Sodium in the structure of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica (pdb 3ngj)

The binding sites of Sodium atom in the structure of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica (pdb code 3ngj). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ngj structure was solved by SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.4-1.7 Space group P1211 a (A) 50.260 b (A) 70.780 c (A) 126.750 alpha (°) 90.00 beta (°) 92.46 gamma (°) 90.00 Rfactor (%) 14.6 Rfree (%) 17.5 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3ngj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ngj. 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: Val116, A: Ser119, A: Gly120, A: Lys121, A: Ala122, A: Leu123, A: Thr124, A: Glu151, A: Hoh263, A: Hoh276, A: Hoh306, A: Hoh593, A: Hoh818, A: Hoh821, A: Hoh822, conact list: Atom Atom Distance (A) Na O A:Val116 4.09 Na O A:Ser119 4.24 Na CB A:Ser119 3.50 Na OG A:Ser119 2.37 Na C A:Ser119 3.93 Na CA A:Ser119 4.33 Na O A:Gly120 2.42 Na N A:Gly120 3.91 Na C A:Gly120 3.51 Na CA A:Gly120 4.28 Na O A:Lys121 4.66 Na N A:Lys121 4.44 Na C A:Lys121 4.24 Na CA A:Lys121 4.64 Na O A:Ala122 2.29 Na N A:Ala122 4.06 Na C A:Ala122 3.47 Na CA A:Ala122 4.37 Na N A:Leu123 4.39 Na C A:Leu123 4.76 Na CA A:Leu123 4.51 Na N A:Thr124 4.78 Na OG1 A:Thr124 4.21 Na OE1 A:Glu151 4.54 Na OE2 A:Glu151 4.46 Na CD A:Glu151 4.96 Na O A:Hoh263 2.45 Na O A:Hoh276 2.42 Na O A:Hoh306 2.56 Na O A:Hoh593 4.46 Na O A:Hoh818 4.34 Na O A:Hoh821 4.39 Na O A:Hoh822 4.00 interactive model: Sodium binding site 2 out of 4 in 3ngj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ngj. 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: Val116, B: Ser119, B: Gly120, B: Lys121, B: Ala122, B: Leu123, B: Thr124, B: Glu151, B: Hoh226, B: Hoh227, B: Hoh355, B: Hoh780, B: Hoh847, conact list: Atom Atom Distance (A) Na O B:Val116 4.11 Na O B:Ser119 4.27 Na CB B:Ser119 3.39 Na OG B:Ser119 2.32 Na C B:Ser119 3.96 Na CA B:Ser119 4.29 Na O B:Gly120 2.45 Na N B:Gly120 4.00 Na C B:Gly120 3.55 Na CA B:Gly120 4.34 Na O B:Lys121 4.65 Na N B:Lys121 4.48 Na C B:Lys121 4.24 Na CA B:Lys121 4.67 Na O B:Ala122 2.22 Na N B:Ala122 4.05 Na C B:Ala122 3.41 Na CA B:Ala122 4.34 Na N B:Leu123 4.28 Na C B:Leu123 4.64 Na CA B:Leu123 4.33 Na N B:Thr124 4.64 Na OG1 B:Thr124 4.21 Na OE1 B:Glu151 4.47 Na OE2 B:Glu151 4.36 Na CD B:Glu151 4.85 Na O B:Hoh226 2.39 Na O B:Hoh227 2.48 Na O B:Hoh355 2.50 Na O B:Hoh780 3.98 Na O B:Hoh847 4.20 interactive model: Sodium binding site 3 out of 4 in 3ngj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3ngj. 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: C: Val116, C: Ser119, C: Gly120, C: Lys121, C: Ala122, C: Leu123, C: Thr124, C: Glu151, C: Hoh220, C: Hoh240, C: Hoh318, C: Hoh436, conact list: Atom Atom Distance (A) Na O C:Val116 4.15 Na O C:Ser119 4.06 Na CB C:Ser119 3.41 Na OG C:Ser119 2.37 Na C C:Ser119 3.78 Na CA C:Ser119 4.22 Na O C:Gly120 2.34 Na N C:Gly120 3.81 Na C C:Gly120 3.46 Na CA C:Gly120 4.17 Na O C:Lys121 4.62 Na N C:Lys121 4.45 Na C C:Lys121 4.22 Na CA C:Lys121 4.71 Na O C:Ala122 2.16 Na N C:Ala122 4.00 Na C C:Ala122 3.36 Na CA C:Ala122 4.28 Na N C:Leu123 4.27 Na C C:Leu123 4.74 Na CA C:Leu123 4.39 Na N C:Thr124 4.81 Na OG1 C:Thr124 4.38 Na OE1 C:Glu151 4.69 Na OE2 C:Glu151 4.48 Na O C:Hoh220 2.57 Na O C:Hoh240 2.66 Na O C:Hoh318 2.44 Na O C:Hoh436 4.42 interactive model: Sodium binding site 4 out of 4 in 3ngj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3ngj. 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: D: Val116, D: Ser119, D: Gly120, D: Lys121, D: Ala122, D: Leu123, D: Thr124, D: Glu151, D: Hoh220, D: Hoh433, D: Hoh462, D: Hoh733, D: Hoh734, conact list: Atom Atom Distance (A) Na O D:Val116 4.11 Na O D:Ser119 4.23 Na CB D:Ser119 3.47 Na OG D:Ser119 2.34 Na C D:Ser119 3.95 Na CA D:Ser119 4.33 Na O D:Gly120 2.44 Na N D:Gly120 3.92 Na C D:Gly120 3.51 Na CA D:Gly120 4.29 Na O D:Lys121 4.69 Na N D:Lys121 4.43 Na C D:Lys121 4.24 Na CA D:Lys121 4.61 Na O D:Ala122 2.21 Na N D:Ala122 4.03 Na C D:Ala122 3.42 Na CA D:Ala122 4.34 Na N D:Leu123 4.33 Na C D:Leu123 4.72 Na CA D:Leu123 4.41 Na N D:Thr124 4.70 Na OG1 D:Thr124 4.27 Na OE1 D:Glu151 4.57 Na OE2 D:Glu151 4.47 Na CD D:Glu151 4.97 Na O D:Hoh220 2.51 Na O D:Hoh433 2.42 Na O D:Hoh462 2.43 Na O D:Hoh733 4.38 Na O D:Hoh734 3.96 interactive model: