Chemical elements
  Sodium
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    PDB 131d-1bli
    PDB 1bph-1d10
    PDB 1d11-1ej2
    PDB 1eja-1gb5
    PDB 1gb6-1goh
    PDB 1gq2-1ikp
    PDB 1ikq-1jz1
    PDB 1jz2-1kvs
    PDB 1kvt-1me8
    PDB 1mg2-1nsz
    PDB 1nta-1oyt
    PDB 1p0s-1qjs
    PDB 1qnj-1s5d
    PDB 1s5e-1tjp
    PDB 1tk6-1uxt
    PDB 1uxu-1vzq
    PDB 1w15-1xc6
    PDB 1xcu-1yf1
    PDB 1ygg-1zko
    PDB 1zkp-2afh
    PDB 2agv-2bhc
    PDB 2bhp-2cc6
    PDB 2cc7-2dec
    PDB 2deg-2ein
    PDB 2eit-2fjb
    PDB 2fld-2gg8
    PDB 2gg9-2h9j
    PDB 2h9k-2ien
    PDB 2ieo-2jih
    PDB 2jin-2omd
    PDB 2omg-2p77
    PDB 2p78-2q68
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    PDB 2qzi-2v35
    PDB 2v3h-2vwo
    PDB 2vx4-2wig
    PDB 2wij-2x1z
    PDB 2x20-2xmk
    PDB 2xmm-2zfq
    PDB 2zfr-3a6s
      2zfr
      2zg0
      2zgb
      2zgx
      2zhe
      2zhf
      2zhi
      2zhj
      2zhq
      2zhw
      2zi2
      2zij
      2zik
      2zil
      2ziq
      2zj9
      2zk9
      2zka
      2zkb
      2zn8
      2znb
      2znd
      2zne
      2znk
      2zo3
      2zo5
      2zoq
      2zq3
      2zs7
      2zs9
      2zsa
      2zsd
      2zse
      2zsf
      2zsg
      2zxk
      2zxl
      2zxs
      2zxw
      2zyl
      2zyp
      352d
      378d
      3a03
      3a07
      3a0i
      3a34
      3a65
      3a66
      3a6s
    PDB 3a6t-3b1e
    PDB 3b2n-3bos
    PDB 3bov-3ccr
    PDB 3ccs-3d7r
    PDB 3d97-3e3y
    PDB 3e40-3erp
    PDB 3euw-3fgw
    PDB 3fh4-3g3r
    PDB 3g3s-3gxw
    PDB 3gyz-3hwt
    PDB 3hww-3ijp
    PDB 3imm-3k0g
    PDB 3k13-3l7x
    PDB 3l88-3max
    PDB 3mbb-3mr1
    PDB 3mty-3nu3
    PDB 3nu4-3ot1
    PDB 3ow2-3qwc
    PDB 3qx5-3tfr
    PDB 3tfs-3v6o
    PDB 3v72-4ag2
    PDB 4aga-4eae
    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Thrombin Inhibition (pdb 2zgx)






The binding sites of Sodium atom in the structure of Thrombin Inhibition (pdb code 2zgx). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2zgx structure was solved by B.BAUM, A.HEINE, G.KLEBE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)10.0-1.8
Space groupC121
a (A)70.420
b (A)71.450
c (A)72.460
alpha (°)90.00
beta (°)100.70
gamma (°)90.00
Rfactor (%)18.4
Rfree (%)24.9


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 2zgx


Sodium binding site 1 out of 2 in 2zgx
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 2zgx
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2zgx. 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: Hoh2018, H: Hoh2029, H: Hoh2030, H: Hoh2034, H: Hoh2044, H: Hoh2065, H: Hoh2093, H: Hoh2109,

conact list:


AtomAtomDistance (A)
NaO H:Tyr184A4.16
NaO H:Asp2214.71
NaC H:Asp2214.14
NaOD1 H:Asp2214.72
NaCA H:Asp2214.39
NaO H:Arg221A2.34
NaN H:Arg221A3.90
NaC H:Arg221A3.34
NaCA H:Arg221A4.25
NaN H:Asp2224.13
NaC H:Asp2224.39
NaCA H:Asp2224.19
NaN H:Gly2234.32
NaC H:Gly2234.78
NaO H:Lys2242.32
NaN H:Lys2243.80
NaCB H:Lys2244.61
NaC H:Lys2243.39
NaCA H:Lys2244.11
NaN H:Tyr2254.45
NaCA H:Tyr2254.75
NaO H:Hoh20184.25
NaO H:Hoh20292.27
NaO H:Hoh20303.90
NaO H:Hoh20343.89
NaO H:Hoh20442.38
NaO H:Hoh20652.63
NaO H:Hoh20932.58
NaO H:Hoh21094.73

interactive model:


Sodium binding site 2 out of 2 in 2zgx


Sodium binding site 2 out of 2 in 2zgx
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 2zgx
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2zgx. 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: Hoh2035, H: Hoh2049, H: Hoh2078, H: Hoh2149,

conact list:


AtomAtomDistance (A)
NaO H:Lys1692.41
NaCB H:Lys1694.90
NaC H:Lys1693.47
NaCA H:Lys1694.52
NaO H:Asp1704.74
NaN H:Asp1704.17
NaC H:Asp1704.36
NaOD1 H:Asp1704.57
NaCA H:Asp1704.00
NaN H:Ser1714.82
NaO H:Thr1722.37
NaN H:Thr1724.31
NaCG2 H:Thr1724.78
NaC H:Thr1723.58
NaCA H:Thr1724.54
NaN H:Arg1734.45
NaC H:Arg1734.94
NaCA H:Arg1734.42
NaO H:Hoh20352.85
NaO H:Hoh20492.36
NaO H:Hoh20782.41
NaO H:Hoh21494.51

interactive model:




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