Sodium in the structure of High Resolution Structure of Thermus Thermophilus Enoyl- Acyl Carrier Protein Reductase Apo-Form (pdb 2wyu)

The binding sites of Sodium atom in the structure of High Resolution Structure of Thermus Thermophilus Enoyl- Acyl Carrier Protein Reductase Apo-Form (pdb code 2wyu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2wyu structure was solved by J.M.OTERO, A.J.NOEL, P.GUARDADO-CALVO, A.L.LLAMAS-SAIZ, M.J.VAN RAAIJ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-1.5 Space group P1211 a (A) 54.270 b (A) 107.800 c (A) 85.980 alpha (°) 90.00 beta (°) 95.89 gamma (°) 90.00 Rfactor (%) 16.995 Rfree (%) 19.972 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2wyu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wyu. 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: Glu100, A: Ala101, A: Met102, A: Glu103, A: Gly104, A: Arg105, A: Asp108, A: Hoh2036, A: Hoh2084, A: Hoh2191, A: Hoh2197, A: Hoh2200, A: Hoh2203, A: Hoh2212, conact list: Atom Atom Distance (A) Na O A:Glu100 2.22 Na CB A:Glu100 4.91 Na OE2 A:Glu100 4.56 Na CD A:Glu100 4.50 Na C A:Glu100 3.41 Na CG A:Glu100 4.19 Na CA A:Glu100 4.44 Na O A:Ala101 4.14 Na N A:Ala101 4.22 Na C A:Ala101 4.23 Na CA A:Ala101 4.15 Na N A:Met102 4.98 Na O A:Glu103 2.53 Na N A:Glu103 4.57 Na CB A:Glu103 4.73 Na C A:Glu103 3.65 Na CA A:Glu103 4.54 Na N A:Gly104 4.48 Na C A:Gly104 4.62 Na CA A:Gly104 4.41 Na O A:Arg105 4.51 Na N A:Arg105 4.58 Na O A:Asp108 4.58 Na CB A:Asp108 4.81 Na C A:Asp108 4.93 Na O A:Hoh2036 4.92 Na O A:Hoh2084 2.49 Na O A:Hoh2191 2.43 Na O A:Hoh2197 2.25 Na O A:Hoh2200 4.25 Na O A:Hoh2203 2.30 Na O A:Hoh2212 4.40 interactive model: Sodium binding site 2 out of 3 in 2wyu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wyu. 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: Glu100, B: Ala101, B: Glu103, B: Gly104, B: Arg105, B: Asp108, B: Hoh2155, B: Hoh2158, B: Hoh2160, B: Hoh2164, B: Hoh2166, B: Hoh2171, conact list: Atom Atom Distance (A) Na O B:Glu100 2.47 Na CB B:Glu100 4.87 Na C B:Glu100 3.51 Na CG B:Glu100 4.13 Na CA B:Glu100 4.52 Na O B:Ala101 4.38 Na N B:Ala101 4.25 Na C B:Ala101 4.42 Na CA B:Ala101 4.18 Na O B:Glu103 2.69 Na N B:Glu103 4.76 Na CB B:Glu103 4.97 Na C B:Glu103 3.89 Na CA B:Glu103 4.78 Na N B:Gly104 4.80 Na CA B:Gly104 4.76 Na O B:Arg105 4.58 Na N B:Arg105 4.91 Na O B:Asp108 4.27 Na CB B:Asp108 4.70 Na C B:Asp108 4.67 Na O B:Hoh2155 4.01 Na O B:Hoh2158 2.56 Na O B:Hoh2160 2.24 Na O B:Hoh2164 1.96 Na O B:Hoh2166 4.50 Na O B:Hoh2171 4.06 interactive model: Sodium binding site 3 out of 3 in 2wyu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2wyu. 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: D: Glu100, D: Ala101, D: Glu103, D: Gly104, D: Arg105, D: Asp108, D: Hoh2054, D: Hoh2137, D: Hoh2139, D: Hoh2142, D: Hoh2147, conact list: Atom Atom Distance (A) Na O D:Glu100 2.31 Na CB D:Glu100 4.70 Na C D:Glu100 3.40 Na CA D:Glu100 4.42 Na O D:Ala101 4.40 Na N D:Ala101 4.16 Na C D:Ala101 4.40 Na CA D:Ala101 4.13 Na O D:Glu103 2.84 Na N D:Glu103 4.75 Na CB D:Glu103 4.85 Na C D:Glu103 3.93 Na CA D:Glu103 4.77 Na N D:Gly104 4.79 Na CA D:Gly104 4.76 Na O D:Arg105 4.64 Na N D:Arg105 4.87 Na O D:Asp108 4.44 Na CB D:Asp108 4.86 Na C D:Asp108 4.83 Na O D:Hoh2054 2.57 Na O D:Hoh2137 2.27 Na O D:Hoh2139 2.18 Na O D:Hoh2142 4.45 Na O D:Hoh2147 3.99 interactive model: