Chemical elements
  Rubidium
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    Chemical Properties
    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 Use of A Halide Binding Site To Bypass the 1000-Atom Limit to Ab Initio Structure Determination (pdb 1swy)






The binding sites of Rubidium atom in the structure of Use of A Halide Binding Site To Bypass the 1000-Atom Limit to Ab Initio Structure Determination (pdb code 1swy). This binding sites where shown with 5.0 Angstroms radius around Rubidium atom.
The 1swy structure was solved by B.H.M.MOOERS, B.W.MATTHEWS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)22.0-1.1
Space groupP3221
a (A)60.199
b (A)60.199
c (A)95.242
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)12.3
Rfree (%)14.7


Rubidium Binding Sites:

Rubidium binding site 1 out of 6 in 1swy


Rubidium binding site 1 out of 6 in 1swy
Click to enlarge
stereopicture of Rubidium binding site 1 out of 6 in 1swy
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Rubidium in the PDB 1swy. 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: Tyr88, A: Asp89, A: Ser90, A: Leu91, A: Asp92, A: Glu96, A: Hoh1008, A: Hoh1142, A: Hoh1179,

conact list:


AtomAtomDistance (A)
RbO A:Tyr883.98
RbC A:Tyr884.95
RbO A:Asp892.99
RbC A:Asp893.80
RbCA A:Asp894.18
RbN A:Ser904.80
RbC A:Ser904.76
RbO A:Leu912.75
RbN A:Leu914.44
RbC A:Leu913.85
RbCA A:Leu914.78
RbN A:Asp924.71
RbCA A:Asp924.80
RbOE1 A:Glu964.29
RbOE2 A:Glu962.93
RbCD A:Glu963.87
RbCG A:Glu964.88
RbO A:Hoh10084.69
RbO A:Hoh11422.93
RbO A:Hoh11792.92

interactive model:


Rubidium binding site 2 out of 6 in 1swy


Rubidium binding site 2 out of 6 in 1swy
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stereopicture of Rubidium binding site 2 out of 6 in 1swy
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Rubidium in the PDB 1swy. 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: Asp10, A: Glu11, A: Tyr18, A: Asp20, A: Gly30, A: Hoh1028, A: Hoh1068, A: Hoh1077, A: Hoh1139, A: Hoh1193, A: Hoh1208, A: Hoh1304, A: Hoh1405,

conact list:


AtomAtomDistance (A)
RbO A:Asp104.83
RbO A:Glu112.95
RbOE1 A:Glu113.04
RbCB A:Glu114.31
RbCD A:Glu114.23
RbC A:Glu113.81
RbCG A:Glu114.87
RbCA A:Glu113.88
RbCZ A:Tyr183.89
RbCE1 A:Tyr184.12
RbOH A:Tyr182.80
RbCB A:Asp204.89
RbN A:Gly304.97
RbCA A:Gly304.77
RbO A:Hoh10282.84
RbO A:Hoh10682.95
RbO A:Hoh10772.61
RbO A:Hoh10772.94
RbO A:Hoh11393.58
RbO A:Hoh11933.89
RbO A:Hoh12084.44
RbO A:Hoh13043.59
RbO A:Hoh14054.12

interactive model:


Rubidium binding site 3 out of 6 in 1swy


Rubidium binding site 3 out of 6 in 1swy
Click to enlarge
stereopicture of Rubidium binding site 3 out of 6 in 1swy
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Rubidium in the PDB 1swy. 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: Gly30, A: His31, A: Leu32, A: Asp70, A: Phe104, A: Gln105, A: Rb603, A: Hoh1031, A: Hoh1033, A: Hoh1048, A: Hoh1138, A: Hoh1150, A: Hoh1176, A: Hoh1205,

conact list:


AtomAtomDistance (A)
RbO A:Gly302.82
RbC A:Gly304.03
RbCA A:Gly304.91
RbN A:His314.88
RbCA A:His314.77
RbN A:Leu324.42
RbCB A:Leu324.85
RbOD2 A:Asp704.94
RbO A:Phe1042.83
RbCB A:Phe1044.82
RbCE2 A:Phe1043.34
RbCD1 A:Phe1044.35
RbCD2 A:Phe1043.45
RbCZ A:Phe1043.80
RbC A:Phe1043.89
RbCE1 A:Phe1044.31
RbCG A:Phe1043.97
RbCA A:Phe1044.48
RbN A:Gln1054.90
RbRB A:Rb6030.00
RbRB A:Rb6032.43
RbO A:Hoh10313.09
RbO A:Hoh10334.14
RbO A:Hoh10482.62
RbO A:Hoh11384.41
RbO A:Hoh11502.56
RbO A:Hoh11504.80
RbO A:Hoh11764.30
RbO A:Hoh12054.68

interactive model:


Rubidium binding site 4 out of 6 in 1swy


Rubidium binding site 4 out of 6 in 1swy
Click to enlarge
stereopicture of Rubidium binding site 4 out of 6 in 1swy
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Rubidium in the PDB 1swy. 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: Glu11, A: Gly30, A: His31, A: Leu32, A: Phe104, A: Gln105, A: Rb603, A: Hoh1032, A: Hoh1048, A: Hoh1049, A: Hoh1068, A: Hoh1134, A: Hoh1138, A: Hoh1150, A: Hoh1176,

conact list:


AtomAtomDistance (A)
RbOE1 A:Glu114.96
RbOE2 A:Glu114.66
RbCD A:Glu114.99
RbO A:Gly302.87
RbC A:Gly303.88
RbCA A:Gly304.39
RbN A:His314.89
RbC A:His314.97
RbN A:Leu324.16
RbCB A:Leu324.10
RbCA A:Leu324.65
RbO A:Phe1043.72
RbCE2 A:Phe1044.44
RbCD2 A:Phe1044.59
RbC A:Phe1044.77
RbO A:Gln1054.53
RbCA A:Gln1054.73
RbRB A:Rb6032.43
RbRB A:Rb6030.00
RbO A:Hoh10324.38
RbO A:Hoh10482.75
RbO A:Hoh10494.70
RbO A:Hoh10683.92
RbO A:Hoh11343.04
RbO A:Hoh11382.69
RbO A:Hoh11503.87
RbO A:Hoh11762.90

interactive model:


Rubidium binding site 5 out of 6 in 1swy


Rubidium binding site 5 out of 6 in 1swy
Click to enlarge
stereopicture of Rubidium binding site 5 out of 6 in 1swy
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Rubidium in the PDB 1swy. 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: Ala112, A: Gly113, A: Thr115, A: Hoh1057, A: Hoh1169,

conact list:


AtomAtomDistance (A)
RbO A:Ala1124.98
RbO A:Gly1133.18
RbC A:Gly1133.94
RbCA A:Gly1134.03
RbN A:Thr1154.44
RbCB A:Thr1153.82
RbCG2 A:Thr1154.86
RbOG1 A:Thr1152.77
RbCA A:Thr1154.79
RbO A:Hoh10573.61
RbO A:Hoh11694.87

interactive model:


Rubidium binding site 6 out of 6 in 1swy


Rubidium binding site 6 out of 6 in 1swy
Click to enlarge
stereopicture of Rubidium binding site 6 out of 6 in 1swy
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Rubidium in the PDB 1swy. 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: Lys19, A: Tyr25, A: Pro37, A: Ser38, A: Leu39, A: Hoh1006, A: Hoh1038, A: Hoh1056, A: Hoh1064, A: Hoh1111,

conact list:


AtomAtomDistance (A)
RbCE A:Lys194.69
RbNZ A:Lys194.51
RbCE2 A:Tyr254.19
RbCZ A:Tyr253.81
RbCE1 A:Tyr254.94
RbOH A:Tyr252.65
RbO A:Pro372.63
RbCB A:Pro374.63
RbC A:Pro373.79
RbCA A:Pro374.45
RbN A:Ser384.86
RbN A:Leu394.70
RbO A:Hoh10063.33
RbO A:Hoh10382.93
RbO A:Hoh10562.73
RbO A:Hoh10645.00
RbO A:Hoh11114.18

interactive model:




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