Sodium in the structure of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii (pdb 1lk5)

The binding sites of Sodium atom in the structure of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii (pdb code 1lk5). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1lk5 structure was solved by K.ISHIKAWA, I.MATSUI, F.PAYAN, C.CAMBILLAU, H.ISHIDA, Y.KAWARABAYASI, H.KIKUCHI, A.ROUSSEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-1.8 Space group P212121 a (A) 73.548 b (A) 114.932 c (A) 119.017 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 21.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1lk5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1lk5. 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: Asn175, A: Gly176, A: Asn177, B: Asn175, B: Gly176, B: Asn177, A: Hoh1016, A: Hoh1024, A: Hoh1052, A: Hoh1070, A: Hoh1092, A: Hoh1143, A: Hoh1194, A: Hoh1197, B: Hoh1016, B: Hoh1025, B: Hoh1026, B: Hoh1044, B: Hoh1057, B: Hoh1104, conact list: Atom Atom Distance (A) Na O A:Asn175 2.29 Na CB A:Asn175 4.57 Na C A:Asn175 3.48 Na CA A:Asn175 4.33 Na N A:Gly176 4.42 Na C A:Gly176 4.96 Na CA A:Gly176 4.53 Na ND2 A:Asn177 4.77 Na OD1 A:Asn177 4.66 Na O B:Asn175 2.32 Na CB B:Asn175 4.53 Na C B:Asn175 3.49 Na CA B:Asn175 4.35 Na N B:Gly176 4.41 Na C B:Gly176 4.95 Na CA B:Gly176 4.49 Na ND2 B:Asn177 4.87 Na OD1 B:Asn177 4.63 Na O A:Hoh1016 2.53 Na O A:Hoh1024 2.35 Na O A:Hoh1052 4.24 Na O A:Hoh1070 4.50 Na O A:Hoh1092 4.30 Na O A:Hoh1143 4.27 Na O A:Hoh1194 4.62 Na O A:Hoh1197 4.93 Na O B:Hoh1016 2.52 Na O B:Hoh1025 4.49 Na O B:Hoh1026 2.37 Na O B:Hoh1044 3.48 Na O B:Hoh1057 4.53 Na O B:Hoh1104 4.60 interactive model: Sodium binding site 2 out of 2 in 1lk5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1lk5. 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: Asn175, C: Gly176, C: Asn177, D: Asn175, D: Gly176, D: Asn177, A: Hoh1052, A: Hoh1143, C: Hoh1039, C: Hoh1047, C: Hoh1055, C: Hoh1074, C: Hoh1113, D: Hoh1014, D: Hoh1022, D: Hoh1047, D: Hoh1069, D: Hoh1121, conact list: Atom Atom Distance (A) Na O C:Asn175 2.35 Na CB C:Asn175 4.70 Na C C:Asn175 3.54 Na CA C:Asn175 4.44 Na N C:Gly176 4.46 Na C C:Gly176 4.89 Na CA C:Gly176 4.50 Na ND2 C:Asn177 4.73 Na OD1 C:Asn177 4.57 Na CG C:Asn177 4.96 Na O D:Asn175 2.34 Na CB D:Asn175 4.64 Na C D:Asn175 3.53 Na CA D:Asn175 4.44 Na N D:Gly176 4.44 Na C D:Gly176 4.87 Na CA D:Gly176 4.47 Na ND2 D:Asn177 4.70 Na OD1 D:Asn177 4.58 Na CG D:Asn177 4.95 Na O A:Hoh1052 4.23 Na O A:Hoh1143 4.18 Na O C:Hoh1039 2.54 Na O C:Hoh1047 2.40 Na O C:Hoh1055 4.53 Na O C:Hoh1074 4.52 Na O C:Hoh1113 4.40 Na O D:Hoh1014 2.47 Na O D:Hoh1022 3.45 Na O D:Hoh1047 4.42 Na O D:Hoh1069 2.25 Na O D:Hoh1121 4.71 interactive model: