Sodium in the structure of Atomic Resolution Structure Of Apo-Form of Rafe From Streptococcus Pneumoniae (pdb 2heu)

The binding sites of Sodium atom in the structure of Atomic Resolution Structure Of Apo-Form of Rafe From Streptococcus Pneumoniae (pdb code 2heu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2heu structure was solved by N.G.PATERSON, A.RIBOLDI-TUNNICLIFFE, T.J.MITCHELL, N.W.ISAACS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-1.0 Space group C121 a (A) 77.219 b (A) 129.315 c (A) 119.420 alpha (°) 90.00 beta (°) 94.21 gamma (°) 90.00 Rfactor (%) 13 Rfree (%) 15.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2heu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2heu. 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: Lys103, A: Arg104, A: Val105, A: Asn107, A: Glu335, A: Hoh4229, A: Hoh4251, A: Hoh4346, A: Hoh4380, A: Hoh4503, A: Hoh4599, A: Hoh4691, A: Hoh4750, A: Hoh4754, conact list: Atom Atom Distance (A) Na O A:Lys103 2.34 Na CB A:Lys103 4.55 Na C A:Lys103 3.55 Na CA A:Lys103 4.40 Na N A:Arg104 4.51 Na C A:Arg104 4.94 Na CA A:Arg104 4.68 Na O A:Val105 4.33 Na OD1 A:Asn107 4.29 Na OE1 A:Glu335 2.54 Na OE2 A:Glu335 2.37 Na CD A:Glu335 2.79 Na CG A:Glu335 4.29 Na O A:Hoh4229 4.55 Na O A:Hoh4251 4.34 Na O A:Hoh4346 2.41 Na O A:Hoh4380 4.48 Na O A:Hoh4503 2.36 Na O A:Hoh4599 4.61 Na O A:Hoh4691 4.66 Na O A:Hoh4750 2.34 Na O A:Hoh4754 4.84 interactive model: Sodium binding site 2 out of 2 in 2heu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2heu. 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: C: Lys103, C: Arg104, C: Val105, C: Asn107, C: Glu335, C: Hoh5270, C: Hoh5285, C: Hoh5324, C: Hoh5348, C: Hoh5390, C: Hoh5410, C: Hoh5440, C: Hoh5523, conact list: Atom Atom Distance (A) Na O C:Lys103 2.38 Na O C:Lys103 2.30 Na CB C:Lys103 4.56 Na CB C:Lys103 4.55 Na C C:Lys103 3.58 Na C C:Lys103 3.55 Na CA C:Lys103 4.40 Na CA C:Lys103 4.40 Na N C:Arg104 4.49 Na C C:Arg104 4.85 Na CA C:Arg104 4.57 Na O C:Val105 4.37 Na OD1 C:Asn107 4.31 Na OE1 C:Glu335 2.41 Na OE2 C:Glu335 2.50 Na CD C:Glu335 2.83 Na CG C:Glu335 4.29 Na O C:Hoh5270 4.61 Na O C:Hoh5285 4.55 Na O C:Hoh5324 2.40 Na O C:Hoh5348 2.28 Na O C:Hoh5390 4.49 Na O C:Hoh5410 4.85 Na O C:Hoh5440 2.27 Na O C:Hoh5523 4.13 interactive model: