Sodium in the structure of Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation With Benzylhydantoin (pdb 2jlo)

The binding sites of Sodium atom in the structure of Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation With Benzylhydantoin (pdb code 2jlo). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2jlo structure was solved by S.WEYAND, T.SHIMAMURA, S.YAJIMA, S.SUZUKI, O.MIRZA, K.KRUSONG, E.P.CARPENTER, N.G.RUTHERFORD, J.M.HADDEN, J.O'REILLY, P.MA, M.SAIDIJAM, S.G.PATCHING, R.J.HOPE, H.T.NORBERTCZAK, P.C.J.ROACH, S.IWATA, P.J.F.HENDERSON, A.D.CAMERON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.9-4.0 Space group P212121 a (A) 88.550 b (A) 106.618 c (A) 110.320 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 35.2 Rfree (%) 40 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2jlo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2jlo. 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: Ala38, A: Met39, A: Ala40, A: Ile41, A: Leu175, A: Leu308, A: Ala309, A: Thr310, A: Ser312, A: Thr313, conact list: Atom Atom Distance (A) Na O A:Ala38 2.84 Na C A:Ala38 3.07 Na CB A:Ala38 3.66 Na CA A:Ala38 3.74 Na N A:Met39 3.56 Na C A:Met39 4.45 Na CA A:Met39 3.89 Na N A:Ala40 4.72 Na O A:Ile41 2.79 Na N A:Ile41 4.44 Na CB A:Ile41 4.56 Na CD1 A:Ile41 4.22 Na C A:Ile41 3.91 Na CG1 A:Ile41 3.39 Na CA A:Ile41 4.50 Na CD1 A:Leu175 4.31 Na O A:Leu308 4.14 Na C A:Leu308 4.85 Na O A:Ala309 2.56 Na N A:Ala309 4.66 Na C A:Ala309 3.20 Na CB A:Ala309 4.27 Na CA A:Ala309 3.49 Na O A:Thr310 4.98 Na N A:Thr310 4.25 Na C A:Thr310 4.95 Na CA A:Thr310 4.78 Na O A:Ser312 3.70 Na N A:Ser312 4.45 Na CB A:Ser312 3.60 Na OG A:Ser312 2.62 Na C A:Ser312 3.76 Na CA A:Ser312 4.15 Na N A:Thr313 4.19 Na CB A:Thr313 3.92 Na OG1 A:Thr313 2.65 Na CA A:Thr313 4.57 interactive model: