The binding sites of Sodium atom in the structure of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant With Coenzyme A. (pdb code 2wl4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2wl4 structure was solved by G.MERILAINEN, V.POIKELA, P.KURSULA, R.K.WIERENGA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 19.6-1.8 | Space group | P1211 | a (A) | 84.310 | b (A) | 79.140 | c (A) | 149.410 | alpha (°) | 90.00 | beta (°) | 92.68 | gamma (°) | 90.00 | Rfactor (%) | 23.07 | Rfree (%) | 27.02 |
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Sodium binding site 1 out of 3 in 2wl4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wl4. 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: C: Ala27, C: Gln56, C: Leu58, C: Pro59, C: Glu62, C: Met116, C: Glu117, C: Ser118, C: Met119, C: Hoh2011, C: Hoh2026, C: Hoh2027, | conact list:
Atom | Atom | Distance (A) | Na | CB C:Ala27 | 3.73 | Na | CA C:Ala27 | 4.94 | Na | NE2 C:Gln56 | 3.34 | Na | CD C:Gln56 | 4.30 | Na | CG C:Gln56 | 4.29 | Na | O C:Leu58 | 3.13 | Na | N C:Leu58 | 4.64 | Na | CB C:Leu58 | 4.28 | Na | C C:Leu58 | 4.02 | Na | CG C:Leu58 | 4.96 | Na | CA C:Leu58 | 4.56 | Na | N C:Pro59 | 5.00 | Na | OE1 C:Glu62 | 4.55 | Na | O C:Met116 | 4.74 | Na | O C:Glu117 | 4.98 | Na | N C:Glu117 | 4.73 | Na | OE1 C:Glu117 | 4.83 | Na | CB C:Glu117 | 4.38 | Na | OE2 C:Glu117 | 3.21 | Na | CD C:Glu117 | 3.84 | Na | C C:Glu117 | 3.78 | Na | CG C:Glu117 | 3.95 | Na | CA C:Glu117 | 3.64 | Na | O C:Ser118 | 3.60 | Na | N C:Ser118 | 2.94 | Na | CB C:Ser118 | 4.17 | Na | C C:Ser118 | 3.81 | Na | CA C:Ser118 | 3.82 | Na | N C:Met119 | 4.64 | Na | O C:Hoh2011 | 3.52 | Na | O C:Hoh2026 | 4.68 | Na | O C:Hoh2027 | 2.85 |
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| Sodium binding site 2 out of 3 in 2wl4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wl4. 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: C: Val34, C: Ile35, C: Val38, C: Val112, C: Ala113, C: Ala255, C: Ala256, C: Leu257, | conact list:
Atom | Atom | Distance (A) | Na | O C:Val34 | 3.48 | Na | C C:Val34 | 4.00 | Na | CG1 C:Val34 | 4.07 | Na | O C:Ile35 | 4.21 | Na | N C:Ile35 | 4.00 | Na | CB C:Ile35 | 4.19 | Na | CG2 C:Ile35 | 4.21 | Na | C C:Ile35 | 4.34 | Na | CG1 C:Ile35 | 4.29 | Na | CA C:Ile35 | 3.46 | Na | N C:Val38 | 4.85 | Na | CB C:Val38 | 3.44 | Na | CG2 C:Val38 | 3.70 | Na | CG1 C:Val38 | 3.88 | Na | CA C:Val38 | 4.71 | Na | CB C:Val112 | 4.05 | Na | CG2 C:Val112 | 3.71 | Na | C C:Val112 | 4.87 | Na | CG1 C:Val112 | 3.41 | Na | CA C:Val112 | 4.60 | Na | N C:Ala113 | 4.77 | Na | C C:Ala255 | 4.32 | Na | CB C:Ala255 | 3.45 | Na | CA C:Ala255 | 4.45 | Na | O C:Ala256 | 4.35 | Na | N C:Ala256 | 3.91 | Na | C C:Ala256 | 4.32 | Na | CA C:Ala256 | 4.49 | Na | N C:Leu257 | 4.76 |
| interactive model:
| Sodium binding site 3 out of 3 in 2wl4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2wl4. 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: Gly289, D: Thr290, D: Pro292, D: Ile293, D: Gln322, D: Ala323, D: Ala325, D: Val326, D: Hoh2150, | conact list:
Atom | Atom | Distance (A) | Na | O D:Gly289 | 3.19 | Na | C D:Gly289 | 3.98 | Na | N D:Thr290 | 4.27 | Na | CB D:Thr290 | 4.64 | Na | CG2 D:Thr290 | 4.64 | Na | C D:Thr290 | 4.70 | Na | CA D:Thr290 | 3.83 | Na | CD D:Pro292 | 4.55 | Na | N D:Ile293 | 4.93 | Na | CB D:Ile293 | 4.77 | Na | CD1 D:Ile293 | 3.55 | Na | CG1 D:Ile293 | 3.44 | Na | O D:Gln322 | 3.07 | Na | CB D:Gln322 | 4.49 | Na | C D:Gln322 | 3.88 | Na | CA D:Gln322 | 4.26 | Na | N D:Ala323 | 4.92 | Na | O D:Ala325 | 4.13 | Na | N D:Ala325 | 4.67 | Na | C D:Ala325 | 3.63 | Na | CB D:Ala325 | 3.63 | Na | CA D:Ala325 | 4.16 | Na | N D:Val326 | 3.26 | Na | CB D:Val326 | 4.18 | Na | CG2 D:Val326 | 3.43 | Na | CA D:Val326 | 3.67 | Na | O D:Hoh2150 | 4.31 |
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