Chemical elements
  Rubidium
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    PDB 1dge-461d
      1dge
      1hxe
      1i0m
      1i0n
      1jvm
      1nhh
      1r3i
      1swy
      1swz
      1sx2
      1sx7
      1ud5
      1w5u
      1x2w
      2dwe
      2gj9
      2hfe
      2r35
      3b8e
      3c34
      3e8b
      3fb7
      3fb8
      3ggk
      3hwb
      3jxd
      3kdp
      3mgr
      3mku
      460d
      461d

Rubidium in the structure of Cation Selective Pathway of Ompf Porin Revealed By Anomalous Diffraction (pdb 3hwb)






The binding sites of Rubidium atom in the structure of Cation Selective Pathway of Ompf Porin Revealed By Anomalous Diffraction (pdb code 3hwb). This binding sites where shown with 5.0 Angstroms radius around Rubidium atom.
The 3hwb structure was solved by D.BALASUNDARESAN, S.RAYCHAUDHURY, L.BLACHOWICZ, B.ROUX, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)46.5-3.0
Space groupP63
a (A)117.192
b (A)117.192
c (A)116.885
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)23.1
Rfree (%)28.5


Rubidium Binding Sites:

Rubidium binding site 1 out of 19 in 3hwb


Rubidium binding site 1 out of 19 in 3hwb
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stereopicture of Rubidium binding site 1 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Rubidium binding site 2 out of 19 in 3hwb


Rubidium binding site 2 out of 19 in 3hwb
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stereopicture of Rubidium binding site 2 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Rubidium binding site 3 out of 19 in 3hwb


Rubidium binding site 3 out of 19 in 3hwb
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stereopicture of Rubidium binding site 3 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Tyr98, A: Gly135, A: Gly159, A: Lys160, A: Asn161,

conact list:


AtomAtomDistance (A)
RbOH A:Tyr984.22
RbO A:Gly1354.95
RbCA A:Gly1354.08
RbO A:Gly1594.47
RbN A:Gly1594.88
RbC A:Gly1593.91
RbCA A:Gly1593.88
RbO A:Lys1603.45
RbN A:Lys1603.96
RbC A:Lys1604.29
RbCA A:Lys1604.73
RbOD1 A:Asn1613.76
RbCG A:Asn1614.84

interactive model:


Rubidium binding site 4 out of 19 in 3hwb


Rubidium binding site 4 out of 19 in 3hwb
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stereopicture of Rubidium binding site 4 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Tyr98, A: Gly99, A: Arg100, A: Val133, A: Gly134, A: Gly135, A: Val136, A: Hoh369,

conact list:


AtomAtomDistance (A)
RbCE2 A:Tyr983.94
RbCD2 A:Tyr984.52
RbCZ A:Tyr983.95
RbCE1 A:Tyr984.52
RbOH A:Tyr984.06
RbO A:Gly993.86
RbN A:Gly993.94
RbC A:Gly993.43
RbCA A:Gly993.57
RbN A:Arg1003.57
RbCB A:Arg1004.92
RbCA A:Arg1004.21
RbO A:Val1334.87
RbO A:Gly1344.87
RbC A:Gly1343.73
RbCA A:Gly1343.80
RbN A:Gly1352.80
RbC A:Gly1354.19
RbCA A:Gly1353.55
RbO A:Val1364.80
RbN A:Val1363.76
RbCG2 A:Val1364.68
RbCA A:Val1364.95
RbO A:Hoh3692.77

interactive model:


Rubidium binding site 5 out of 19 in 3hwb


Rubidium binding site 5 out of 19 in 3hwb
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stereopicture of Rubidium binding site 5 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Rubidium binding site 6 out of 19 in 3hwb


Rubidium binding site 6 out of 19 in 3hwb
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stereopicture of Rubidium binding site 6 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Rubidium binding site 7 out of 19 in 3hwb


Rubidium binding site 7 out of 19 in 3hwb
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stereopicture of Rubidium binding site 7 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Tyr102, A: Tyr106,

conact list:


AtomAtomDistance (A)
RbCE2 A:Tyr1024.35
RbCZ A:Tyr1024.24
RbCE1 A:Tyr1024.92
RbOH A:Tyr1024.08
RbCE2 A:Tyr1064.61
RbOH A:Tyr1064.48

interactive model:


Rubidium binding site 8 out of 19 in 3hwb


Rubidium binding site 8 out of 19 in 3hwb
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stereopicture of Rubidium binding site 8 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Rubidium binding site 9 out of 19 in 3hwb


Rubidium binding site 9 out of 19 in 3hwb
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stereopicture of Rubidium binding site 9 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gly268, A: Tyr302, A: Asn304,

conact list:


AtomAtomDistance (A)
RbCA A:Gly2684.89
RbO A:Tyr3024.61
RbCB A:Tyr3024.78
RbCA A:Asn3044.84

interactive model:


Rubidium binding site 10 out of 19 in 3hwb


Rubidium binding site 10 out of 19 in 3hwb
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stereopicture of Rubidium binding site 10 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gln264, A: Gly268, A: Leu269, A: Arg270, A: Thr300, A: Tyr301, A: Tyr302,

conact list:


AtomAtomDistance (A)
RbNE2 A:Gln2643.33
RbOE1 A:Gln2643.68
RbCD A:Gln2643.93
RbO A:Gly2683.52
RbC A:Gly2683.60
RbCA A:Gly2684.35
RbO A:Leu2694.51
RbN A:Leu2693.71
RbC A:Leu2693.71
RbCA A:Leu2693.76
RbN A:Arg2703.39
RbCB A:Arg2703.68
RbCA A:Arg2704.15
RbO A:Thr3002.94
RbCB A:Thr3004.46
RbCG2 A:Thr3004.75
RbC A:Thr3003.64
RbCA A:Thr3004.68
RbN A:Tyr3014.07
RbC A:Tyr3014.07
RbCA A:Tyr3013.91
RbN A:Tyr3023.37
RbCB A:Tyr3023.99
RbCE2 A:Tyr3023.94
RbCD1 A:Tyr3024.31
RbCD2 A:Tyr3023.44
RbCZ A:Tyr3024.55
RbCE1 A:Tyr3024.72
RbCG A:Tyr3023.64
RbCA A:Tyr3024.29

interactive model:


Rubidium binding site 11 out of 19 in 3hwb


Rubidium binding site 11 out of 19 in 3hwb
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stereopicture of Rubidium binding site 11 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Met114, A: Leu115, A: Pro116, A: Gln262, A: Arg270, A: Thr300, A: Tyr302,

conact list:


AtomAtomDistance (A)
RbO A:Met1143.20
RbC A:Met1144.22
RbO A:Leu1154.47
RbN A:Leu1154.91
RbC A:Leu1154.25
RbCA A:Leu1154.82
RbN A:Pro1164.13
RbCD A:Pro1164.64
RbCG A:Pro1164.84
RbCA A:Pro1164.21
RbNE2 A:Gln2624.74
RbOE1 A:Gln2624.97
RbCD A:Arg2704.27
RbNE A:Arg2704.80
RbCB A:Thr3004.59
RbCG2 A:Thr3004.60
RbOG1 A:Thr3003.88
RbOH A:Tyr3023.98

interactive model:


Rubidium binding site 12 out of 19 in 3hwb


Rubidium binding site 12 out of 19 in 3hwb
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stereopicture of Rubidium binding site 12 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp288, A: Val289, A: Asp290, A: Asn322, A: Lys323,

conact list:


AtomAtomDistance (A)
RbO A:Asp2884.86
RbCB A:Val2894.48
RbC A:Val2894.61
RbCG1 A:Val2894.00
RbCA A:Val2894.23
RbN A:Asp2903.88
RbCB A:Asp2904.56
RbOD2 A:Asp2903.78
RbCG A:Asp2904.49
RbCA A:Asp2904.81
RbN A:Asn3224.69
RbCB A:Asn3224.90
RbND2 A:Asn3224.57
RbCG A:Asn3224.81
RbCA A:Asn3224.26
RbN A:Lys3234.83
RbNZ A:Lys3234.79

interactive model:


Rubidium binding site 13 out of 19 in 3hwb


Rubidium binding site 13 out of 19 in 3hwb
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stereopicture of Rubidium binding site 13 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu201, A: Gln203, A: Pro204, A: Gly206, A: Asn207,

conact list:


AtomAtomDistance (A)
RbO A:Glu2013.29
RbOE1 A:Glu2014.92
RbC A:Glu2014.40
RbO A:Gln2033.04
RbN A:Gln2034.99
RbC A:Gln2034.25
RbO A:Pro2044.47
RbC A:Pro2044.68
RbCA A:Pro2044.91
RbO A:Gly2063.04
RbC A:Gly2064.13
RbN A:Asn2074.76
RbCB A:Asn2074.45
RbND2 A:Asn2073.84
RbCG A:Asn2074.34
RbCA A:Asn2074.52

interactive model:


Rubidium binding site 14 out of 19 in 3hwb


Rubidium binding site 14 out of 19 in 3hwb
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stereopicture of Rubidium binding site 14 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asn316, A: Ile318, A: Ser328, A: Asp330,

conact list:


AtomAtomDistance (A)
RbO A:Asn3163.20
RbCB A:Asn3164.94
RbC A:Asn3164.33
RbO A:Ile3183.92
RbC A:Ile3184.97
RbO A:Ser3283.27
RbC A:Ser3284.36
RbOD1 A:Asp3304.29

interactive model:


Rubidium binding site 15 out of 19 in 3hwb


Rubidium binding site 15 out of 19 in 3hwb
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stereopicture of Rubidium binding site 15 out of 19 in 3hwb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Rubidium binding site 16 out of 19 in 3hwb


Rubidium binding site 16 out of 19 in 3hwb
Click to enlarge
stereopicture of Rubidium binding site 16 out of 19 in 3hwb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Asp172, B: Gly173, B: Asp195, B: Lys210,

conact list:


AtomAtomDistance (A)
RbO B:Asp1724.02
RbCB B:Asp1724.72
RbC B:Asp1724.50
RbN B:Gly1734.86
RbCA B:Gly1734.82
RbOD2 B:Asp1954.27
RbOD1 B:Asp1953.56
RbCG B:Asp1954.21
RbCE B:Lys2104.51
RbNZ B:Lys2104.79

interactive model:


Rubidium binding site 17 out of 19 in 3hwb


Rubidium binding site 17 out of 19 in 3hwb
Click to enlarge
stereopicture of Rubidium binding site 17 out of 19 in 3hwb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Asn316, B: Gln317, B: Ile318, B: Ser328, B: Asp330,

conact list:


AtomAtomDistance (A)
RbO B:Asn3163.13
RbC B:Asn3164.16
RbO B:Gln3174.83
RbN B:Gln3174.72
RbC B:Gln3174.44
RbCA B:Gln3174.44
RbO B:Ile3183.35
RbN B:Ile3184.61
RbC B:Ile3184.36
RbO B:Ser3283.30
RbCB B:Ser3284.52
RbC B:Ser3284.32
RbCA B:Ser3284.77
RbOD1 B:Asp3304.82

interactive model:


Rubidium binding site 18 out of 19 in 3hwb


Rubidium binding site 18 out of 19 in 3hwb
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stereopicture of Rubidium binding site 18 out of 19 in 3hwb
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Glu201, B: Ala202, B: Gln203, B: Gly206, B: Asn207,

conact list:


AtomAtomDistance (A)
RbO B:Glu2012.76
RbOE1 B:Glu2014.45
RbC B:Glu2013.85
RbCA B:Glu2014.48
RbN B:Ala2024.89
RbC B:Ala2024.91
RbO B:Gln2033.29
RbN B:Gln2034.85
RbC B:Gln2034.34
RbO B:Gly2063.43
RbC B:Gly2064.62
RbND2 B:Asn2074.18
RbCG B:Asn2074.94
RbCA B:Asn2074.93

interactive model:


Rubidium binding site 19 out of 19 in 3hwb


Rubidium binding site 19 out of 19 in 3hwb
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stereopicture of Rubidium binding site 19 out of 19 in 3hwb
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Rubidium in the PDB 3hwb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Tyr106, B: Asp113, B: Gly120, B: Ala123, B: Arg132, B: Hoh355,

conact list:


AtomAtomDistance (A)
RbCZ B:Tyr1064.55
RbCE1 B:Tyr1064.19
RbOH B:Tyr1064.02
RbOD2 B:Asp1133.00
RbOD1 B:Asp1134.16
RbCG B:Asp1133.89
RbO B:Gly1204.84
RbO B:Ala1234.38
RbCB B:Ala1234.58
RbNH1 B:Arg1324.30
RbO B:Hoh3552.83

interactive model:




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