Sodium in the structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) With Pentachlorophenol Bound (pdb 2wdr)

The binding sites of Sodium atom in the structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) With Pentachlorophenol Bound (pdb code 2wdr). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2wdr 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) 46.5-3.2 Space group P212121 a (A) 119.955 b (A) 186.128 c (A) 204.034 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.7 Rfree (%) 22.8 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2wdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wdr. 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 4.41 Na CZ A:Tyr355 4.31 Na OH A:Tyr355 3.72 Na O A:Met356 2.66 Na CE A:Met356 4.48 Na C A:Met356 3.81 Na CG A:Met356 4.82 Na O A:Met357 2.96 Na N A:Met357 4.37 Na C A:Met357 3.36 Na CA A:Met357 3.98 Na O A:Gly358 2.44 Na N A:Gly358 3.92 Na C A:Gly358 3.57 Na CA A:Gly358 4.27 Na N A:Gly359 4.61 Na CA A:Gly359 4.82 Na O A:Gly387 4.50 Na O A:Glu388 2.53 Na CB A:Glu388 4.86 Na C A:Glu388 3.52 Na CG A:Glu388 4.48 Na CA A:Glu388 4.00 Na N A:Ile389 4.63 Na C A:Ile389 4.60 Na CA A:Ile389 5.00 Na O A:Ala390 2.70 Na N A:Ala390 4.31 Na C A:Ala390 3.71 Na CA A:Ala390 4.64 Na N A:Cys391 4.44 Na CB A:Cys391 4.75 Na CA A:Cys391 4.46 interactive model: Sodium binding site 2 out of 3 in 2wdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wdr. 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 4.46 Na CZ E:Tyr355 4.39 Na OH E:Tyr355 3.76 Na O E:Met356 2.75 Na CE E:Met356 4.51 Na C E:Met356 3.88 Na CG E:Met356 4.97 Na O E:Met357 2.90 Na N E:Met357 4.41 Na C E:Met357 3.33 Na CA E:Met357 3.99 Na O E:Gly358 2.44 Na N E:Gly358 3.90 Na C E:Gly358 3.52 Na CA E:Gly358 4.21 Na N E:Gly359 4.52 Na CA E:Gly359 4.75 Na O E:Gly387 4.44 Na O E:Glu388 2.62 Na CB E:Glu388 4.99 Na C E:Glu388 3.60 Na CG E:Glu388 4.65 Na CA E:Glu388 4.09 Na N E:Ile389 4.69 Na C E:Ile389 4.60 Na O E:Ala390 2.61 Na N E:Ala390 4.24 Na C E:Ala390 3.59 Na CA E:Ala390 4.56 Na N E:Cys391 4.28 Na CB E:Cys391 4.58 Na CA E:Cys391 4.28 interactive model: Sodium binding site 3 out of 3 in 2wdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2wdr. 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 4.19 Na CZ I:Tyr355 4.03 Na OH I:Tyr355 3.42 Na O I:Met356 2.64 Na CE I:Met356 4.58 Na C I:Met356 3.79 Na CG I:Met356 4.95 Na O I:Met357 3.21 Na N I:Met357 4.36 Na C I:Met357 3.50 Na CA I:Met357 3.98 Na O I:Gly358 2.70 Na N I:Gly358 4.08 Na C I:Gly358 3.84 Na CA I:Gly358 4.51 Na N I:Gly359 4.88 Na O I:Gly387 4.36 Na O I:Glu388 2.54 Na N I:Glu388 4.96 Na CB I:Glu388 4.68 Na C I:Glu388 3.46 Na CG I:Glu388 4.33 Na CA I:Glu388 3.84 Na N I:Ile389 4.60 Na C I:Ile389 4.72 Na O I:Ala390 2.73 Na N I:Ala390 4.37 Na C I:Ala390 3.82 Na CA I:Ala390 4.74 Na N I:Cys391 4.61 Na CA I:Cys391 4.64 interactive model: