Chemical elements
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      2wij
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      2wp0
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      2wp9
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      2wqt
      2wrx
      2ws3
      2wsj
      2wsl
      2wsy
      2wu2
      2wu5
      2wuv
      2wuw
      2wv7
      2ww2
      2wwf
      2wwh
      2wwt
      2wx5
      2wxy
      2wy0
      2wyu
      2wyv
      2wz7
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      2x0a
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Sodium in the structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant (pdb 2wu2)






The binding sites of Sodium atom in the structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant (pdb code 2wu2). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2wu2 structure was solved by J.RUPRECHT, V.YANKOVSKAYA, E.MAKLASHINA, S.IWATA, G.CECCHINI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)48.0-2.5
Space groupP212121
a (A)120.033
b (A)183.363
c (A)202.720
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)17.689
Rfree (%)21.431


Sodium Binding Sites:

Sodium binding site 1 out of 3 in 2wu2


Sodium binding site 1 out of 3 in 2wu2
Click to enlarge
stereopicture of Sodium binding site 1 out of 3 in 2wu2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wu2. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Tyr355, A: Met356, A: Met357, A: Gly358, A: Gly359, A: Gly387, A: Glu388, A: Ile389, A: Ala390, A: Cys391, A: Hoh2157, A: Hoh2171, A: Hoh2176,

conact list:


AtomAtomDistance (A)
NaCE2 A:Tyr3554.56
NaCZ A:Tyr3554.46
NaOH A:Tyr3553.88
NaO A:Met3562.64
NaCB A:Met3564.92
NaCE A:Met3564.60
NaC A:Met3563.77
NaCG A:Met3564.84
NaCA A:Met3564.97
NaO A:Met3573.05
NaN A:Met3574.36
NaC A:Met3573.36
NaCA A:Met3573.96
NaO A:Gly3582.44
NaN A:Gly3583.91
NaC A:Gly3583.52
NaCA A:Gly3584.28
NaN A:Gly3594.47
NaCA A:Gly3594.62
NaO A:Gly3874.34
NaO A:Glu3882.45
NaCB A:Glu3884.91
NaC A:Glu3883.46
NaCG A:Glu3884.47
NaCA A:Glu3884.02
NaO A:Ile3894.70
NaN A:Ile3894.51
NaC A:Ile3894.38
NaCA A:Ile3894.81
NaO A:Ala3902.44
NaN A:Ala3904.26
NaC A:Ala3903.62
NaCA A:Ala3904.60
NaN A:Cys3914.45
NaCB A:Cys3914.90
NaCA A:Cys3914.51
NaO A:Hoh21574.41
NaO A:Hoh21714.90
NaO A:Hoh21764.15

interactive model:


Sodium binding site 2 out of 3 in 2wu2


Sodium binding site 2 out of 3 in 2wu2
Click to enlarge
stereopicture of Sodium binding site 2 out of 3 in 2wu2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wu2. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: Tyr355, E: Met356, E: Met357, E: Gly358, E: Gly359, E: Gly387, E: Glu388, E: Ile389, E: Ala390, E: Cys391, E: Hoh2125,

conact list:


AtomAtomDistance (A)
NaCE2 E:Tyr3554.58
NaCZ E:Tyr3554.50
NaOH E:Tyr3553.92
NaO E:Met3562.60
NaCB E:Met3564.92
NaCE E:Met3564.69
NaC E:Met3563.74
NaCG E:Met3564.80
NaCA E:Met3564.93
NaO E:Met3572.92
NaN E:Met3574.32
NaC E:Met3573.31
NaCA E:Met3573.94
NaO E:Gly3582.35
NaN E:Gly3583.90
NaC E:Gly3583.45
NaCA E:Gly3584.20
NaN E:Gly3594.43
NaCA E:Gly3594.59
NaO E:Gly3874.44
NaO E:Glu3882.44
NaCB E:Glu3884.98
NaC E:Glu3883.50
NaCG E:Glu3884.54
NaCA E:Glu3884.11
NaO E:Ile3894.74
NaN E:Ile3894.54
NaC E:Ile3894.37
NaCA E:Ile3894.83
NaO E:Ala3902.44
NaN E:Ala3904.15
NaC E:Ala3903.63
NaCA E:Ala3904.56
NaN E:Cys3914.49
NaCB E:Cys3914.80
NaCA E:Cys3914.49
NaO E:Hoh21254.98

interactive model:


Sodium binding site 3 out of 3 in 2wu2


Sodium binding site 3 out of 3 in 2wu2
Click to enlarge
stereopicture of Sodium binding site 3 out of 3 in 2wu2
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2wu2. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: I: Tyr355, I: Met356, I: Met357, I: Gly358, I: Gly359, I: Gly387, I: Glu388, I: Ile389, I: Ala390, I: Cys391, I: Hoh2102, I: Hoh2116, I: Hoh2123,

conact list:


AtomAtomDistance (A)
NaCE2 I:Tyr3554.49
NaCZ I:Tyr3554.35
NaOH I:Tyr3553.78
NaO I:Met3562.52
NaCB I:Met3564.81
NaCE I:Met3564.64
NaC I:Met3563.69
NaCG I:Met3564.77
NaCA I:Met3564.86
NaO I:Met3573.03
NaN I:Met3574.31
NaC I:Met3573.37
NaCA I:Met3573.95
NaO I:Gly3582.52
NaN I:Gly3583.94
NaC I:Gly3583.59
NaCA I:Gly3584.30
NaN I:Gly3594.55
NaCA I:Gly3594.71
NaO I:Gly3874.30
NaO I:Glu3882.43
NaCB I:Glu3884.82
NaC I:Glu3883.43
NaCG I:Glu3884.38
NaCA I:Glu3883.95
NaO I:Ile3894.81
NaN I:Ile3894.52
NaC I:Ile3894.47
NaCA I:Ile3894.87
NaO I:Ala3902.48
NaN I:Ala3904.30
NaC I:Ala3903.69
NaCA I:Ala3904.64
NaN I:Cys3914.56
NaCB I:Cys3914.91
NaCA I:Cys3914.59
NaO I:Hoh21024.44
NaO I:Hoh21164.94
NaO I:Hoh21233.91

interactive model:




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