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Sodium in the structure of Complex of Recombinant Human Thrombin With A Inhibitor (pdb 2cf8)

The binding sites of Sodium atom in the structure of Complex of Recombinant Human Thrombin With A Inhibitor (pdb code 2cf8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2cf8 structure was solved by E.SCHWEIZER, A.HOFFMANN-ROEDER, J.A.OLSEN, U.OBST-SANDER, B.WAGNER, M.KANSY, D.W.BANNER, F.DIEDERICH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)71.2-1.3
Space groupC121
a (A)71.070
b (A)71.510
c (A)72.400
alpha (°)90.00
beta (°)100.25
gamma (°)90.00
Rfactor (%)18
Rfree (%)19.9

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2cf8

Sodium binding site 1 out of 1 in 2cf8
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2cf8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2cf8. 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: Tyr184A, H: Asp221, H: Arg221A, H: Asp222, H: Gly223, H: Lys224, H: Tyr225, H: Hoh2261, H: Hoh2273, H: Hoh2274, H: Hoh2275, H: Hoh2297, H: Hoh2304, H: Hoh2308, H: Hoh2312, H: Hoh2313,

conact list:

AtomAtomDistance (A)
NaO H:Tyr184A4.06
NaO H:Asp2214.58
NaHA H:Asp2213.73
NaH H:Asp2214.99
NaOD1 H:Asp2214.71
NaC H:Asp2214.09
NaCA H:Asp2214.41
NaHB2 H:Arg221A4.78
NaN H:Arg221A3.85
NaC H:Arg221A3.34
NaCA H:Arg221A4.23
NaO H:Arg221A2.28
NaHA H:Arg221A4.95
NaH H:Arg221A3.87
NaN H:Asp2224.20
NaHA H:Asp2223.73
NaH H:Asp2224.98
NaC H:Asp2224.46
NaCA H:Asp2224.29
NaN H:Gly2234.22
NaH H:Gly2233.89
NaC H:Gly2234.81
NaHB2 H:Lys2243.88
NaN H:Lys2243.80
NaCB H:Lys2244.53
NaC H:Lys2243.42
NaCA H:Lys2244.13
NaO H:Lys2242.28
NaH H:Lys2243.17
NaN H:Tyr2254.46
NaCA H:Tyr2254.78
NaHA H:Tyr2254.10
NaO H:Hoh22612.76
NaO H:Hoh22734.01
NaO H:Hoh22744.33
NaO H:Hoh22754.45
NaO H:Hoh22974.95
NaO H:Hoh23042.55
NaO H:Hoh23084.02
NaO H:Hoh23122.48
NaO H:Hoh23132.30

interactive model:

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