Sodium in the structure of Crystal Structure Of The Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B (pdb 3jpy)

The binding sites of Sodium atom in the structure of Crystal Structure Of The Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B (pdb code 3jpy). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3jpy structure was solved by E.KARAKAS, N.SIMOROWSKI, H.FURUKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.3-3.2 Space group P3121 a (A) 143.368 b (A) 143.368 c (A) 88.467 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.4 Rfree (%) 23.3 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3jpy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3jpy. 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: Ser131, A: Met132, A: Ile133, A: Gln145, A: Phe146, A: Gly147, A: Pro148, A: Cl601, conact list: Atom Atom Distance (A) Na O A:Ser131 2.32 Na CB A:Ser131 4.13 Na OG A:Ser131 3.79 Na C A:Ser131 3.49 Na CA A:Ser131 4.37 Na N A:Met132 4.40 Na C A:Met132 4.77 Na CA A:Met132 4.47 Na N A:Ile133 4.53 Na CB A:Gln145 4.94 Na O A:Phe146 2.46 Na N A:Phe146 4.99 Na C A:Phe146 3.57 Na CA A:Phe146 4.86 Na O A:Gly147 4.20 Na N A:Gly147 4.06 Na C A:Gly147 3.80 Na CA A:Gly147 3.62 Na O A:Pro148 4.20 Na N A:Pro148 4.12 Na CD A:Pro148 3.89 Na CL A:Cl601 3.81 interactive model: