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Sodium in the structure of Crystal Structure of A Peptide-Hla Complex (pdb 3spv)

The binding sites of Sodium atom in the structure of Crystal Structure of A Peptide-Hla Complex (pdb code 3spv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3spv structure was solved by S.GRAS, J.ROSSJOHN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.6-1.3
Space groupP212121
a (A)50.560
b (A)81.460
c (A)110.020
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)19.6
Rfree (%)21.9

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 3spv

Sodium binding site 1 out of 1 in 3spv
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 3spv
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3spv. 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: Asp9, A: Thr10, A: Ala11, A: Phe22, A: Asp74, A: Leu95, A: Gln96, A: Ser97, A: Tyr116, C: Lys5, A: Hoh346,

conact list:

AtomAtomDistance (A)
NaO A:Asp93.46
NaCB A:Asp93.64
NaOD2 A:Asp94.95
NaC A:Asp93.75
NaCG A:Asp94.87
NaCA A:Asp94.38
NaN A:Thr104.14
NaC A:Thr104.26
NaCA A:Thr104.28
NaN A:Ala113.86
NaCB A:Ala114.13
NaCA A:Ala114.64
NaCE1 A:Phe224.88
NaCB A:Asp744.76
NaOD2 A:Asp742.91
NaOD1 A:Asp744.23
NaCG A:Asp743.75
NaO A:Leu952.91
NaCB A:Leu954.34
NaCD2 A:Leu954.24
NaC A:Leu953.56
NaCG A:Leu953.90
NaCA A:Leu954.60
NaO A:Gln964.54
NaN A:Gln963.96
NaC A:Gln963.81
NaCA A:Gln963.74
NaN A:Ser973.70
NaN A:Ser973.69
NaCB A:Ser974.22
NaCB A:Ser974.06
NaOG A:Ser973.73
NaOG A:Ser973.03
NaCA A:Ser974.59
NaCA A:Ser974.52
NaCE1 A:Tyr1164.95
NaCE C:Lys54.54
NaCE C:Lys54.67
NaNZ C:Lys53.17
NaNZ C:Lys53.30
NaO A:Hoh3462.93

interactive model:

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