Sodium in the structure of Crystal Structure Of A Member of the Enolase Superfamily From Agrobacterium Tumefaciens (pdb 2nql)

The binding sites of Sodium atom in the structure of Crystal Structure Of A Member of the Enolase Superfamily From Agrobacterium Tumefaciens (pdb code 2nql). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2nql structure was solved by Y.PATSKOVSKY, U.RAMAGOPAL, R.TORO, J.M.SAUDER, M.DICKEY, J.M.ADAMS, S.OZYURT, S.R.WASSERMAN, J.GERLT, S.K.BURLEY, S.C.ALMO, NEW YORK SGXRESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.8 Space group P6522 a (A) 102.071 b (A) 102.071 c (A) 369.202 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.9 Rfree (%) 20.1 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2nql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2nql. 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: Lys184, A: Glu240, A: Glu266, A: Gln287, A: His315, A: Glu341, A: Hoh1224, A: Hoh1241, A: Hoh1360, A: Hoh1398, A: Hoh1478, conact list: Atom Atom Distance (A) Na NZ A:Lys184 3.91 Na OE1 A:Glu240 3.50 Na OE2 A:Glu240 2.27 Na CD A:Glu240 3.08 Na CG A:Glu240 4.13 Na N A:Glu266 4.97 Na OE1 A:Glu266 2.15 Na CB A:Glu266 3.59 Na OE2 A:Glu266 4.28 Na CD A:Glu266 3.26 Na CG A:Glu266 3.78 Na CA A:Glu266 4.83 Na O A:Gln287 4.96 Na NE2 A:Gln287 4.01 Na OE1 A:Gln287 3.73 Na CB A:Gln287 4.31 Na CD A:Gln287 3.92 Na CG A:Gln287 4.71 Na NE2 A:His315 4.11 Na CB A:His315 4.44 Na CD2 A:His315 3.23 Na CG A:His315 4.09 Na OE1 A:Glu341 4.57 Na O A:Hoh1224 2.91 Na O A:Hoh1241 4.71 Na O A:Hoh1360 2.37 Na O A:Hoh1398 3.96 Na O A:Hoh1478 4.10 interactive model: Sodium binding site 2 out of 2 in 2nql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2nql. 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: Tyr156, B: Lys184, B: Glu240, B: Glu266, B: Gln287, B: His315, B: Glu341, B: Hoh1217, B: Hoh1239, B: Hoh1483, B: Hoh1531, conact list: Atom Atom Distance (A) Na OH B:Tyr156 4.57 Na CE B:Lys184 4.80 Na NZ B:Lys184 3.39 Na OE1 B:Glu240 3.46 Na OE2 B:Glu240 2.93 Na CD B:Glu240 3.47 Na CG B:Glu240 4.71 Na OE1 B:Glu266 3.35 Na CB B:Glu266 4.29 Na CD B:Glu266 4.39 Na CG B:Glu266 4.85 Na O B:Gln287 4.80 Na NE2 B:Gln287 3.29 Na OE1 B:Gln287 3.51 Na CB B:Gln287 3.72 Na CD B:Gln287 3.34 Na CG B:Gln287 3.99 Na NE2 B:His315 4.70 Na N B:His315 4.96 Na CB B:His315 4.11 Na CD2 B:His315 3.52 Na CG B:His315 4.16 Na CA B:His315 4.45 Na OE1 B:Glu341 4.01 Na OE2 B:Glu341 2.29 Na CD B:Glu341 3.46 Na CG B:Glu341 4.63 Na O B:Hoh1217 3.60 Na O B:Hoh1239 3.42 Na O B:Hoh1483 3.77 Na O B:Hoh1531 3.86 interactive model: