Sodium in the structure of Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex With Pyruvate (pdb 3fkr)

The binding sites of Sodium atom in the structure of Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex With Pyruvate (pdb code 3fkr). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3fkr structure was solved by N.SHIMADA, B.MIKAMI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-1.8 Space group P3121 a (A) 79.259 b (A) 79.259 c (A) 206.527 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.6 Rfree (%) 23.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3fkr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3fkr. 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: Gln154, A: Kpi182, A: Glu184, A: Gly209, A: Glu210, A: Glu211, A: Hoh1087, A: Hoh1088, conact list: Atom Atom Distance (A) Na OE1 A:Gln154 4.41 Na CX1 A:Kpi182 2.92 Na CX2 A:Kpi182 2.96 Na C1 A:Kpi182 4.38 Na O1 A:Kpi182 2.38 Na CD A:Kpi182 4.17 Na O2 A:Kpi182 4.14 Na CE A:Kpi182 3.12 Na NZ A:Kpi182 2.23 Na OE1 A:Glu184 2.71 Na CB A:Glu184 4.99 Na OE2 A:Glu184 2.04 Na CD A:Glu184 2.69 Na CG A:Glu184 4.08 Na C A:Gly209 4.84 Na CA A:Gly209 4.72 Na N A:Glu210 3.97 Na CA A:Glu210 4.68 Na OE2 A:Glu211 4.08 Na O A:Hoh1087 2.36 Na O A:Hoh1088 3.83 interactive model: Sodium binding site 2 out of 2 in 3fkr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3fkr. 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: Gln154, B: Kpi182, B: Glu184, B: Gly209, B: Glu210, B: Glu211, B: Hoh895, B: Hoh997, B: Hoh1041, B: Hoh1046, conact list: Atom Atom Distance (A) Na OE1 B:Gln154 4.38 Na CX1 B:Kpi182 2.98 Na CX2 B:Kpi182 3.04 Na C1 B:Kpi182 4.42 Na O1 B:Kpi182 4.19 Na CD B:Kpi182 4.22 Na O2 B:Kpi182 2.41 Na CE B:Kpi182 3.05 Na NZ B:Kpi182 2.26 Na OE1 B:Glu184 2.78 Na OE2 B:Glu184 2.11 Na CD B:Glu184 2.75 Na CG B:Glu184 4.17 Na C B:Gly209 4.81 Na CA B:Gly209 4.65 Na N B:Glu210 3.99 Na CA B:Glu210 4.76 Na OE2 B:Glu211 4.01 Na O B:Hoh895 2.73 Na O B:Hoh997 3.97 Na O B:Hoh1041 3.41 Na O B:Hoh1046 2.31 interactive model: