Chemical elements
  Sodium
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      3qx5
      3r57
      3r9b
      3r9c
      3ra3
      3rga
      3rlw
      3rly
      3rm0
      3rm2
      3rml
      3rmm
      3rmn
      3rmo
      3rn1
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      3rwg
      3rwk
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      3s0t
      3s45
      3s54
      3s9o
      3sha
      3shc
      3shh
      3shx
      3si3
      3si4
      3sjl
      3sko
      3sla
      3spv
      3spx
      3suj
      3sv2
      3svw
      3sws
      3sxt
      3syu
      3szs
      3t34
      3t4u
      3t5f
      3t7z
      3t8j
      3t90
      3t9g
      3tbh
      3tfr
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    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Human Thrombin in Complex With MI328 (pdb 3rlw)






The binding sites of Sodium atom in the structure of Human Thrombin in Complex With MI328 (pdb code 3rlw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3rlw structure was solved by A.BIELA, A.HEINE, G.KLEBE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)34.6-1.7
Space groupC121
a (A)70.500
b (A)71.300
c (A)72.500
alpha (°)90.00
beta (°)100.60
gamma (°)90.00
Rfactor (%)16.3
Rfree (%)19.2


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 3rlw


Sodium binding site 1 out of 2 in 3rlw
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 3rlw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3rlw. 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: Lys169, H: Asp170, H: Ser171, H: Thr172, H: Arg173, H: Ile174, H: Hoh1062, H: Hoh1064, H: Hoh1076, H: Hoh1169,

conact list:


AtomAtomDistance (A)
NaO H:Lys1692.41
NaCB H:Lys1694.90
NaC H:Lys1693.49
NaCA H:Lys1694.53
NaO H:Asp1704.85
NaN H:Asp1704.22
NaC H:Asp1704.47
NaOD1 H:Asp1704.77
NaCA H:Asp1704.11
NaN H:Ser1714.93
NaO H:Thr1722.35
NaN H:Thr1724.31
NaCG2 H:Thr1724.65
NaC H:Thr1723.58
NaCA H:Thr1724.54
NaN H:Arg1734.44
NaC H:Arg1734.90
NaCA H:Arg1734.41
NaO H:Ile1744.95
NaO H:Hoh10622.49
NaO H:Hoh10642.32
NaO H:Hoh10762.44
NaO H:Hoh11694.46

interactive model:


Sodium binding site 2 out of 2 in 3rlw


Sodium binding site 2 out of 2 in 3rlw
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 3rlw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3rlw. 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: Hoh1052, H: Hoh1054, H: Hoh1079, H: Hoh1086, H: Hoh1093, H: Hoh1103, H: Hoh1120, H: Hoh1167,

conact list:


AtomAtomDistance (A)
NaO H:Tyr184A4.00
NaO H:Asp2214.65
NaC H:Asp2214.16
NaOD1 H:Asp2214.65
NaCA H:Asp2214.45
NaO H:Arg221A2.32
NaN H:Arg221A3.98
NaC H:Arg221A3.37
NaCA H:Arg221A4.31
NaN H:Asp2224.17
NaC H:Asp2224.44
NaCA H:Asp2224.24
NaN H:Gly2234.12
NaC H:Gly2234.80
NaO H:Lys2242.38
NaN H:Lys2243.82
NaCB H:Lys2244.55
NaC H:Lys2243.48
NaCA H:Lys2244.17
NaN H:Tyr2254.51
NaCA H:Tyr2254.78
NaO H:Hoh10524.29
NaO H:Hoh10543.90
NaO H:Hoh10793.92
NaO H:Hoh10862.44
NaO H:Hoh10932.55
NaO H:Hoh11032.44
NaO H:Hoh11204.80
NaO H:Hoh11672.37

interactive model:




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