Sodium in the structure of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia (pdb 1nd4)

The binding sites of Sodium atom in the structure of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia (pdb code 1nd4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1nd4 structure was solved by D.NURIZZO, S.C.SHEWRY, E.N.BAKER, C.A.SMITH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.0-2.1 Space group P1211 a (A) 43.048 b (A) 101.893 c (A) 71.972 alpha (°) 90.00 beta (°) 105.58 gamma (°) 90.00 Rfactor (%) 20.6 Rfree (%) 23.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1nd4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1nd4. 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: Asp190, A: Cys192, A: Pro194, A: Asn195, A: Mg400, A: Kan1300, A: Hoh1627, A: Hoh1637, A: Hoh1645, A: Hoh1688, A: Hoh1794, conact list: Atom Atom Distance (A) Na O A:Asp190 4.78 Na OD2 A:Asp190 3.92 Na OD1 A:Asp190 3.46 Na CG A:Asp190 3.99 Na CB A:Cys192 3.54 Na SG A:Cys192 2.49 Na CA A:Cys192 4.96 Na CG A:Pro194 4.24 Na ND2 A:Asn195 3.81 Na OD1 A:Asn195 4.73 Na CG A:Asn195 4.53 Na MG A:Mg400 4.49 Na C1 A:Kan1300 4.57 Na C2 A:Kan1300 3.17 Na O9 A:Kan1300 4.90 Na C4 A:Kan1300 4.78 Na O7 A:Kan1300 2.66 Na C3 A:Kan1300 3.39 Na O6 A:Kan1300 2.29 Na O A:Hoh1627 4.02 Na O A:Hoh1637 2.41 Na O A:Hoh1645 4.19 Na O A:Hoh1688 3.88 Na O A:Hoh1794 4.98 interactive model: Sodium binding site 2 out of 2 in 1nd4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1nd4. 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: Asp190, B: Cys192, B: Pro194, B: Asn195, B: Mg400, B: Kan2300, B: Hoh2612, B: Hoh2636, B: Hoh2646, B: Hoh2670, B: Hoh2697, conact list: Atom Atom Distance (A) Na O B:Asp190 4.22 Na CB B:Asp190 4.80 Na OD2 B:Asp190 3.85 Na C B:Asp190 4.89 Na OD1 B:Asp190 2.72 Na CG B:Asp190 3.56 Na N B:Cys192 4.43 Na CB B:Cys192 2.93 Na SG B:Cys192 2.23 Na CA B:Cys192 4.28 Na CD B:Pro194 4.94 Na CG B:Pro194 4.37 Na ND2 B:Asn195 3.62 Na OD1 B:Asn195 4.76 Na CG B:Asn195 4.38 Na MG B:Mg400 4.94 Na C1 B:Kan2300 4.91 Na C2 B:Kan2300 3.58 Na O7 B:Kan2300 2.88 Na C3 B:Kan2300 3.62 Na O6 B:Kan2300 2.63 Na O B:Hoh2612 3.96 Na O B:Hoh2636 4.53 Na O B:Hoh2646 3.87 Na O B:Hoh2670 4.05 Na O B:Hoh2697 3.44 interactive model: