Chemical elements
  Sodium
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Sodium in the structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb 2eij)






The binding sites of Sodium atom in the structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eij). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2eij structure was solved by K.MURAMOTO, K.HIRATA, K.SHINZAWA-ITOH, S.YOKO-O, E.YAMASHITA, H.AOYAMA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)40.0-1.9
Space groupP212121
a (A)183.060
b (A)206.584
c (A)178.298
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)20.6
Rfree (%)23.4


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 2eij


Sodium binding site 1 out of 2 in 2eij
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 2eij
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2eij. 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: Glu40, A: Leu41, A: Gln43, A: Gly45, A: Thr46, A: Leu47, A: Ser441, A: Asp442, A: Hoh2026, A: Hoh2060, A: Hoh2069,

conact list:


AtomAtomDistance (A)
NaO A:Glu402.29
NaOE1 A:Glu402.23
NaCB A:Glu404.39
NaOE2 A:Glu404.28
NaCD A:Glu403.14
NaC A:Glu403.33
NaCG A:Glu403.43
NaCA A:Glu404.19
NaN A:Leu414.21
NaCD2 A:Leu414.57
NaCA A:Leu414.31
NaO A:Gln434.09
NaO A:Gly452.38
NaN A:Gly454.56
NaC A:Gly453.54
NaCA A:Gly454.69
NaN A:Thr464.20
NaC A:Thr464.64
NaCA A:Thr463.98
NaN A:Leu474.49
NaO A:Ser4412.31
NaCB A:Ser4414.99
NaC A:Ser4413.51
NaCA A:Ser4414.66
NaN A:Asp4424.20
NaCB A:Asp4424.13
NaOD2 A:Asp4424.21
NaOD1 A:Asp4424.77
NaCG A:Asp4424.18
NaCA A:Asp4423.99
NaO A:Hoh20262.51
NaO A:Hoh20603.55
NaO A:Hoh20693.85

interactive model:


Sodium binding site 2 out of 2 in 2eij


Sodium binding site 2 out of 2 in 2eij
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 2eij
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2eij. 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: N: Glu40, N: Leu41, N: Gln43, N: Gly45, N: Thr46, N: Leu47, N: Ser441, N: Asp442, N: Hoh3026, N: Hoh3060, N: Hoh3069,

conact list:


AtomAtomDistance (A)
NaO N:Glu402.28
NaOE1 N:Glu402.19
NaCB N:Glu404.29
NaOE2 N:Glu404.21
NaCD N:Glu403.06
NaC N:Glu403.33
NaCG N:Glu403.30
NaCA N:Glu404.13
NaN N:Leu414.26
NaCD2 N:Leu414.66
NaCA N:Leu414.42
NaO N:Gln434.23
NaO N:Gly452.38
NaN N:Gly454.66
NaC N:Gly453.53
NaCA N:Gly454.73
NaN N:Thr464.12
NaCB N:Thr464.94
NaC N:Thr464.48
NaCA N:Thr463.82
NaN N:Leu474.33
NaO N:Ser4412.33
NaCB N:Ser4414.97
NaC N:Ser4413.53
NaCA N:Ser4414.65
NaN N:Asp4424.26
NaCB N:Asp4424.24
NaOD2 N:Asp4424.49
NaOD1 N:Asp4424.88
NaCG N:Asp4424.36
NaCA N:Asp4424.10
NaO N:Hoh30262.55
NaO N:Hoh30603.52
NaO N:Hoh30693.89

interactive model:




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