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
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    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
      3gyz
      3gz5
      3gz6
      3gza
      3gzh
      3h09
      3h0n
      3h0u
      3h12
      3h1v
      3h2z
      3h42
      3h4z
      3h5b
      3h5i
      3h7c
      3h7k
      3h7m
      3h84
      3h8j
      3hab
      3hac
      3hb7
      3hbz
      3hc9
      3hh3
      3hh5
      3hhq
      3hij
      3hiu
      3hjb
      3hjz
      3hk7
      3hkv
      3hlj
      3hlt
      3hpt
      3hsc
      3hss
      3htl
      3hup
      3hvi
      3hvu
      3hvy
      3hw8
      3hwd
      3hwe
      3hwf
      3hwg
      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 Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression (pdb 3h7c)






The binding sites of Sodium atom in the structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression (pdb code 3h7c). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3h7c structure was solved by E.S.BURGIE, C.A.BINGMAN, G.N.PHILLIPS JR., CENTER FOREUKARYOTIC STRUCTURAL GENOMICS (CESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)50.0-1.5
Space groupC121
a (A)123.715
b (A)69.932
c (A)50.917
alpha (°)90.00
beta (°)98.40
gamma (°)90.00
Rfactor (%)14.6
Rfree (%)17.4


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 3h7c


Sodium binding site 1 out of 2 in 3h7c
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 3h7c
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3h7c. 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: X: Arg73, X: Lys74, X: Gln75, X: Leu76, X: Pro77, X: Glu78, X: Hoh602, X: Hoh723,

conact list:


AtomAtomDistance (A)
NaO X:Arg732.77
NaCZ X:Arg735.00
NaC X:Arg733.91
NaNE X:Arg734.56
NaNH2 X:Arg734.50
NaO X:Lys742.98
NaN X:Lys744.39
NaC X:Lys743.50
NaCA X:Lys743.82
NaN X:Gln754.42
NaC X:Gln754.78
NaO X:Leu762.49
NaN X:Leu764.10
NaC X:Leu763.60
NaCA X:Leu764.47
NaN X:Pro774.48
NaC X:Pro774.64
NaCA X:Pro774.47
NaN X:Glu784.77
NaO X:Hoh6023.93
NaO X:Hoh7232.78

interactive model:


Sodium binding site 2 out of 2 in 3h7c


Sodium binding site 2 out of 2 in 3h7c
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 3h7c
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3h7c. 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: X: Gly304, X: 1pe391,

conact list:


AtomAtomDistance (A)
NaCA X:Gly3044.62
NaOH2 X:1pe3913.09
NaC12 X:1pe3913.86
NaOH3 X:1pe3912.71
NaOH6 X:1pe3913.02
NaOH4 X:1pe3912.84
NaC14 X:1pe3913.54
NaC24 X:1pe3913.75
NaOH5 X:1pe3912.78
NaC25 X:1pe3913.48
NaC13 X:1pe3913.60
NaC23 X:1pe3913.57
NaC26 X:1pe3914.16
NaC22 X:1pe3913.73
NaC15 X:1pe3913.58

interactive model:




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