Sodium in the structure of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex With Amp-Pnp (pdb 2onj)

The binding sites of Sodium atom in the structure of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex With Amp-Pnp (pdb code 2onj). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2onj structure was solved by R.J.P.DAWSON, K.P.LOCHER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.4 Space group C121 a (A) 160.961 b (A) 104.447 c (A) 181.391 alpha (°) 90.00 beta (°) 98.23 gamma (°) 90.00 Rfactor (%) 25.4 Rfree (%) 27.8 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2onj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2onj. 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: Gly367, A: Glu368, A: Thr369, A: Ser524, A: Lys525, A: Asp526, A: Arg527, A: Thr528, A: Thr529, A: Asp543, conact list: Atom Atom Distance (A) Na O A:Gly367 2.92 Na C A:Gly367 3.45 Na CA A:Gly367 4.06 Na O A:Glu368 3.58 Na N A:Glu368 4.15 Na C A:Glu368 3.73 Na CA A:Glu368 4.37 Na N A:Thr369 4.00 Na CB A:Thr369 4.03 Na CG2 A:Thr369 4.97 Na OG1 A:Thr369 2.77 Na CA A:Thr369 4.24 Na O A:Ser524 2.68 Na CB A:Ser524 4.52 Na C A:Ser524 3.80 Na CA A:Ser524 4.52 Na O A:Lys525 3.78 Na N A:Lys525 4.79 Na C A:Lys525 4.29 Na CA A:Lys525 4.88 Na N A:Asp526 4.87 Na C A:Asp526 4.95 Na O A:Arg527 2.76 Na N A:Arg527 4.05 Na C A:Arg527 3.91 Na CA A:Arg527 4.59 Na N A:Thr528 4.93 Na N A:Thr529 4.48 Na CB A:Thr529 4.30 Na OG1 A:Thr529 3.83 Na OD2 A:Asp543 4.68 interactive model: Sodium binding site 2 out of 4 in 2onj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2onj. 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: Ser381, A: Gln422, A: Asp502, A: Glu503, A: Val532, B: Gly480, A: Anp701, A: Hoh818, conact list: Atom Atom Distance (A) Na N A:Ser381 4.75 Na CB A:Ser381 3.78 Na OG A:Ser381 2.40 Na CA A:Ser381 4.64 Na NE2 A:Gln422 4.26 Na OE1 A:Gln422 2.50 Na CB A:Gln422 4.39 Na CD A:Gln422 3.63 Na CG A:Gln422 4.60 Na OD2 A:Asp502 3.85 Na OD1 A:Asp502 3.39 Na CG A:Asp502 3.92 Na OE2 A:Glu503 3.41 Na CD A:Glu503 4.27 Na CG A:Glu503 4.64 Na CG1 A:Val532 4.99 Na N B:Gly480 4.52 Na CA B:Gly480 4.99 Na PG A:Anp701 3.02 Na O2G A:Anp701 3.11 Na O2B A:Anp701 3.44 Na O3A A:Anp701 4.52 Na N3B A:Anp701 2.90 Na O3G A:Anp701 2.82 Na PB A:Anp701 3.85 Na O1G A:Anp701 4.67 Na O A:Hoh818 3.16 interactive model: Sodium binding site 3 out of 4 in 2onj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2onj. 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: Gly480, B: Ser381, B: Gln422, B: Asp502, B: Glu503, B: Anp700, B: Hoh808, conact list: Atom Atom Distance (A) Na N A:Gly480 4.35 Na CA A:Gly480 4.75 Na CB B:Ser381 4.02 Na OG B:Ser381 2.66 Na CA B:Ser381 4.93 Na NE2 B:Gln422 3.95 Na OE1 B:Gln422 2.15 Na CB B:Gln422 4.13 Na CD B:Gln422 3.30 Na CG B:Gln422 4.29 Na OD2 B:Asp502 4.00 Na OD1 B:Asp502 3.52 Na CG B:Asp502 4.03 Na OE2 B:Glu503 3.29 Na CD B:Glu503 4.12 Na CG B:Glu503 4.57 Na PG B:Anp700 3.05 Na O2G B:Anp700 3.13 Na O2B B:Anp700 3.48 Na O3A B:Anp700 4.53 Na N3B B:Anp700 2.93 Na O3G B:Anp700 2.82 Na PB B:Anp700 3.88 Na O1G B:Anp700 4.69 Na O B:Hoh808 2.79 interactive model: Sodium binding site 4 out of 4 in 2onj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2onj. 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: Gly367, B: Glu368, B: Thr369, B: Ser524, B: Lys525, B: Asp526, B: Arg527, B: Thr528, B: Thr529, B: Asp543, conact list: Atom Atom Distance (A) Na O B:Gly367 2.84 Na N B:Gly367 4.89 Na C B:Gly367 3.28 Na CA B:Gly367 3.86 Na O B:Glu368 3.40 Na N B:Glu368 3.97 Na C B:Glu368 3.62 Na CA B:Glu368 4.25 Na N B:Thr369 3.98 Na CB B:Thr369 4.13 Na OG1 B:Thr369 2.92 Na CA B:Thr369 4.24 Na O B:Ser524 2.86 Na CB B:Ser524 4.67 Na C B:Ser524 3.95 Na CA B:Ser524 4.64 Na O B:Lys525 3.87 Na N B:Lys525 4.93 Na C B:Lys525 4.38 Na N B:Asp526 4.89 Na C B:Asp526 4.84 Na O B:Arg527 2.53 Na N B:Arg527 3.91 Na C B:Arg527 3.67 Na CA B:Arg527 4.40 Na N B:Thr528 4.67 Na C B:Thr528 4.90 Na CA B:Thr528 4.78 Na N B:Thr529 4.29 Na CB B:Thr529 4.25 Na OG1 B:Thr529 3.79 Na CA B:Thr529 4.94 Na OD2 B:Asp543 4.75 interactive model: