Sodium in the structure of Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 (pdb 3l8m)

The binding sites of Sodium atom in the structure of Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 (pdb code 3l8m). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3l8m structure was solved by J.SEETHARAMAN, S.LEW, D.WANG, H.JANJUA, K.CUNNINGHAM, L.OWENS, R.XIAO, J.LIU, M.C.BARAN, T.B.ACTON, G.T.MONTELIONE, J.F.HUNT, L.TONG, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.4-2.4 Space group P63 a (A) 101.873 b (A) 101.873 c (A) 88.024 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.8 Rfree (%) 27.1 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3l8m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3l8m. 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: Asn92, A: Ile93, A: Asp94, A: Asn124, A: Ile125, A: Lys126, conact list: Atom Atom Distance (A) Na CB A:Asn92 4.22 Na C A:Asn92 4.20 Na OD1 A:Asn92 4.64 Na CG A:Asn92 4.90 Na CA A:Asn92 4.24 Na O A:Ile93 3.31 Na N A:Ile93 3.72 Na C A:Ile93 3.83 Na CA A:Ile93 4.39 Na N A:Asp94 4.52 Na OD2 A:Asp94 4.74 Na OD1 A:Asp94 2.85 Na CG A:Asp94 4.06 Na CA A:Asp94 4.83 Na O A:Asn124 2.98 Na CB A:Asn124 4.17 Na ND2 A:Asn124 3.87 Na C A:Asn124 3.85 Na OD1 A:Asn124 3.12 Na CG A:Asn124 3.44 Na CA A:Asn124 4.69 Na N A:Ile125 4.56 Na C A:Ile125 4.48 Na CA A:Ile125 4.59 Na N A:Lys126 4.04 Na CB A:Lys126 3.94 Na CE A:Lys126 4.09 Na CD A:Lys126 3.74 Na CG A:Lys126 3.64 Na CA A:Lys126 4.63 Na NZ A:Lys126 4.87 interactive model: Sodium binding site 2 out of 3 in 3l8m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3l8m. 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: Asn11, A: Gly100, A: Gly101, B: Arg10, B: Asn11, B: Gly100, A: Hoh220, A: Hoh232, A: Hoh237, A: Hoh250, B: Hoh222, conact list: Atom Atom Distance (A) Na ND2 A:Asn11 3.31 Na OD1 A:Asn11 3.84 Na CG A:Asn11 3.99 Na N A:Gly100 4.43 Na C A:Gly100 4.80 Na CA A:Gly100 3.64 Na N A:Gly101 4.85 Na NH1 B:Arg10 4.74 Na ND2 B:Asn11 4.11 Na OD1 B:Asn11 3.31 Na CG B:Asn11 4.11 Na N B:Gly100 4.64 Na CA B:Gly100 3.90 Na O A:Hoh220 4.80 Na O A:Hoh232 2.88 Na O A:Hoh237 4.98 Na O A:Hoh250 4.26 Na O B:Hoh222 2.96 interactive model: Sodium binding site 3 out of 3 in 3l8m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3l8m. 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: B: Gln43, B: Phe44, B: Arg88, B: Tyr90, conact list: Atom Atom Distance (A) Na O B:Gln43 4.95 Na OE1 B:Gln43 3.96 Na CB B:Gln43 3.66 Na CD B:Gln43 4.54 Na C B:Gln43 4.99 Na CG B:Gln43 4.19 Na CA B:Gln43 4.78 Na CE2 B:Phe44 4.52 Na CD2 B:Phe44 4.25 Na CB B:Arg88 4.96 Na CD B:Arg88 3.72 Na CZ B:Arg88 4.20 Na CG B:Arg88 4.96 Na NE B:Arg88 4.42 Na NH1 B:Arg88 3.12 Na CE2 B:Tyr90 3.94 Na CZ B:Tyr90 4.07 Na OH B:Tyr90 3.27 interactive model: