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Sodium in the structure of Human Thrombin Complexed With D-Phe-Pro-D-Arg-D-Thr (pdb 3u8o)

The binding sites of Sodium atom in the structure of Human Thrombin Complexed With D-Phe-Pro-D-Arg-D-Thr (pdb code 3u8o). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3u8o 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)36.3-1.3
Space groupP212121
a (A)57.446
b (A)72.680
c (A)83.090
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)12.8
Rfree (%)14.9

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 3u8o

Sodium binding site 1 out of 1 in 3u8o
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 3u8o
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3u8o. 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: Gly509, H: Tyr510, H: Asp552, H: Arg553, H: Asp554, H: Gly555, H: Lys556, H: Tyr557, H: Hoh715, H: Hoh731, H: Hoh736, H: Hoh756, H: Hoh759, H: Hoh760, H: Hoh764, H: Hoh788,

conact list:

AtomAtomDistance (A)
NaHA3 H:Gly5095.00
NaO H:Tyr5104.11
NaO H:Asp5524.45
NaHA H:Asp5523.63
NaH H:Asp5524.97
NaOD1 H:Asp5524.59
NaC H:Asp5524.06
NaCA H:Asp5524.34
NaHB2 H:Arg5534.95
NaN H:Arg5533.97
NaC H:Arg5533.46
NaCA H:Arg5534.35
NaO H:Arg5532.38
NaH H:Arg5534.08
NaN H:Asp5544.33
NaHA H:Asp5543.79
NaC H:Asp5544.57
NaCA H:Asp5544.37
NaN H:Gly5554.24
NaH H:Gly5553.85
NaC H:Gly5554.85
NaHB2 H:Lys5563.87
NaN H:Lys5563.83
NaCB H:Lys5564.53
NaC H:Lys5563.49
NaCA H:Lys5564.17
NaO H:Lys5562.40
NaH H:Lys5563.18
NaN H:Tyr5574.50
NaCA H:Tyr5574.78
NaHA H:Tyr5574.08
NaO H:Hoh7154.23
NaO H:Hoh7312.43
NaO H:Hoh7362.45
NaO H:Hoh7563.92
NaO H:Hoh7592.60
NaO H:Hoh7602.36
NaO H:Hoh7644.45
NaO H:Hoh7884.00

interactive model:

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