Sodium in the structure of Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima At 1.60 A Resolution (pdb 1o1z)

The binding sites of Sodium atom in the structure of Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima At 1.60 A Resolution (pdb code 1o1z). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1o1z structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 48.2-1.6 Space group P21212 a (A) 132.410 b (A) 41.790 c (A) 51.720 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.9 Rfree (%) 18 Sodium Binding Sites: Sodium binding site 1 out of 1 in 1o1z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1o1z. 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: Ser111, A: Lys112, A: Lys113, A: Arg114, A: Lys115, A: Leu117, A: Hoh653, A: Hoh656, A: Hoh738, A: Hoh765, A: Hoh921, conact list: Atom Atom Distance (A) Na O A:Ser111 2.37 Na CB A:Ser111 4.51 Na C A:Ser111 3.50 Na CA A:Ser111 4.50 Na O A:Lys112 3.64 Na N A:Lys112 4.25 Na C A:Lys112 3.90 Na CA A:Lys112 4.11 Na N A:Lys113 4.59 Na C A:Lys113 4.66 Na O A:Arg114 2.22 Na N A:Arg114 3.75 Na CB A:Arg114 4.59 Na C A:Arg114 3.31 Na CA A:Arg114 4.07 Na N A:Lys115 4.28 Na CA A:Lys115 4.52 Na CD1 A:Leu117 4.23 Na CG A:Leu117 4.92 Na O A:Hoh653 4.48 Na O A:Hoh656 2.38 Na O A:Hoh738 4.96 Na O A:Hoh765 4.91 Na O A:Hoh921 4.42 interactive model: