Sodium in the structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed With Nad+ and MG2+ Showing Dual Nad(H) Conformations (pdb 1o00)

The binding sites of Sodium atom in the structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed With Nad+ and MG2+ Showing Dual Nad(H) Conformations (pdb code 1o00). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1o00 structure was solved by S.J.PEREZ-MILLER, T.D.HURLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.8-2.6 Space group P212121 a (A) 141.911 b (A) 150.671 c (A) 177.133 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 23.2 Sodium Binding Sites: Sodium binding site 1 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1o00. 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: Thr39, A: Val40, A: Asn41, A: Pro42, A: Asp109, A: Asn110, A: Gln196, A: Thr197, A: Val345, conact list: Atom Atom Distance (A) Na CB A:Thr39 4.93 Na OG1 A:Thr39 3.70 Na C A:Thr39 4.61 Na O A:Val40 2.23 Na N A:Val40 3.93 Na CB A:Val40 4.88 Na C A:Val40 3.42 Na CA A:Val40 4.17 Na N A:Asn41 4.47 Na CA A:Asn41 4.73 Na N A:Pro42 4.88 Na CD A:Pro42 4.11 Na CG A:Pro42 4.22 Na O A:Asp109 2.38 Na CB A:Asp109 4.19 Na OD2 A:Asp109 4.24 Na C A:Asp109 3.42 Na OD1 A:Asp109 2.26 Na CG A:Asp109 3.38 Na CA A:Asp109 3.83 Na N A:Asn110 4.61 Na O A:Gln196 2.56 Na CB A:Gln196 4.82 Na C A:Gln196 3.76 Na CA A:Gln196 4.52 Na N A:Thr197 4.75 Na CG2 A:Thr197 4.37 Na CA A:Thr197 4.86 Na O A:Val345 4.54 interactive model: Sodium binding site 2 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1o00. 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: Thr39, B: Val40, B: Asn41, B: Pro42, B: Asp109, B: Asn110, B: Gln196, B: Thr197, B: Val345, B: Hoh2859, conact list: Atom Atom Distance (A) Na CB B:Thr39 4.78 Na OG1 B:Thr39 3.52 Na C B:Thr39 4.58 Na CA B:Thr39 4.94 Na O B:Val40 2.38 Na N B:Val40 3.87 Na CB B:Val40 4.88 Na C B:Val40 3.53 Na CA B:Val40 4.19 Na N B:Asn41 4.63 Na CA B:Asn41 4.93 Na CD B:Pro42 4.23 Na O B:Asp109 2.45 Na CB B:Asp109 4.26 Na OD2 B:Asp109 4.28 Na C B:Asp109 3.50 Na OD1 B:Asp109 2.25 Na CG B:Asp109 3.42 Na CA B:Asp109 3.94 Na N B:Asn110 4.68 Na O B:Gln196 2.41 Na CB B:Gln196 4.73 Na C B:Gln196 3.61 Na CA B:Gln196 4.37 Na N B:Thr197 4.62 Na CG2 B:Thr197 4.34 Na CA B:Thr197 4.76 Na O B:Val345 4.54 Na CG2 B:Val345 4.99 Na O B:Hoh2859 3.15 interactive model: Sodium binding site 3 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1o00. 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: Thr39, C: Val40, C: Asn41, C: Pro42, C: Asp109, C: Asn110, C: Gln196, C: Thr197, C: Val345, C: Hoh3570, C: Hoh3571, conact list: Atom Atom Distance (A) Na OG1 C:Thr39 4.07 Na C C:Thr39 4.98 Na O C:Val40 2.43 Na N C:Val40 4.17 Na CB C:Val40 4.93 Na C C:Val40 3.62 Na CA C:Val40 4.36 Na N C:Asn41 4.67 Na CA C:Asn41 4.94 Na N C:Pro42 4.81 Na CD C:Pro42 3.92 Na CG C:Pro42 4.79 Na O C:Asp109 2.37 Na CB C:Asp109 4.55 Na OD2 C:Asp109 4.73 Na C C:Asp109 3.51 Na OD1 C:Asp109 2.77 Na CG C:Asp109 3.85 Na CA C:Asp109 4.11 Na N C:Asn110 4.61 Na CA C:Asn110 4.88 Na O C:Gln196 2.53 Na CB C:Gln196 4.49 Na C C:Gln196 3.65 Na CA C:Gln196 4.34 Na N C:Thr197 4.68 Na CG2 C:Thr197 4.28 Na CA C:Thr197 4.90 Na O C:Val345 4.07 Na CG2 C:Val345 4.67 Na O C:Hoh3570 4.08 Na O C:Hoh3571 3.86 interactive model: Sodium binding site 4 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1o00. 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: D: Thr39, D: Val40, D: Asn41, D: Pro42, D: Asp109, D: Asn110, D: Gln196, D: Thr197, D: Val345, conact list: Atom Atom Distance (A) Na CB D:Thr39 4.74 Na OG1 D:Thr39 3.48 Na C D:Thr39 4.53 Na CA D:Thr39 4.87 Na O D:Val40 2.35 Na N D:Val40 3.76 Na CB D:Val40 4.74 Na C D:Val40 3.49 Na CA D:Val40 4.11 Na N D:Asn41 4.61 Na CA D:Asn41 4.96 Na CD D:Pro42 4.28 Na O D:Asp109 2.60 Na CB D:Asp109 4.41 Na OD2 D:Asp109 4.38 Na C D:Asp109 3.66 Na OD1 D:Asp109 2.40 Na CG D:Asp109 3.55 Na CA D:Asp109 4.08 Na N D:Asn110 4.83 Na O D:Gln196 2.42 Na CB D:Gln196 4.61 Na C D:Gln196 3.59 Na CA D:Gln196 4.30 Na N D:Thr197 4.62 Na CG2 D:Thr197 4.43 Na CA D:Thr197 4.80 Na O D:Val345 4.51 interactive model: Sodium binding site 5 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1o00. 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: E: Thr39, E: Val40, E: Asn41, E: Pro42, E: Asp109, E: Asn110, E: Gln196, E: Thr197, E: Val345, E: Hoh845, conact list: Atom Atom Distance (A) Na OG1 E:Thr39 3.82 Na C E:Thr39 4.91 Na O E:Val40 2.53 Na N E:Val40 4.15 Na C E:Val40 3.71 Na CA E:Val40 4.42 Na N E:Asn41 4.77 Na N E:Pro42 4.93 Na CD E:Pro42 4.08 Na CG E:Pro42 4.96 Na O E:Asp109 2.29 Na CB E:Asp109 4.31 Na OD2 E:Asp109 4.38 Na C E:Asp109 3.39 Na OD1 E:Asp109 2.38 Na CG E:Asp109 3.51 Na CA E:Asp109 3.94 Na N E:Asn110 4.53 Na CA E:Asn110 4.87 Na O E:Gln196 2.43 Na CB E:Gln196 4.58 Na C E:Gln196 3.60 Na CA E:Gln196 4.36 Na N E:Thr197 4.61 Na CG2 E:Thr197 4.16 Na CA E:Thr197 4.76 Na O E:Val345 4.23 Na CG2 E:Val345 4.71 Na O E:Hoh845 3.42 interactive model: Sodium binding site 6 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1o00. 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: F: Thr39, F: Val40, F: Asn41, F: Pro42, F: Asp109, F: Gln196, F: Thr197, F: Val345, F: Hoh1032, F: Hoh1333, F: Hoh1489, conact list: Atom Atom Distance (A) Na CB F:Thr39 4.60 Na OG1 F:Thr39 3.37 Na C F:Thr39 4.29 Na CA F:Thr39 4.69 Na O F:Val40 2.21 Na N F:Val40 3.56 Na CB F:Val40 4.61 Na C F:Val40 3.31 Na CA F:Val40 3.90 Na N F:Asn41 4.47 Na CA F:Asn41 4.91 Na CD F:Pro42 4.44 Na CG F:Pro42 4.48 Na O F:Asp109 2.80 Na CB F:Asp109 4.54 Na OD2 F:Asp109 4.46 Na C F:Asp109 3.85 Na OD1 F:Asp109 2.49 Na CG F:Asp109 3.65 Na CA F:Asp109 4.24 Na O F:Gln196 2.42 Na CB F:Gln196 4.62 Na C F:Gln196 3.59 Na CA F:Gln196 4.28 Na N F:Thr197 4.65 Na CG2 F:Thr197 4.61 Na CA F:Thr197 4.88 Na O F:Val345 4.62 Na O F:Hoh1032 4.85 Na O F:Hoh1333 4.11 Na O F:Hoh1489 3.19 interactive model: Sodium binding site 7 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1o00. 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: G: Thr39, G: Val40, G: Asn41, G: Pro42, G: Ile48, G: Asp109, G: Asn110, G: Gln196, G: Thr197, G: Val345, conact list: Atom Atom Distance (A) Na CB G:Thr39 4.61 Na OG1 G:Thr39 3.36 Na C G:Thr39 4.38 Na CA G:Thr39 4.74 Na O G:Val40 2.27 Na N G:Val40 3.66 Na CB G:Val40 4.70 Na C G:Val40 3.39 Na CA G:Val40 4.01 Na N G:Asn41 4.52 Na CA G:Asn41 4.91 Na CD G:Pro42 4.60 Na CD1 G:Ile48 4.95 Na O G:Asp109 2.67 Na CB G:Asp109 4.37 Na OD2 G:Asp109 4.25 Na C G:Asp109 3.69 Na OD1 G:Asp109 2.34 Na CG G:Asp109 3.47 Na CA G:Asp109 4.07 Na N G:Asn110 4.89 Na O G:Gln196 2.44 Na CB G:Gln196 4.77 Na C G:Gln196 3.63 Na CA G:Gln196 4.36 Na N G:Thr197 4.65 Na CG2 G:Thr197 4.50 Na CA G:Thr197 4.79 Na O G:Val345 4.67 interactive model: Sodium binding site 8 out of 8 in 1o00 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1o00. 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: H: Thr39, H: Val40, H: Asn41, H: Pro42, H: Asp109, H: Asn110, H: Gln196, H: Thr197, H: Val345, H: Hoh8679, conact list: Atom Atom Distance (A) Na CB H:Thr39 4.87 Na OG1 H:Thr39 3.64 Na C H:Thr39 4.54 Na CA H:Thr39 4.95 Na O H:Val40 2.24 Na N H:Val40 3.83 Na CB H:Val40 4.72 Na C H:Val40 3.40 Na CA H:Val40 4.09 Na N H:Asn41 4.49 Na CA H:Asn41 4.82 Na N H:Pro42 4.91 Na CD H:Pro42 4.24 Na CG H:Pro42 4.27 Na O H:Asp109 2.49 Na CB H:Asp109 4.36 Na OD2 H:Asp109 4.39 Na C H:Asp109 3.55 Na OD1 H:Asp109 2.38 Na CG H:Asp109 3.53 Na CA H:Asp109 3.99 Na N H:Asn110 4.72 Na O H:Gln196 2.55 Na CB H:Gln196 4.77 Na C H:Gln196 3.73 Na CA H:Gln196 4.45 Na N H:Thr197 4.75 Na CG2 H:Thr197 4.45 Na CA H:Thr197 4.91 Na O H:Val345 4.42 Na CG2 H:Val345 4.95 Na O H:Hoh8679 4.96 interactive model: