Sodium in the structure of The Structure of Rat Cytosolic Pepck in Complex With Phosphoglycolate and Gdp (pdb 3dtb)

The binding sites of Sodium atom in the structure of The Structure of Rat Cytosolic Pepck in Complex With Phosphoglycolate and Gdp (pdb code 3dtb). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3dtb structure was solved by S.M.SULLIVAN, T.HOLYOAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.8-1.3 Space group P1211 a (A) 62.154 b (A) 119.683 c (A) 86.849 alpha (°) 90.00 beta (°) 107.05 gamma (°) 90.00 Rfactor (%) 16.8 Rfree (%) 19.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3dtb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3dtb. 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: Leu79, A: Thr80, A: Asn208, A: Asn209, A: Trp210, A: Hoh3508, A: Hoh3545, A: Hoh3780, A: Hoh3782, A: Hoh4068, conact list: Atom Atom Distance (A) Na O A:Gly64 4.46 Na O A:Val65 4.00 Na C A:Val65 4.69 Na CA A:Val65 4.92 Na CA A:Val65 4.85 Na O A:Leu79 2.26 Na N A:Leu79 3.82 Na CB A:Leu79 3.89 Na C A:Leu79 3.37 Na CG A:Leu79 4.99 Na CA A:Leu79 3.91 Na N A:Thr80 4.50 Na CA A:Thr80 4.82 Na O A:Asn208 2.22 Na CB A:Asn208 3.98 Na C A:Asn208 3.40 Na CA A:Asn208 4.24 Na O A:Asn209 4.48 Na N A:Asn209 4.39 Na CB A:Asn209 4.33 Na C A:Asn209 4.36 Na CA A:Asn209 4.57 Na N A:Trp210 4.67 Na CB A:Trp210 4.58 Na CE3 A:Trp210 4.97 Na O A:Hoh3508 2.33 Na O A:Hoh3545 4.24 Na O A:Hoh3780 2.25 Na O A:Hoh3782 2.36 Na O A:Hoh4068 4.16 interactive model: Sodium binding site 2 out of 2 in 3dtb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3dtb. 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: Hoh1202, B: Hoh1353, B: Hoh1568, B: Hoh1569, B: Hoh1570, B: Hoh1722, conact list: Atom Atom Distance (A) Na O B:Gly64 4.28 Na O B:Val65 4.02 Na C B:Val65 4.74 Na CA B:Val65 4.90 Na C B:Ala78 4.96 Na O B:Leu79 2.22 Na N B:Leu79 3.79 Na CB B:Leu79 4.01 Na C B:Leu79 3.34 Na CA B:Leu79 3.92 Na N B:Thr80 4.47 Na CA B:Thr80 4.79 Na O B:Asn208 2.26 Na CB B:Asn208 3.90 Na C B:Asn208 3.40 Na CA B:Asn208 4.17 Na O B:Asn209 4.36 Na N B:Asn209 4.39 Na CB B:Asn209 4.27 Na C B:Asn209 4.31 Na CA B:Asn209 4.55 Na N B:Trp210 4.67 Na CB B:Trp210 4.59 Na O B:Hoh1202 2.38 Na O B:Hoh1353 2.46 Na O B:Hoh1568 4.07 Na O B:Hoh1569 4.18 Na O B:Hoh1570 2.30 Na O B:Hoh1722 4.48 interactive model: