Sodium in the structure of Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae (pdb 3io1)

The binding sites of Sodium atom in the structure of Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae (pdb code 3io1). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3io1 structure was solved by D.KUMARAN, K.BAUMANN, S.K.BURLEY, S.SWAMINATHAN, NEW YORK SGXRESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 43.0-2.5 Space group P21212 a (A) 183.390 b (A) 48.519 c (A) 107.998 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.4 Rfree (%) 26 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3io1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3io1. 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: Asp116, A: Asp118, A: His150, A: Asp151, A: His153, A: Glu183, A: Glu184, conact list: Atom Atom Distance (A) Na CB A:Asp116 4.38 Na OD2 A:Asp116 2.38 Na OD1 A:Asp116 3.94 Na CG A:Asp116 3.35 Na O A:Asp118 4.58 Na OD2 A:Asp118 4.50 Na O A:His150 4.59 Na CD2 A:His150 4.83 Na CB A:Asp151 4.16 Na OD2 A:Asp151 2.27 Na OD1 A:Asp151 2.39 Na CG A:Asp151 2.65 Na CA A:Asp151 4.95 Na ND1 A:His153 4.78 Na CE1 A:His153 4.71 Na OE1 A:Glu183 2.44 Na CB A:Glu183 4.03 Na OE2 A:Glu183 4.34 Na CD A:Glu183 3.39 Na CG A:Glu183 3.93 Na N A:Glu184 4.88 Na OE1 A:Glu184 4.14 Na OE2 A:Glu184 3.64 Na CD A:Glu184 4.17 interactive model: Sodium binding site 2 out of 2 in 3io1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3io1. 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: Asp116, B: Asp118, B: Asp151, B: His153, B: Glu183, B: Glu184, conact list: Atom Atom Distance (A) Na CB B:Asp116 4.31 Na OD2 B:Asp116 3.26 Na OD1 B:Asp116 3.50 Na CG B:Asp116 3.42 Na O B:Asp118 3.86 Na OD2 B:Asp118 4.01 Na C B:Asp118 4.71 Na OD1 B:Asp118 4.62 Na CG B:Asp118 4.48 Na CB B:Asp151 3.96 Na OD2 B:Asp151 2.30 Na OD1 B:Asp151 1.97 Na CG B:Asp151 2.45 Na CA B:Asp151 4.88 Na ND1 B:His153 4.81 Na CE1 B:His153 4.78 Na OE1 B:Glu183 2.50 Na CB B:Glu183 3.92 Na OE2 B:Glu183 4.68 Na CD B:Glu183 3.64 Na C B:Glu183 4.86 Na CG B:Glu183 4.18 Na CA B:Glu183 4.90 Na N B:Glu184 4.58 Na OE1 B:Glu184 4.85 Na OE2 B:Glu184 2.76 Na CD B:Glu184 3.77 Na CG B:Glu184 4.14 interactive model: