Sodium in the structure of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex With (S)-Lysine (pdb 4dpq)

The binding sites of Sodium atom in the structure of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex With (S)-Lysine (pdb code 4dpq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 4dpq structure was solved by M.D.W.GRIFFIN, J.M.BILLAKANTI, J.A.GERRARD, R.C.J.DOBSON, F.G.PEARCE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.6-2.2 Space group P41212 a (A) 95.480 b (A) 95.480 c (A) 174.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.9 Rfree (%) 17.7 Sodium Binding Sites: Sodium binding site 1 out of 5 in 4dpq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4dpq. 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: Arg342, A: Glu343, A: Phe345, A: Val346, A: Gly347, A: Glu348, A: Na402, A: Hoh542, A: Hoh545, A: Hoh553, A: Hoh566, A: Hoh588, A: Hoh643, A: Hoh647, conact list: Atom Atom Distance (A) Na O A:Arg342 4.69 Na CZ A:Arg342 4.84 Na NH1 A:Arg342 3.96 Na O A:Glu343 4.49 Na O A:Phe345 2.40 Na N A:Phe345 4.85 Na C A:Phe345 3.58 Na CA A:Phe345 4.83 Na O A:Val346 4.23 Na N A:Val346 4.17 Na C A:Val346 3.64 Na CA A:Val346 3.87 Na O A:Gly347 2.38 Na N A:Gly347 3.42 Na C A:Gly347 3.40 Na CA A:Gly347 4.00 Na N A:Glu348 4.50 Na OE1 A:Glu348 4.48 Na OE2 A:Glu348 4.60 Na CD A:Glu348 4.54 Na CA A:Glu348 4.92 Na NA A:Na402 3.43 Na O A:Hoh542 2.31 Na O A:Hoh545 2.54 Na O A:Hoh553 2.49 Na O A:Hoh566 4.36 Na O A:Hoh588 2.25 Na O A:Hoh643 4.24 Na O A:Hoh647 4.88 interactive model: Sodium binding site 2 out of 5 in 4dpq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4dpq. 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: Glu343, A: His344, A: Phe345, A: Na401, A: Hoh542, A: Hoh545, A: Hoh553, A: Hoh566, A: Hoh588, A: Hoh643, A: Hoh647, conact list: Atom Atom Distance (A) Na O A:Glu343 2.41 Na CB A:Glu343 4.30 Na C A:Glu343 3.44 Na CA A:Glu343 3.88 Na N A:His344 4.61 Na O A:Phe345 4.57 Na NA A:Na401 3.43 Na O A:Hoh542 2.78 Na O A:Hoh545 4.91 Na O A:Hoh553 2.41 Na O A:Hoh566 4.58 Na O A:Hoh588 2.73 Na O A:Hoh643 4.74 Na O A:Hoh647 2.35 interactive model: Sodium binding site 3 out of 5 in 4dpq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 4dpq. 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: Arg252, A: Trp253, A: Gly256, A: Ala257, A: Hoh525, A: Hoh532, A: Hoh533, A: Hoh543, A: Hoh565, A: Hoh589, conact list: Atom Atom Distance (A) Na O A:Arg252 2.71 Na C A:Arg252 3.87 Na NH1 A:Arg252 3.90 Na N A:Trp253 4.49 Na C A:Trp253 4.21 Na CE3 A:Trp253 4.79 Na CA A:Trp253 4.23 Na O A:Trp253 3.89 Na N A:Gly256 4.16 Na C A:Gly256 4.55 Na CA A:Gly256 3.89 Na O A:Ala257 4.69 Na O A:Hoh525 2.22 Na O A:Hoh532 2.40 Na O A:Hoh533 4.47 Na O A:Hoh543 2.29 Na O A:Hoh565 2.35 Na O A:Hoh589 3.66 interactive model: Sodium binding site 4 out of 5 in 4dpq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 4dpq. 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: Arg342, B: Glu343, B: Phe345, B: Val346, B: Gly347, B: Glu348, B: Na402, B: Hoh520, B: Hoh556, B: Hoh557, B: Hoh580, B: Hoh617, conact list: Atom Atom Distance (A) Na O B:Arg342 4.48 Na CZ B:Arg342 4.99 Na NH1 B:Arg342 3.97 Na O B:Glu343 4.28 Na C B:Glu343 4.96 Na O B:Phe345 2.40 Na N B:Phe345 4.76 Na C B:Phe345 3.58 Na CA B:Phe345 4.75 Na O B:Val346 4.19 Na N B:Val346 4.19 Na C B:Val346 3.59 Na CA B:Val346 3.86 Na O B:Gly347 2.38 Na N B:Gly347 3.36 Na C B:Gly347 3.39 Na CA B:Gly347 3.91 Na N B:Glu348 4.50 Na OE2 B:Glu348 4.73 Na CD B:Glu348 4.74 Na CA B:Glu348 4.92 Na NA B:Na402 3.12 Na O B:Hoh520 2.37 Na O B:Hoh556 2.64 Na O B:Hoh557 2.54 Na O B:Hoh580 4.25 Na O B:Hoh617 2.35 interactive model: Sodium binding site 5 out of 5 in 4dpq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 4dpq. 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: Arg342, B: Glu343, B: His344, B: Phe345, B: Na401, B: Hoh520, B: Hoh556, B: Hoh557, B: Hoh580, B: Hoh617, B: Hoh629, B: Hoh637, conact list: Atom Atom Distance (A) Na O B:Arg342 4.56 Na O B:Glu343 2.33 Na N B:Glu343 4.93 Na CB B:Glu343 4.22 Na C B:Glu343 3.31 Na CA B:Glu343 3.67 Na N B:His344 4.50 Na CA B:His344 4.97 Na O B:Phe345 4.41 Na NA B:Na401 3.12 Na O B:Hoh520 2.45 Na O B:Hoh556 2.66 Na O B:Hoh557 4.86 Na O B:Hoh580 4.47 Na O B:Hoh617 2.49 Na O B:Hoh629 2.70 Na O B:Hoh637 3.89 interactive model: