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Sodium in the structure of Unliganded Wild-Type Human Thrombin (pdb 3u69)

The binding sites of Sodium atom in the structure of Unliganded Wild-Type Human Thrombin (pdb code 3u69). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3u69 structure was solved by A.C.FIGUEIREDO, C.C.CLEMENT, M.PHILIPP, P.J.BARBOSA PEREIRA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)47.3-1.6
Space groupP212121
a (A)57.555
b (A)72.995
c (A)83.042
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)13.3
Rfree (%)16.7

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 3u69

Sodium binding site 1 out of 1 in 3u69
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 3u69
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3u69. 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: Hoh6, H: Hoh11, H: Hoh18, H: Hoh19, H: Hoh27, H: Hoh29, H: Hoh52, H: Hoh65, H: Hoh66,

conact list:

AtomAtomDistance (A)
NaO H:Tyr5104.09
NaO H:Asp5524.57
NaHA H:Asp5523.66
NaH H:Asp5525.00
NaOD1 H:Asp5524.60
NaC H:Asp5524.08
NaCA H:Asp5524.36
NaHB2 H:Arg5534.85
NaN H:Arg5533.88
NaC H:Arg5533.38
NaCA H:Arg5534.24
NaO H:Arg5532.30
NaHA H:Arg5534.94
NaH H:Arg5533.94
NaN H:Asp5544.28
NaHA H:Asp5543.81
NaC H:Asp5544.61
NaCA H:Asp5544.39
NaN H:Gly5554.29
NaH H:Gly5553.89
NaC H:Gly5554.91
NaHB2 H:Lys5563.85
NaN H:Lys5563.90
NaCB H:Lys5564.50
NaHB3 H:Lys5564.96
NaC H:Lys5563.44
NaCA H:Lys5564.15
NaO H:Lys5562.35
NaH H:Lys5563.30
NaN H:Tyr5574.46
NaCA H:Tyr5574.75
NaHA H:Tyr5574.04
NaO H:Hoh62.38
NaO H:Hoh112.42
NaO H:Hoh183.90
NaO H:Hoh192.44
NaO H:Hoh274.20
NaO H:Hoh292.61
NaO H:Hoh524.99
NaO H:Hoh654.92
NaO H:Hoh664.01

interactive model:

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