Sodium in the structure of The Structure of Rat Cytosolic Pepck in Complex With Phosphonoformate (pdb 2rk8)

The binding sites of Sodium atom in the structure of The Structure of Rat Cytosolic Pepck in Complex With Phosphonoformate (pdb code 2rk8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2rk8 structure was solved by S.M.SULLIVAN, R.M.STIFFIN, G.M.CARLSON, T.HOLYOAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.1-2.0 Space group P1211 a (A) 62.251 b (A) 119.470 c (A) 86.870 alpha (°) 90.00 beta (°) 107.06 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 24.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2rk8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2rk8. 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: Gly64, A: Val65, A: Ala78, A: Leu79, A: Thr80, A: Asn208, A: Asn209, A: Trp210, A: Hoh5839, A: Hoh5930, A: Hoh6047, A: Hoh6164, conact list: Atom Atom Distance (A) Na O A:Gly64 4.15 Na O A:Val65 3.62 Na C A:Val65 4.41 Na CA A:Val65 4.72 Na C A:Ala78 4.98 Na O A:Leu79 2.51 Na N A:Leu79 3.81 Na CB A:Leu79 4.05 Na C A:Leu79 3.58 Na CA A:Leu79 4.02 Na N A:Thr80 4.76 Na O A:Asn208 2.31 Na CB A:Asn208 4.22 Na CB A:Asn208 4.22 Na C A:Asn208 3.51 Na CA A:Asn208 4.43 Na CA A:Asn208 4.43 Na O A:Asn209 4.40 Na N A:Asn209 4.42 Na CB A:Asn209 4.24 Na C A:Asn209 4.35 Na CA A:Asn209 4.52 Na N A:Trp210 4.76 Na CB A:Trp210 4.78 Na O A:Hoh5839 2.75 Na O A:Hoh5930 2.28 Na O A:Hoh6047 2.18 Na O A:Hoh6164 4.34 interactive model: Sodium binding site 2 out of 2 in 2rk8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2rk8. 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: Gly64, B: Val65, B: Ala78, B: Leu79, B: Thr80, B: Asn208, B: Asn209, B: Trp210, B: Hoh3970, B: Hoh4138, B: Hoh4249, conact list: Atom Atom Distance (A) Na O B:Gly64 4.31 Na O B:Val65 3.88 Na C B:Val65 4.62 Na CA B:Val65 4.84 Na C B:Ala78 4.96 Na O B:Leu79 2.47 Na N B:Leu79 3.79 Na CB B:Leu79 4.09 Na C B:Leu79 3.53 Na CA B:Leu79 4.00 Na N B:Thr80 4.69 Na O B:Asn208 2.22 Na CB B:Asn208 4.03 Na C B:Asn208 3.40 Na CA B:Asn208 4.26 Na O B:Asn209 4.36 Na N B:Asn209 4.34 Na CB B:Asn209 4.29 Na C B:Asn209 4.29 Na CA B:Asn209 4.51 Na N B:Trp210 4.65 Na CB B:Trp210 4.78 Na O B:Hoh3970 2.32 Na O B:Hoh4138 2.53 Na O B:Hoh4249 2.25 interactive model: