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 |
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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:
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