Chemical elements
  Sodium
    Isotopes
    Energy
    Preparation
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    Physical Properties
    Chemical Properties
    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
      2cc7
      2cc8
      2cc9
      2ccb
      2ccc
      2cd7
      2cf8
      2cf9
      2cfd
      2cfg
      2cfk
      2cfl
      2cfw
      2cg0
      2cg1
      2cie
      2cif
      2ciq
      2cjc
      2ckr
      2cks
      2cl4
      2cle
      2clf
      2clh
      2cli
      2clk
      2cll
      2clm
      2clo
      2cn0
      2czs
      2d16
      2d1e
      2d3l
      2d3n
      2d4d
      2d4e
      2d4f
      2d4i
      2d4k
      2d6b
      2db4
      2dct
      2dda
      2ddb
      2ddc
      2ddd
      2dea
      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 Complexes of Dodecin With Flavin and Flavin-Like Ligands (pdb 2cc8)






The binding sites of Sodium atom in the structure of Complexes of Dodecin With Flavin and Flavin-Like Ligands (pdb code 2cc8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2cc8 structure was solved by M.GRININGER, K.ZETH, D.OESTERHELT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-1.9
Space groupF4132
a (A)142.350
b (A)142.350
c (A)142.350
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)19.2
Rfree (%)22.5


Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2cc8


Sodium binding site 1 out of 1 in 2cc8
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2cc8
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2cc8. 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: Lys5, A: Leu7, A: Gln59, A: Cl104, A: Hoh2003, A: Hoh2008, A: Hoh2074,

conact list:


AtomAtomDistance (A)
NaO A:Lys54.76
NaCB A:Leu74.37
NaCD2 A:Leu74.85
NaNE2 A:Gln594.60
NaOE1 A:Gln594.66
NaCL A:Cl1042.40
NaO A:Hoh20032.95
NaO A:Hoh20084.23
NaO A:Hoh20742.36

interactive model:




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