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:
|
|