Sodium in the structure of Carboxypeptidase A Liganded to An Organic Small-Molecule: Conformational Changes (pdb 3kgq)

The binding sites of Sodium atom in the structure of Carboxypeptidase A Liganded to An Organic Small-Molecule: Conformational Changes (pdb code 3kgq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3kgq structure was solved by D.FERNANDEZ, E.BOIX, I.PALLARES, F.X.AVILES, J.VENDRELL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.2-1.7 Space group P1211 a (A) 40.604 b (A) 57.006 c (A) 60.604 alpha (°) 90.00 beta (°) 102.04 gamma (°) 90.00 Rfactor (%) 18 Rfree (%) 20.4 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3kgq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3kgq. 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: Thr14, A: Leu15, A: Phe116, A: Ala117, A: His120, A: Hoh381, A: Hoh390, conact list: Atom Atom Distance (A) Na CB A:Thr14 3.79 Na CG2 A:Thr14 4.60 Na OG1 A:Thr14 4.81 Na C A:Thr14 4.06 Na CA A:Thr14 3.92 Na N A:Leu15 3.21 Na CB A:Leu15 3.76 Na CA A:Leu15 4.09 Na O A:Phe116 4.43 Na CD2 A:Phe116 4.86 Na C A:Phe116 4.72 Na O A:Ala117 4.46 Na N A:Ala117 4.47 Na C A:Ala117 4.66 Na CB A:Ala117 4.43 Na CA A:Ala117 3.82 Na NE2 A:His120 4.54 Na CB A:His120 3.80 Na ND1 A:His120 3.49 Na CD2 A:His120 4.29 Na CE1 A:His120 4.10 Na CG A:His120 3.62 Na O A:Hoh381 3.48 Na O A:Hoh390 3.25 interactive model: