Sodium in the structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant (pdb 2wp9)

The binding sites of Sodium atom in the structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant (pdb code 2wp9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2wp9 structure was solved by J.RUPRECHT, V.YANKOVSKAYA, E.MAKLASHINA, S.IWATA, G.CECCHINI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 48.9-2.7 Space group P212121 a (A) 119.853 b (A) 183.803 c (A) 202.777 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.032 Rfree (%) 22.247 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2wp9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wp9. 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: Tyr355, A: Met356, A: Met357, A: Gly358, A: Gly359, A: Gly387, A: Glu388, A: Ile389, A: Ala390, A: Cys391, conact list: Atom Atom Distance (A) Na CE2 A:Tyr355 4.74 Na CZ A:Tyr355 4.60 Na OH A:Tyr355 4.04 Na O A:Met356 2.66 Na CE A:Met356 4.81 Na C A:Met356 3.84 Na CG A:Met356 4.77 Na O A:Met357 3.08 Na N A:Met357 4.45 Na C A:Met357 3.46 Na CA A:Met357 4.07 Na O A:Gly358 2.48 Na N A:Gly358 4.04 Na C A:Gly358 3.53 Na CA A:Gly358 4.29 Na N A:Gly359 4.45 Na CA A:Gly359 4.59 Na O A:Gly387 4.22 Na O A:Glu388 2.52 Na CB A:Glu388 4.89 Na C A:Glu388 3.45 Na CG A:Glu388 4.51 Na CA A:Glu388 3.97 Na O A:Ile389 4.75 Na N A:Ile389 4.50 Na C A:Ile389 4.37 Na CA A:Ile389 4.82 Na O A:Ala390 2.33 Na N A:Ala390 4.12 Na C A:Ala390 3.53 Na CA A:Ala390 4.49 Na N A:Cys391 4.39 Na CB A:Cys391 4.69 Na CA A:Cys391 4.45 interactive model: Sodium binding site 2 out of 3 in 2wp9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wp9. 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: E: Tyr355, E: Met356, E: Met357, E: Gly358, E: Gly359, E: Gly387, E: Glu388, E: Ile389, E: Ala390, E: Cys391, conact list: Atom Atom Distance (A) Na CE2 E:Tyr355 4.70 Na CZ E:Tyr355 4.61 Na OH E:Tyr355 4.12 Na O E:Met356 2.50 Na CB E:Met356 4.91 Na CE E:Met356 4.81 Na C E:Met356 3.63 Na CG E:Met356 4.63 Na CA E:Met356 4.86 Na O E:Met357 2.73 Na N E:Met357 4.21 Na C E:Met357 3.18 Na CA E:Met357 3.84 Na O E:Gly358 2.29 Na N E:Gly358 3.83 Na C E:Gly358 3.35 Na CA E:Gly358 4.10 Na N E:Gly359 4.33 Na CA E:Gly359 4.56 Na O E:Gly387 4.51 Na O E:Glu388 2.60 Na C E:Glu388 3.59 Na CG E:Glu388 4.64 Na CA E:Glu388 4.17 Na O E:Ile389 4.82 Na N E:Ile389 4.63 Na C E:Ile389 4.53 Na CA E:Ile389 4.96 Na O E:Ala390 2.52 Na N E:Ala390 4.40 Na C E:Ala390 3.70 Na CA E:Ala390 4.67 Na N E:Cys391 4.51 Na CB E:Cys391 4.67 Na CA E:Cys391 4.47 interactive model: Sodium binding site 3 out of 3 in 2wp9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2wp9. 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: I: Tyr355, I: Met356, I: Met357, I: Gly358, I: Gly359, I: Gly387, I: Glu388, I: Ile389, I: Ala390, I: Cys391, conact list: Atom Atom Distance (A) Na CE2 I:Tyr355 4.47 Na CZ I:Tyr355 4.29 Na OH I:Tyr355 3.69 Na O I:Met356 2.57 Na C I:Met356 3.75 Na CG I:Met356 4.82 Na CA I:Met356 4.98 Na O I:Met357 2.99 Na N I:Met357 4.35 Na C I:Met357 3.43 Na CA I:Met357 3.96 Na O I:Gly358 2.69 Na N I:Gly358 4.10 Na C I:Gly358 3.74 Na CA I:Gly358 4.46 Na N I:Gly359 4.71 Na CA I:Gly359 4.89 Na O I:Gly387 4.18 Na O I:Glu388 2.54 Na N I:Glu388 4.96 Na CB I:Glu388 4.81 Na C I:Glu388 3.46 Na CG I:Glu388 4.43 Na CA I:Glu388 3.90 Na O I:Ile389 4.98 Na N I:Ile389 4.55 Na C I:Ile389 4.57 Na CA I:Ile389 4.96 Na O I:Ala390 2.46 Na N I:Ala390 4.34 Na C I:Ala390 3.69 Na CA I:Ala390 4.66 Na N I:Cys391 4.54 Na CB I:Cys391 4.81 Na CA I:Cys391 4.53 interactive model: