Sodium in the structure of Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei With Bound Pyrophosphate (pdb 3eiy)

The binding sites of Sodium atom in the structure of Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei With Bound Pyrophosphate (pdb code 3eiy). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3eiy structure was solved by SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.1 Space group P6322 a (A) 100.952 b (A) 100.952 c (A) 111.233 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.1 Rfree (%) 24.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3eiy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3eiy. 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: Asp98, A: Asp103, A: Lys105, A: Tyr142, A: Lys143, A: Pop179, A: Hoh201, A: Hoh220, A: Hoh231, A: Hoh239, A: Hoh257, conact list: Atom Atom Distance (A) Na CB A:Asp98 4.50 Na OD2 A:Asp98 2.65 Na OD1 A:Asp98 4.67 Na CG A:Asp98 3.78 Na CB A:Asp103 4.52 Na OD2 A:Asp103 2.58 Na OD1 A:Asp103 4.20 Na CG A:Asp103 3.57 Na CE A:Lys105 4.47 Na NZ A:Lys105 3.78 Na OH A:Tyr142 4.28 Na CE A:Lys143 4.70 Na NZ A:Lys143 3.52 Na O A:Pop179 4.00 Na O5 A:Pop179 4.30 Na P2 A:Pop179 3.72 Na O2 A:Pop179 3.97 Na P1 A:Pop179 3.45 Na O1 A:Pop179 4.67 Na O3 A:Pop179 2.20 Na O4 A:Pop179 4.98 Na O6 A:Pop179 2.56 Na O A:Hoh201 2.50 Na O A:Hoh220 4.42 Na O A:Hoh231 4.00 Na O A:Hoh239 3.75 Na O A:Hoh257 2.65 interactive model: Sodium binding site 2 out of 2 in 3eiy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3eiy. 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: Ser64, A: Asp66, A: Asp71, A: Asp103, A: Ala104, A: Lys105, A: Hoh221, A: Hoh245, A: Hoh247, A: Hoh257, A: Hoh263, A: Hoh277, conact list: Atom Atom Distance (A) Na OG A:Ser64 4.56 Na OD2 A:Asp66 3.70 Na CG A:Asp66 4.73 Na N A:Asp71 4.70 Na CB A:Asp71 4.21 Na OD2 A:Asp71 2.81 Na OD1 A:Asp71 4.75 Na CG A:Asp71 3.77 Na CB A:Asp103 4.59 Na OD2 A:Asp103 4.63 Na C A:Asp103 4.31 Na OD1 A:Asp103 2.53 Na CG A:Asp103 3.76 Na CA A:Asp103 4.22 Na O A:Ala104 2.92 Na N A:Ala104 3.92 Na C A:Ala104 3.96 Na CA A:Ala104 4.58 Na N A:Lys105 4.96 Na CG A:Lys105 4.61 Na NZ A:Lys105 4.17 Na O A:Hoh221 4.01 Na O A:Hoh245 2.65 Na O A:Hoh247 2.85 Na O A:Hoh257 4.53 Na O A:Hoh263 2.50 Na O A:Hoh277 4.26 interactive model: