Sodium in the structure of Crystal Structure of A Thermostable Serine Protease (pdb 1dbi)

The binding sites of Sodium atom in the structure of Crystal Structure of A Thermostable Serine Protease (pdb code 1dbi). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1dbi structure was solved by C.A.SMITH, H.S.TOOGOOD, H.M.BAKER, R.M.DANIEL, E.N.BAKER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.8 Space group P1211 a (A) 44.050 b (A) 51.680 c (A) 52.780 alpha (°) 90.00 beta (°) 96.10 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 1 in 1dbi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1dbi. 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: Tyr176, A: Glu177, A: Asn178, A: Val179, A: Ile180, A: Ala181, A: Trp200, A: Asp202, A: Hoh301, A: Hoh302, A: Hoh303, A: Hoh496, A: Hoh569, conact list: Atom Atom Distance (A) Na O A:Tyr176 2.97 Na C A:Tyr176 4.14 Na O A:Glu177 3.80 Na N A:Glu177 4.76 Na C A:Glu177 4.21 Na CA A:Glu177 4.39 Na N A:Asn178 4.92 Na O A:Val179 2.61 Na N A:Val179 4.33 Na C A:Val179 3.75 Na CA A:Val179 4.67 Na N A:Ile180 4.58 Na CA A:Ile180 4.56 Na N A:Ala181 4.65 Na O A:Trp200 4.80 Na OD2 A:Asp202 2.88 Na OD1 A:Asp202 3.56 Na CG A:Asp202 3.60 Na O A:Hoh301 2.50 Na O A:Hoh302 2.72 Na O A:Hoh303 2.18 Na O A:Hoh496 4.75 Na O A:Hoh569 3.67 interactive model: