Sodium in the structure of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant With Coenzyme A. (pdb 2wl4)

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 Sodium Binding Sites: 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 interactive model: 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 interactive model: