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
    PDB 2q69-2qz7
    PDB 2qzi-2v35
    PDB 2v3h-2vwo
    PDB 2vx4-2wig
    PDB 2wij-2x1z
    PDB 2x20-2xmk
    PDB 2xmm-2zfq
      2xmm
      2xn4
      2xn9
      2xna
      2xnj
      2xvx
      2xvz
      2xw7
      2xxr
      2xxt
      2xxu
      2xxz
      2xyn
      2xz2
      2xzi
      2xzj
      2xzk
      2y00
      2y02
      2y03
      2y04
      2y4j
      2y85
      2y8k
      2yeq
      2yfa
      2ygj
      2yj7
      2yxt
      2yxu
      2yyk
      2z12
      2z18
      2z19
      2z1n
      2z2f
      2z3b
      2z4o
      2z5d
      2z68
      2z8f
      2zak
      2zal
      2zc9
      2zda
      2zdv
      2zf0
      2zff
      2zfp
      2zfq
    PDB 2zfr-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
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    PDB 3hww-3ijp
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    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 Crystal Structure of the Ternary Complex Between Human T Cell Receptor, Staphylococcal Enterotoxin H and Human Major Histocompatibility Complex Class II (pdb 2xn9)






The binding sites of Sodium atom in the structure of Crystal Structure of the Ternary Complex Between Human T Cell Receptor, Staphylococcal Enterotoxin H and Human Major Histocompatibility Complex Class II (pdb code 2xn9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2xn9 structure was solved by M.SALINE, K.E.J.RODSTROM, G.FISCHER, V.Y.OREKHOV, B.G.KARLSSON, K.LINDKVIST-PETERSSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)152.5-2.3
Space groupC121
a (A)191.180
b (A)48.890
c (A)166.720
alpha (°)90.00
beta (°)113.55
gamma (°)90.00
Rfactor (%)22.15
Rfree (%)27.236


Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2xn9


Sodium binding site 1 out of 1 in 2xn9
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2xn9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2xn9. 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: A: Thr51, C: Gly19, C: Gln20, C: His23, C: Pro24, C: Phe25, C: Ala76, C: Ser77, C: Phe78, A: Hoh2029, A: Hoh2030, C: Hoh2011, C: Hoh2028,

conact list:


AtomAtomDistance (A)
NaOG1 A:Thr514.33
NaO C:Gly194.20
NaO C:Gln204.60
NaNE2 C:Gln204.14
NaOE1 C:Gln204.12
NaCD C:Gln204.44
NaCA C:Gln204.72
NaO C:His232.22
NaN C:His234.91
NaCB C:His233.98
NaC C:His233.35
NaCA C:His234.22
NaN C:Pro244.25
NaC C:Pro244.71
NaCA C:Pro244.29
NaN C:Phe255.00
NaC C:Ala764.73
NaO C:Ser772.47
NaN C:Ser773.59
NaCB C:Ser773.68
NaOG C:Ser772.50
NaC C:Ser773.44
NaCA C:Ser773.78
NaN C:Phe784.65
NaO A:Hoh20294.97
NaO A:Hoh20302.18
NaO C:Hoh20112.47
NaO C:Hoh20282.71

interactive model:




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