Sodium in the structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein (pdb 4gdu)

The binding sites of Sodium atom in the structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein (pdb code 4gdu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 4gdu structure was solved by J.NOMME, A.LAVIE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:

Resolution (A)	30.0-2.1
Space group	P65
a (A)	59.220
b (A)	59.220
c (A)	298.500
alpha (°)	90.00
beta (°)	90.00
gamma (°)	120.00
Rfactor (%)	16.6
Rfree (%)	22.2

Sodium binding site 1 out of 2 in 4gdu
Click to enlarge	Click to enlarge	Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4gdu. 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: Leu55, A: Glu56, A: Asp57, A: Asp58, A: Pro59, A: Glu60, A: Phe61, A: Asn62, A: Ala63, A: Gly64, A: Cys65, A: Gly66,
conact list: Atom Atom Distance (A) Na O A:Leu55 2.44 Na C A:Leu55 3.51 Na CA A:Leu55 4.82 Na O A:Glu56 2.91 Na N A:Glu56 3.97 Na CB A:Glu56 4.97 Na C A:Glu56 3.38 Na CA A:Glu56 3.57 Na N A:Asp57 4.36 Na C A:Asp57 4.57 Na O A:Asp58 2.28 Na N A:Asp58 3.98 Na CB A:Asp58 4.75 Na C A:Asp58 3.28 Na CA A:Asp58 4.16 Na N A:Pro59 4.10 Na C A:Pro59 4.44 Na CA A:Pro59 4.19 Na N A:Glu60 4.53 Na C A:Glu60 4.99 Na O A:Phe61 2.62 Na N A:Phe61 3.84 Na CB A:Phe61 4.06 Na C A:Phe61 3.58 Na CA A:Phe61 4.01 Na N A:Asn62 4.70 Na O A:Ala63 2.35 Na N A:Ala63 3.95 Na C A:Ala63 3.52 Na CB A:Ala63 4.75 Na CA A:Ala63 4.32 Na O A:Gly64 4.91 Na N A:Gly64 4.48 Na C A:Gly64 4.31 Na CA A:Gly64 4.61 Na O A:Cys65 2.33 Na N A:Cys65 3.92 Na CB A:Cys65 4.65 Na C A:Cys65 3.49 Na CA A:Cys65 4.21 Na N A:Gly66 4.53 Na CA A:Gly66 4.73		interactive model:
Sodium binding site 2 out of 2 in 4gdu
Click to enlarge	Click to enlarge	Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4gdu. 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: B: Leu55, B: Glu56, B: Asp57, B: Asp58, B: Pro59, B: Glu60, B: Phe61, B: Asn62, B: Ala63, B: Gly64, B: Cys65, B: Gly66, B: Ser67,
conact list: Atom Atom Distance (A) Na O B:Leu55 2.80 Na C B:Leu55 3.86 Na O B:Glu56 2.79 Na N B:Glu56 4.26 Na C B:Glu56 3.37 Na CA B:Glu56 3.70 Na O B:Asp57 4.99 Na N B:Asp57 4.30 Na C B:Asp57 4.52 Na CA B:Asp57 4.87 Na O B:Asp58 2.56 Na N B:Asp58 4.24 Na C B:Asp58 3.49 Na CA B:Asp58 4.46 Na O B:Pro59 4.52 Na N B:Pro59 4.20 Na C B:Pro59 4.34 Na CA B:Pro59 4.13 Na N B:Glu60 4.89 Na O B:Phe61 2.54 Na N B:Phe61 4.02 Na CB B:Phe61 4.17 Na C B:Phe61 3.57 Na CA B:Phe61 4.09 Na N B:Asn62 4.68 Na C B:Asn62 4.93 Na O B:Ala63 2.48 Na N B:Ala63 3.95 Na C B:Ala63 3.58 Na CB B:Ala63 4.66 Na CA B:Ala63 4.30 Na O B:Gly64 4.96 Na N B:Gly64 4.56 Na C B:Gly64 4.40 Na CA B:Gly64 4.76 Na O B:Cys65 2.24 Na N B:Cys65 3.98 Na CB B:Cys65 4.89 Na C B:Cys65 3.32 Na CA B:Cys65 4.24 Na N B:Gly66 4.15 Na C B:Gly66 4.55 Na CA B:Gly66 4.14 Na N B:Ser67 4.90		interactive model: