Sodium in the structure of Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis (pdb 3cym)

The binding sites of Sodium atom in the structure of Crystal Structure of Protein BAD_0989 From Bifidobacterium Adolescentis (pdb code 3cym). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3cym structure was solved by Y.PATSKOVSKY, S.OZYURT, J.FREEMAN, S.CHANG, K.BAIN, S.R.WASSERMAN, J.M.SAUDER, S.K.BURLEY, S.C.ALMO, NEW YORK SGX RESEARCH CENTER FORSTRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.1 Space group P212121 a (A) 42.163 b (A) 94.422 c (A) 113.196 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.2 Rfree (%) 29.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3cym Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3cym. 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: Asp42, A: Ala43, A: Glu44, A: Gln59, A: Lys147, A: Tyr166, A: Asp170, A: Na502, A: Hoh601, A: Hoh605, A: Hoh637, A: Hoh699, A: Hoh725, A: Hoh876, conact list: Atom Atom Distance (A) Na CB A:Asp42 4.83 Na OD2 A:Asp42 2.66 Na OD1 A:Asp42 3.82 Na CG A:Asp42 3.56 Na O A:Ala43 4.29 Na OE1 A:Glu44 3.61 Na OE2 A:Glu44 2.67 Na CD A:Glu44 3.53 Na CG A:Glu44 4.97 Na NE2 A:Gln59 4.54 Na NZ A:Lys147 4.16 Na CE2 A:Tyr166 4.30 Na CZ A:Tyr166 4.60 Na OH A:Tyr166 4.09 Na CB A:Asp170 4.16 Na OD2 A:Asp170 2.47 Na OD1 A:Asp170 4.61 Na CG A:Asp170 3.61 Na NA A:Na502 3.94 Na O A:Hoh601 4.83 Na O A:Hoh605 2.36 Na O A:Hoh637 2.36 Na O A:Hoh699 2.48 Na O A:Hoh725 3.90 Na O A:Hoh876 4.79 interactive model: Sodium binding site 2 out of 2 in 3cym Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3cym. 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: Asp42, A: Ala43, A: Arg45, A: His97, A: Gln101, A: Asp102, A: Na501, A: Hoh605, A: Hoh637, A: Hoh642, A: Hoh725, A: Hoh748, A: Hoh749, A: Hoh869, conact list: Atom Atom Distance (A) Na OD2 A:Asp42 4.05 Na OD1 A:Asp42 2.76 Na CG A:Asp42 3.79 Na O A:Ala43 3.99 Na N A:Ala43 4.71 Na NH2 A:Arg45 4.63 Na O A:His97 4.48 Na CB A:Gln101 4.77 Na OD2 A:Asp102 3.03 Na OD1 A:Asp102 3.37 Na CG A:Asp102 3.59 Na NA A:Na501 3.94 Na O A:Hoh605 2.45 Na O A:Hoh637 2.71 Na O A:Hoh642 4.87 Na O A:Hoh725 4.69 Na O A:Hoh748 2.42 Na O A:Hoh749 2.59 Na O A:Hoh869 4.29 interactive model: