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Sodium in the structure of Human Thrombin Complexed With D-Phe-Pro-D-Arg-Ile (pdb 3u8r)

The binding sites of Sodium atom in the structure of Human Thrombin Complexed With D-Phe-Pro-D-Arg-Ile (pdb code 3u8r). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3u8r structure was solved by A.C.FIGUEIREDO, C.C.CLEMENT, M.PHILIPP, P.J.B.PEREIRA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)43.8-1.5
Space groupP212121
a (A)51.563
b (A)76.527
c (A)83.260
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)12.9
Rfree (%)16.1

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 3u8r

Sodium binding site 1 out of 1 in 3u8r
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 3u8r
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3u8r. 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: H: Tyr510, H: Asp552, H: Arg553, H: Asp554, H: Gly555, H: Lys556, H: Tyr557, H: Hoh704, H: Hoh710, H: Hoh721, H: Hoh726, H: Hoh741, H: Hoh744, H: Hoh750, H: Hoh764,

conact list:

AtomAtomDistance (A)
NaO H:Tyr5104.12
NaO H:Asp5524.52
NaHA H:Asp5523.62
NaH H:Asp5524.93
NaOD1 H:Asp5524.57
NaC H:Asp5524.07
NaCA H:Asp5524.33
NaHB2 H:Arg5534.90
NaN H:Arg5533.96
NaC H:Arg5533.41
NaCA H:Arg5534.31
NaO H:Arg5532.29
NaH H:Arg5534.07
NaN H:Asp5544.28
NaHA H:Asp5543.77
NaC H:Asp5544.50
NaCA H:Asp5544.33
NaN H:Gly5554.23
NaH H:Gly5553.89
NaC H:Gly5554.82
NaHB2 H:Lys5563.92
NaN H:Lys5563.81
NaCB H:Lys5564.54
NaC H:Lys5563.46
NaCA H:Lys5564.14
NaO H:Lys5562.36
NaH H:Lys5563.19
NaN H:Tyr5574.50
NaCA H:Tyr5574.79
NaHA H:Tyr5574.09
NaO H:Hoh7044.58
NaO H:Hoh7104.21
NaO H:Hoh7212.50
NaO H:Hoh7262.51
NaO H:Hoh7412.68
NaO H:Hoh7444.01
NaO H:Hoh7502.41
NaO H:Hoh7643.98

interactive model:

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