Chemical elements
  Sodium
    Isotopes
    Energy
    Preparation
    Applications
    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
      1qnj
      1qnx
      1qop
      1qrv
      1qsx
      1qtk
      1qus
      1qut
      1qvf
      1qvg
      1qw7
      1qy0
      1qy1
      1qy2
      1r4p
      1r89
      1r8a
      1r8b
      1r8c
      1riw
      1rjo
      1rlh
      1rm6
      1rrk
      1rs0
      1rtk
      1rtq
      1rv8
      1rvg
      1rw9
      1rwc
      1rwf
      1rwg
      1rwh
      1rwt
      1rys
      1rzt
      1s06
      1s07
      1s08
      1s09
      1s0a
      1s1k
      1s36
      1s3x
      1s45
      1s47
      1s5b
      1s5c
      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
    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 Cholera Holotoxin With An A-Subunit Y30S Mutation, Crystal Form 1 (pdb 1s5c)






The binding sites of Sodium atom in the structure of Cholera Holotoxin With An A-Subunit Y30S Mutation, Crystal Form 1 (pdb code 1s5c). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1s5c structure was solved by C.J.O'NEAL, E.I.AMAYA, M.G.JOBLING, R.K.HOLMES, W.G.HOL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-2.5
Space groupP1211
a (A)58.818
b (A)85.199
c (A)71.255
alpha (°)90.00
beta (°)104.48
gamma (°)90.00
Rfactor (%)19.5
Rfree (%)26.2


Sodium Binding Sites:

Sodium binding site 1 out of 1 in 1s5c


Sodium binding site 1 out of 1 in 1s5c
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 1s5c
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1s5c. 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: Asn1, A: Asp2, A: Asp3, A: Ala89, A: Thr90, A: Ala91, A: Tyr150, A: Ser151, A: Leu153, A: Asp154, A: Hoh253,

conact list:


AtomAtomDistance (A)
NaO A:Asn12.31
NaN A:Asn14.14
NaC A:Asn13.54
NaCA A:Asn14.49
NaN A:Asp24.42
NaC A:Asp24.59
NaCA A:Asp24.42
NaO A:Asp34.16
NaN A:Asp34.27
NaC A:Ala894.60
NaCB A:Ala894.71
NaCA A:Ala894.97
NaO A:Thr902.66
NaN A:Thr903.60
NaCB A:Thr903.74
NaCG2 A:Thr904.64
NaOG1 A:Thr902.57
NaC A:Thr903.58
NaCA A:Thr903.83
NaN A:Ala914.80
NaO A:Tyr1502.35
NaCB A:Tyr1504.78
NaC A:Tyr1503.52
NaCA A:Tyr1504.61
NaO A:Ser1514.73
NaN A:Ser1514.23
NaC A:Ser1514.57
NaCA A:Ser1514.07
NaO A:Leu1532.62
NaN A:Leu1534.47
NaCB A:Leu1534.69
NaC A:Leu1533.61
NaCA A:Leu1534.46
NaN A:Asp1544.45
NaCA A:Asp1544.65
NaO A:Hoh2534.56

interactive model:




© Copyright 2008-2012 by atomistry.com