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 Mannose (pdb 2xjp)

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 Mannose (pdb code 2xjp). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2xjp 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) 20.0-0.9 Space group P212121 a (A) 46.280 b (A) 61.820 c (A) 106.260 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 10.523 Rfree (%) 12.236 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2xjp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2xjp. 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: Hoh2031, A: Hoh2102, A: Hoh2114, A: Hoh2127, A: Hoh2193, A: Hoh2259, A: Hoh2263, A: Hoh2287, A: Hoh2421, conact list: Atom Atom Distance (A) Na CB A:Asp82 4.61 Na HA A:Asp82 4.31 Na OD2 A:Asp82 3.83 Na OD1 A:Asp82 2.26 Na C A:Asp82 4.72 Na CG A:Asp82 3.36 Na CA A:Asp82 4.76 Na N A:Tyr83 4.93 Na C A:Tyr83 4.84 Na O A:Tyr83 4.53 Na HD21 A:Asn84 4.68 Na HD21 A:Asn84 4.72 Na CB A:Asn84 4.84 Na CB A:Asn84 4.74 Na HD22 A:Asn84 3.22 Na HD22 A:Asn84 3.34 Na HB3 A:Asn84 4.98 Na ND2 A:Asn84 3.72 Na ND2 A:Asn84 3.75 Na OD1 A:Asn84 2.48 Na OD1 A:Asn84 2.42 Na CG A:Asn84 3.45 Na CG A:Asn84 3.39 Na HA A:Asn84 4.80 Na HA A:Asn84 4.83 Na HB3 A:Pro97 4.68 Na CA A:Pro97 4.77 Na HA A:Pro97 3.87 Na HB2 A:Gln98 4.80 Na N A:Gln98 4.55 Na HB3 A:Gln98 4.99 Na H A:Gln98 3.72 Na OE1 A:Glu99 4.83 Na CD1 A:Trp228 4.60 Na HD1 A:Trp228 3.86 Na HG21 A:Thr230 4.77 Na HG1 A:Thr230 3.82 Na OG1 A:Thr230 4.47 Na O A:Hoh2031 2.41 Na O A:Hoh2102 4.63 Na O A:Hoh2114 4.54 Na O A:Hoh2127 2.36 Na O A:Hoh2193 4.68 Na O A:Hoh2259 3.28 Na O A:Hoh2263 2.45 Na O A:Hoh2263 2.60 Na O A:Hoh2287 2.60 Na O A:Hoh2287 2.47 Na O A:Hoh2421 2.57 Na O A:Hoh2421 2.00 interactive model: Sodium binding site 2 out of 2 in 2xjp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2xjp. 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: Ile85, A: Pro86, A: Cys87, A: Thr93, A: Phe94, A: Pro95, A: Hoh2012, A: Hoh2023, A: Hoh2138, A: Hoh2168, A: Hoh2291, A: Hoh2310, A: Hoh2399, A: Hoh2416, conact list: Atom Atom Distance (A) Na C A:Ile85 4.94 Na HB2 A:Pro86 4.55 Na N A:Pro86 4.30 Na HG3 A:Pro86 3.08 Na CB A:Pro86 3.64 Na HB3 A:Pro86 3.06 Na CD A:Pro86 4.64 Na CG A:Pro86 3.79 Na CA A:Pro86 3.75 Na HG2 A:Pro86 4.49 Na HD3 A:Pro86 4.81 Na HA A:Pro86 3.10 Na H A:Cys87 4.72 Na CG2 A:Thr93 4.16 Na C A:Thr93 4.58 Na HG21 A:Thr93 4.22 Na O A:Thr93 4.57 Na HG22 A:Thr93 4.56 Na HG23 A:Thr93 3.30 Na N A:Phe94 4.34 Na C A:Phe94 3.68 Na CA A:Phe94 4.13 Na O A:Phe94 4.16 Na HA A:Phe94 3.79 Na H A:Phe94 4.64 Na N A:Pro95 3.50 Na HG3 A:Pro95 4.63 Na CB A:Pro95 4.12 Na HB3 A:Pro95 3.57 Na CD A:Pro95 3.72 Na CG A:Pro95 4.48 Na CA A:Pro95 3.86 Na HD2 A:Pro95 4.47 Na HD3 A:Pro95 3.06 Na HA A:Pro95 3.46 Na O A:Hoh2012 4.90 Na O A:Hoh2023 3.04 Na O A:Hoh2138 3.27 Na O A:Hoh2138 2.89 Na O A:Hoh2168 2.99 Na O A:Hoh2291 4.81 Na O A:Hoh2310 3.22 Na O A:Hoh2399 4.58 Na O A:Hoh2416 4.43 interactive model: