dns. 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: E: Ser121, E: Asp122, E: Glu232, E: Trp233, E: Hoh3051, E: Hoh3062,

conact list:


AtomAtomDistance (A)
BaO E:Ser1213.62
BaN E:Ser1214.84
BaC E:Ser1214.19
BaN E:Asp1224.53
BaCB E:Asp1224.77
BaOD2 E:Asp1224.08
BaOD1 E:Asp1223.38
BaCG E:Asp1223.84
BaCA E:Asp1224.48
BaO E:Glu2322.38
BaCB E:Glu2324.56
BaC E:Glu2323.60
BaCA E:Glu2324.62
BaN E:Trp2334.42
BaC E:Trp2334.08
BaCA E:Trp2334.35
BaO E:Trp2333.47
BaO E:Hoh30511.87
BaO E:Hoh30622.16

interactive model:


Barium binding site 18 out of 20 in 2dns


Barium binding site 18 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 18 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Barium in the PDB 2dns. 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: F: Ala17,

conact list:


AtomAtomDistance (A)
BaO F:Ala173.32
BaC F:Ala174.23
BaCB F:Ala174.89
BaCA F:Ala174.36

interactive model:


Barium binding site 19 out of 20 in 2dns


Barium binding site 19 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 19 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Barium in the PDB 2dns. 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: Glu323, F: Ser301, F: Glu323, A: Ba3007, A: Ba3020, B: Ba3019,

conact list:


AtomAtomDistance (A)
BaOE1 A:Glu3234.37
BaOE2 A:Glu3232.80
BaCD A:Glu3233.92
BaO F:Ser3012.95
BaCB F:Ser3014.33
BaOG F:Ser3014.95
BaC F:Ser3013.93
BaCA F:Ser3014.24
BaOE1 F:Glu3234.06
BaOE2 F:Glu3233.05
BaCD F:Glu3233.92
BaBA A:Ba30073.00
BaBA A:Ba30203.56
BaBA B:Ba30193.14

interactive model:


Barium binding site 20 out of 20 in 2dns


Barium binding site 20 out of 20 in 2dns
Click to enlarge
stereopicture of Barium binding site 20 out of 20 in 2dns
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Barium in the PDB 2dns. 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: F: Ser121, F: Asp122, F: Glu232, F: Trp233, F: Phe234, F: Pro235, F: Hoh3016, F: Hoh3022, F: Hoh3044,

conact list:


AtomAtomDistance (A)
BaO F:Ser1212.88
BaC F:Ser1213.91
BaN F:Asp1224.46
BaCB F:Asp1224.80
BaOD2 F:Asp1224.90
BaOD1 F:Asp1223.14
BaCG F:Asp1224.11
BaCA F:Asp1224.20
BaO F:Glu2323.07
BaCB F:Glu2324.65
BaC F:Glu2323.75
BaCA F:Glu2324.48
BaN F:Trp2334.45
BaC F:Trp2333.86
BaCA F:Trp2334.55
BaO F:Trp2333.22
BaO F:Phe2344.44
BaN F:Phe2344.54
BaC F:Phe2344.26
BaCA F:Phe2344.83
BaN F:Pro2354.18
BaCB F:Pro2354.65
BaCD F:Pro2354.64
BaCA F:Pro2354.37
BaO F:Hoh30163.16
BaO F:Hoh30222.78
BaO F:Hoh30442.22

interactive model:




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