Chemical elements
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    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Effect of Glycine-Amide (Glyad) on Lysozyme (pdb 2zxs)

The binding sites of Sodium atom in the structure of Effect of Glycine-Amide (Glyad) on Lysozyme (pdb code 2zxs). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2zxs structure was solved by L.ITO, K.SHIRAKI, H.YAMAGUCHI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)35.1-1.4
Space groupP43212
a (A)78.482
b (A)78.482
c (A)36.927
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)21.3
Rfree (%)23.8

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2zxs

Sodium binding site 1 out of 1 in 2zxs
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2zxs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2zxs. 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: Ser60, A: Arg61, A: Trp62, A: Cys64, A: Asn65, A: Asp66, A: Thr69, A: Ser72, A: Arg73, A: Asn74, A: Hoh146, A: Hoh166, A: Hoh176, A: Hoh252,

conact list:

AtomAtomDistance (A)
NaO A:Ser602.30
NaCB A:Ser604.25
NaC A:Ser603.45
NaCA A:Ser604.08
NaO A:Arg614.85
NaO A:Arg614.81
NaN A:Arg614.55
NaN A:Arg614.56
NaC A:Arg614.66
NaC A:Arg614.65
NaCA A:Arg614.86
NaCA A:Arg614.88
NaN A:Trp624.84
NaO A:Cys642.58
NaN A:Cys644.64
NaC A:Cys643.69
NaCA A:Cys644.81
NaN A:Asn654.32
NaCB A:Asn654.90
NaC A:Asn654.96
NaOD1 A:Asn654.72
NaCA A:Asn654.07
NaN A:Asp664.71
NaO A:Thr694.70
NaCB A:Thr694.49
NaCG2 A:Thr694.96
NaOG1 A:Thr694.95
NaO A:Ser724.73
NaCB A:Ser723.36
NaOG A:Ser722.48
NaC A:Ser724.18
NaCA A:Ser724.38
NaO A:Arg732.58
NaN A:Arg734.02
NaC A:Arg733.58
NaCA A:Arg734.38
NaN A:Asn744.45
NaCB A:Asn744.85
NaCA A:Asn744.69
NaO A:Hoh1464.58
NaO A:Hoh1662.37
NaO A:Hoh1762.24
NaO A:Hoh2524.74

interactive model:

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