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
      1s5e
      1s5f
      1s5m
      1s5n
      1s72
      1s81
      1s82
      1s9z
      1sa3
      1saz
      1sb1
      1sca
      1scn
      1sed
      1sfh
      1sfq
      1sg8
      1sgw
      1sih
      1sii
      1sk4
      1so8
      1soo
      1spb
      1ss4
      1su3
      1su4
      1sue
      1sup
      1suz
      1sve
      1svy
      1t2x
      1t3m
      1t3p
      1t4b
      1t64
      1t67
      1t6b
      1t76
      1t8u
      1t9i
      1tae
      1tbz
      1tc8
      1tec
      1tg7
      1thm
      1tjo
      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
    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
    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 Crystal Structure of Krait-Venom Phospholipase A2 in A Complex With A Natural Fatty Acid Tridecanoic Acid (pdb 1tc8)






The binding sites of Sodium atom in the structure of Crystal Structure of Krait-Venom Phospholipase A2 in A Complex With A Natural Fatty Acid Tridecanoic Acid (pdb code 1tc8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1tc8 structure was solved by G.SINGH, J.JASTI, K.SARAVANAN, S.SHARMA, P.KAUR, A.SRINIVASAN, T.P.SINGH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-2.7
Space groupP41212
a (A)53.790
b (A)53.790
c (A)82.500
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)20.4
Rfree (%)23.3


Sodium Binding Sites:

Sodium binding site 1 out of 1 in 1tc8


Sodium binding site 1 out of 1 in 1tc8
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 1tc8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1tc8. 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: Tyr28, A: Cys29, A: Gly30, A: Lys31, A: Gly32, A: Gly33, A: Cys45, A: Asp49, A: Arg114, A: Hoh129, A: Hoh159, A: Hoh168,

conact list:


AtomAtomDistance (A)
NaO A:Tyr282.66
NaCB A:Tyr284.49
NaCD2 A:Tyr284.49
NaC A:Tyr283.73
NaCG A:Tyr284.99
NaCA A:Tyr284.18
NaN A:Cys294.88
NaC A:Cys294.96
NaO A:Gly302.70
NaN A:Gly304.39
NaC A:Gly303.78
NaCA A:Gly304.75
NaO A:Lys314.26
NaN A:Lys314.50
NaC A:Lys313.73
NaCA A:Lys314.37
NaO A:Gly322.63
NaN A:Gly323.20
NaC A:Gly322.92
NaCA A:Gly323.37
NaN A:Gly333.64
NaCA A:Gly334.11
NaO A:Cys454.94
NaCB A:Asp494.48
NaOD2 A:Asp492.54
NaOD1 A:Asp492.79
NaCG A:Asp493.00
NaNH2 A:Arg1144.35
NaO A:Hoh1294.45
NaO A:Hoh1593.38
NaO A:Hoh1684.93

interactive model:




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