Sodium in the structure of X-Ray Structure Of The N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex With Calcium and MAN5(D2-D3) (pdb 2xjr)

The binding sites of Sodium atom in the structure of X-Ray Structure Of The N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex With Calcium and MAN5(D2-D3) (pdb code 2xjr). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2xjr structure was solved by M.VEELDERS, S.BRUECKNER, D.OTT, C.UNVERZAGT, H.-U.MOESCH, L.-O.ESSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.4-1.2 Space group P212121 a (A) 46.460 b (A) 61.910 c (A) 106.430 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 11.321 Rfree (%) 13.996 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2xjr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2xjr. 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: Asp82, A: Tyr83, A: Asn84, A: Pro97, A: Gln98, A: Glu99, A: Trp228, A: Thr230, A: Hoh2033, A: Hoh2108, A: Hoh2120, A: Hoh2170, A: Hoh2192, A: Hoh2319, A: Hoh2374, A: Hoh2375, A: Hoh2376, A: Hoh2389, conact list: Atom Atom Distance (A) Na O A:Asp82 4.90 Na CB A:Asp82 4.61 Na OD2 A:Asp82 3.85 Na C A:Asp82 4.65 Na OD1 A:Asp82 2.21 Na CG A:Asp82 3.35 Na CA A:Asp82 4.74 Na O A:Tyr83 4.51 Na N A:Tyr83 4.90 Na C A:Tyr83 4.80 Na CB A:Asn84 4.76 Na ND2 A:Asn84 3.64 Na OD1 A:Asn84 2.44 Na CG A:Asn84 3.37 Na CA A:Pro97 4.79 Na NE2 A:Gln98 3.40 Na N A:Gln98 4.53 Na OE1 A:Gln98 2.27 Na CD A:Gln98 3.17 Na CG A:Gln98 4.59 Na OE1 A:Glu99 4.90 Na CD1 A:Trp228 4.62 Na OG1 A:Thr230 4.58 Na O A:Hoh2033 2.44 Na O A:Hoh2108 2.69 Na O A:Hoh2120 4.72 Na O A:Hoh2170 2.40 Na O A:Hoh2192 2.66 Na O A:Hoh2319 4.59 Na O A:Hoh2374 1.70 Na O A:Hoh2375 3.64 Na O A:Hoh2376 4.58 Na O A:Hoh2389 2.48 Na O A:Hoh2389 4.00 interactive model: Sodium binding site 2 out of 2 in 2xjr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2xjr. 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: Pro86, A: Thr93, A: Phe94, A: Pro95, A: Hoh2016, A: Hoh2047, A: Hoh2186, A: Hoh2225, A: Hoh2338, A: Hoh2372, A: Hoh2403, conact list: Atom Atom Distance (A) Na N A:Pro86 4.32 Na CB A:Pro86 3.62 Na CD A:Pro86 4.64 Na CG A:Pro86 3.79 Na CA A:Pro86 3.78 Na O A:Thr93 4.44 Na CG2 A:Thr93 4.13 Na C A:Thr93 4.50 Na O A:Phe94 4.17 Na N A:Phe94 4.29 Na C A:Phe94 3.66 Na CA A:Phe94 4.06 Na N A:Pro95 3.46 Na CB A:Pro95 4.15 Na CD A:Pro95 3.73 Na CG A:Pro95 4.48 Na CA A:Pro95 3.88 Na O A:Hoh2016 4.85 Na O A:Hoh2047 3.02 Na O A:Hoh2186 3.04 Na O A:Hoh2225 4.43 Na O A:Hoh2338 3.01 Na O A:Hoh2372 4.70 Na O A:Hoh2403 4.08 interactive model: