Sodium in the structure of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed With Nad and Ornithine to 1.6 Angstroms (pdb 1x7d)

The binding sites of Sodium atom in the structure of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed With Nad and Ornithine to 1.6 Angstroms (pdb code 1x7d). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1x7d structure was solved by S.ALAM, J.L.GOODMAN, S.WANG, F.J.RUZICKA, P.A.FREY, J.E.WEDEKIND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-1.6 Space group P212121 a (A) 69.880 b (A) 78.620 c (A) 119.940 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 19 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1x7d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1x7d. 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: Ala224, A: Val225, A: Gly226, A: Gly227, A: Asp228, A: Glu234, A: Glu258, A: Asp292, A: Ser293, A: Val294, A: Nad1302, A: Hoh1513, A: Hoh1530, A: Hoh1879, conact list: Atom Atom Distance (A) Na O A:Ala224 2.55 Na C A:Ala224 3.28 Na CB A:Ala224 4.33 Na CA A:Ala224 4.41 Na O A:Val225 3.36 Na N A:Val225 3.67 Na C A:Val225 3.35 Na CA A:Val225 3.53 Na N A:Gly226 3.94 Na C A:Gly226 4.26 Na CA A:Gly226 4.63 Na O A:Gly227 2.43 Na N A:Gly227 3.50 Na C A:Gly227 3.46 Na CA A:Gly227 3.86 Na N A:Asp228 4.63 Na CA A:Asp228 4.97 Na OE1 A:Glu234 4.72 Na OE2 A:Glu258 4.42 Na CG A:Glu258 4.79 Na C A:Asp292 4.71 Na OD1 A:Asp292 4.27 Na O A:Ser293 2.39 Na N A:Ser293 3.96 Na CB A:Ser293 4.63 Na C A:Ser293 3.46 Na CA A:Ser293 4.16 Na N A:Val294 4.47 Na CG1 A:Val294 4.50 Na CA A:Val294 4.66 Na N7N A:Nad1302 4.81 Na O A:Hoh1513 2.55 Na O A:Hoh1530 4.58 Na O A:Hoh1879 2.57 interactive model: Sodium binding site 2 out of 2 in 1x7d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1x7d. 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: Ala224, B: Val225, B: Gly226, B: Gly227, B: Asp228, B: Glu234, B: Glu258, B: Asp292, B: Ser293, B: Val294, B: Nad1301, B: Hoh3176, B: Hoh3184, B: Hoh3315, conact list: Atom Atom Distance (A) Na O B:Ala224 2.57 Na C B:Ala224 3.28 Na CB B:Ala224 4.31 Na CA B:Ala224 4.40 Na O B:Val225 3.32 Na N B:Val225 3.66 Na C B:Val225 3.33 Na CA B:Val225 3.53 Na N B:Gly226 3.92 Na C B:Gly226 4.22 Na CA B:Gly226 4.59 Na O B:Gly227 2.47 Na N B:Gly227 3.49 Na C B:Gly227 3.48 Na CA B:Gly227 3.85 Na N B:Asp228 4.66 Na OE1 B:Glu234 4.66 Na OE2 B:Glu258 4.41 Na CG B:Glu258 4.77 Na C B:Asp292 4.73 Na OD1 B:Asp292 4.24 Na O B:Ser293 2.41 Na N B:Ser293 3.99 Na CB B:Ser293 4.68 Na C B:Ser293 3.49 Na CA B:Ser293 4.18 Na N B:Val294 4.51 Na CG1 B:Val294 4.51 Na CA B:Val294 4.70 Na N7N B:Nad1301 4.85 Na O B:Hoh3176 2.61 Na O B:Hoh3184 4.58 Na O B:Hoh3315 2.64 interactive model: