Sodium in the structure of The Crystal Structure Of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans (pdb 2poc)

The binding sites of Sodium atom in the structure of The Crystal Structure Of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans (pdb code 2poc). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2poc structure was solved by J.RACZYNSKA, J.OLCHOWY, S.MILEWSKI, W.RYPNIEWSKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-1.8 Space group P1211 a (A) 65.977 b (A) 117.832 c (A) 99.711 alpha (°) 90.00 beta (°) 91.60 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 20.6 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2poc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2poc. 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: Ser484, A: Arg485, A: Gln486, A: Thr487, A: His488, A: Cys489, A: Ud15002, A: Hoh5004, A: Hoh5005, A: Hoh5006, A: Hoh5087, A: Hoh5144, conact list: Atom Atom Distance (A) Na O A:Ser484 2.51 Na C A:Ser484 3.67 Na CA A:Ser484 4.89 Na O A:Arg485 2.87 Na N A:Arg485 4.26 Na C A:Arg485 3.43 Na CA A:Arg485 3.88 Na N A:Gln486 4.25 Na C A:Gln486 4.48 Na CA A:Gln486 4.81 Na O A:Thr487 2.30 Na N A:Thr487 3.92 Na CB A:Thr487 4.57 Na OG1 A:Thr487 3.88 Na C A:Thr487 3.40 Na CA A:Thr487 4.16 Na O A:His488 4.22 Na N A:His488 4.37 Na C A:His488 4.14 Na CA A:His488 4.55 Na N A:Cys489 4.39 Na CA A:Cys489 4.76 Na N3 A:Ud15002 3.75 Na C2 A:Ud15002 3.23 Na C4 A:Ud15002 5.00 Na C1B A:Ud15002 4.46 Na N1 A:Ud15002 4.26 Na O2 A:Ud15002 2.32 Na O A:Hoh5004 2.34 Na O A:Hoh5005 2.46 Na O A:Hoh5006 4.42 Na O A:Hoh5087 4.98 Na O A:Hoh5144 4.21 interactive model: Sodium binding site 2 out of 4 in 2poc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2poc. 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: Ser484, B: Arg485, B: Gln486, B: Thr487, B: His488, B: Cys489, B: Ud15003, B: Hoh5004, B: Hoh5005, B: Hoh5078, B: Hoh5131, conact list: Atom Atom Distance (A) Na O B:Ser484 2.37 Na C B:Ser484 3.56 Na CA B:Ser484 4.79 Na O B:Arg485 2.75 Na N B:Arg485 4.14 Na C B:Arg485 3.29 Na CA B:Arg485 3.76 Na N B:Gln486 4.11 Na C B:Gln486 4.41 Na CA B:Gln486 4.76 Na O B:Thr487 2.25 Na N B:Thr487 3.90 Na CB B:Thr487 4.59 Na OG1 B:Thr487 3.95 Na C B:Thr487 3.41 Na CA B:Thr487 4.12 Na O B:His488 4.18 Na N B:His488 4.45 Na C B:His488 4.26 Na CA B:His488 4.69 Na N B:Cys489 4.62 Na CA B:Cys489 4.93 Na N3 B:Ud15003 3.83 Na C2 B:Ud15003 3.34 Na C1B B:Ud15003 4.60 Na N1 B:Ud15003 4.38 Na O2 B:Ud15003 2.42 Na O B:Hoh5004 2.39 Na O B:Hoh5005 2.42 Na O B:Hoh5078 4.54 Na O B:Hoh5131 4.38 interactive model: Sodium binding site 3 out of 4 in 2poc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2poc. 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: Ser484, C: Arg485, C: Gln486, C: Thr487, C: His488, C: Cys489, C: Ud15004, C: Hoh5005, C: Hoh5006, C: Hoh5009, C: Hoh5224, conact list: Atom Atom Distance (A) Na O C:Ser484 2.37 Na C C:Ser484 3.56 Na CA C:Ser484 4.79 Na O C:Arg485 2.78 Na N C:Arg485 4.16 Na C C:Arg485 3.33 Na CA C:Arg485 3.79 Na N C:Gln486 4.16 Na C C:Gln486 4.41 Na CA C:Gln486 4.78 Na O C:Thr487 2.34 Na N C:Thr487 3.85 Na CB C:Thr487 4.59 Na OG1 C:Thr487 3.89 Na C C:Thr487 3.46 Na CA C:Thr487 4.12 Na O C:His488 4.32 Na N C:His488 4.48 Na C C:His488 4.35 Na CA C:His488 4.71 Na N C:Cys489 4.65 Na N3 C:Ud15004 3.84 Na C2 C:Ud15004 3.32 Na C1B C:Ud15004 4.56 Na N1 C:Ud15004 4.32 Na O2 C:Ud15004 2.37 Na O C:Hoh5005 2.51 Na O C:Hoh5006 2.28 Na O C:Hoh5009 4.57 Na O C:Hoh5224 4.23 interactive model: Sodium binding site 4 out of 4 in 2poc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2poc. 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: Ser484, D: Arg485, D: Gln486, D: Thr487, D: His488, D: Cys489, D: Ud15005, D: Hoh5114, conact list: Atom Atom Distance (A) Na O D:Ser484 2.46 Na C D:Ser484 3.61 Na CA D:Ser484 4.86 Na O D:Arg485 2.69 Na N D:Arg485 4.17 Na C D:Arg485 3.30 Na CA D:Arg485 3.77 Na N D:Gln486 4.20 Na C D:Gln486 4.57 Na CA D:Gln486 4.82 Na O D:Thr487 2.43 Na N D:Thr487 4.02 Na CB D:Thr487 4.58 Na OG1 D:Thr487 3.86 Na C D:Thr487 3.53 Na CA D:Thr487 4.24 Na O D:His488 4.30 Na N D:His488 4.52 Na C D:His488 4.31 Na CA D:His488 4.73 Na N D:Cys489 4.57 Na CA D:Cys489 4.88 Na N3 D:Ud15005 3.76 Na C2 D:Ud15005 3.24 Na C4 D:Ud15005 4.98 Na C1B D:Ud15005 4.48 Na N1 D:Ud15005 4.25 Na O2 D:Ud15005 2.39 Na O D:Hoh5114 4.25 interactive model: