Sodium in the structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed With Crotonaldehyde, Nad(H) and MG2+ (pdb 1o01)

The binding sites of Sodium atom in the structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed With Crotonaldehyde, Nad(H) and MG2+ (pdb code 1o01). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1o01 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) 34.8-2.1 Space group P212121 a (A) 142.133 b (A) 150.571 c (A) 176.782 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 20.6 Sodium Binding Sites: Sodium binding site 1 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1o01. 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: Ile48, A: Asp109, A: Asn110, A: Gln196, A: Thr197, A: Hoh5531, A: Hoh5532, conact list: Atom Atom Distance (A) Na CB A:Thr39 4.22 Na CG2 A:Thr39 4.95 Na OG1 A:Thr39 2.95 Na C A:Thr39 4.20 Na CA A:Thr39 4.47 Na O A:Val40 2.50 Na N A:Val40 3.58 Na CB A:Val40 4.94 Na C A:Val40 3.54 Na CA A:Val40 4.08 Na N A:Asn41 4.65 Na CD A:Pro42 4.45 Na CD1 A:Ile48 4.70 Na O A:Asp109 2.59 Na CB A:Asp109 4.11 Na OD2 A:Asp109 3.99 Na C A:Asp109 3.55 Na OD1 A:Asp109 2.32 Na CG A:Asp109 3.25 Na CA A:Asp109 3.83 Na N A:Asn110 4.79 Na O A:Gln196 2.36 Na CB A:Gln196 4.94 Na C A:Gln196 3.57 Na CA A:Gln196 4.41 Na N A:Thr197 4.54 Na CG2 A:Thr197 4.57 Na CA A:Thr197 4.63 Na O A:Hoh5531 2.75 Na O A:Hoh5532 3.28 interactive model: Sodium binding site 2 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1o01. 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: Ile48, B: Asp109, B: Asn110, B: Gln196, B: Thr197, B: Hoh5981, B: Hoh5982, conact list: Atom Atom Distance (A) Na O B:Thr39 4.99 Na CB B:Thr39 4.19 Na CG2 B:Thr39 4.88 Na OG1 B:Thr39 2.91 Na C B:Thr39 4.19 Na CA B:Thr39 4.48 Na O B:Val40 2.48 Na N B:Val40 3.65 Na CB B:Val40 4.99 Na C B:Val40 3.56 Na CA B:Val40 4.12 Na N B:Asn41 4.68 Na CD B:Pro42 4.58 Na CD1 B:Ile48 4.57 Na O B:Asp109 2.59 Na CB B:Asp109 4.05 Na OD2 B:Asp109 4.04 Na C B:Asp109 3.51 Na OD1 B:Asp109 2.20 Na CG B:Asp109 3.23 Na CA B:Asp109 3.77 Na N B:Asn110 4.75 Na O B:Gln196 2.41 Na C B:Gln196 3.62 Na CA B:Gln196 4.50 Na N B:Thr197 4.55 Na CG2 B:Thr197 4.53 Na CA B:Thr197 4.60 Na O B:Hoh5981 3.32 Na O B:Hoh5982 2.76 interactive model: Sodium binding site 3 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1o01. 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: Ile48, C: Asp109, C: Asn110, C: Gln196, C: Thr197, C: Hoh5665, C: Hoh5666, C: Hoh5669, conact list: Atom Atom Distance (A) Na CB C:Thr39 4.29 Na CG2 C:Thr39 4.96 Na OG1 C:Thr39 2.98 Na C C:Thr39 4.38 Na CA C:Thr39 4.63 Na O C:Val40 2.46 Na N C:Val40 3.75 Na CB C:Val40 4.93 Na C C:Val40 3.58 Na CA C:Val40 4.19 Na N C:Asn41 4.68 Na CD C:Pro42 4.39 Na CD1 C:Ile48 4.80 Na O C:Asp109 2.57 Na CB C:Asp109 4.24 Na OD2 C:Asp109 4.32 Na C C:Asp109 3.54 Na OD1 C:Asp109 2.47 Na CG C:Asp109 3.48 Na CA C:Asp109 3.87 Na N C:Asn110 4.76 Na O C:Gln196 2.33 Na CB C:Gln196 4.82 Na C C:Gln196 3.55 Na CA C:Gln196 4.38 Na N C:Thr197 4.52 Na CG2 C:Thr197 4.52 Na CA C:Thr197 4.63 Na O C:Hoh5665 2.55 Na O C:Hoh5666 2.89 Na O C:Hoh5669 4.68 interactive model: Sodium binding site 4 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1o01. 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: Ile48, D: Asp109, D: Asn110, D: Gln196, D: Thr197, D: Val345, D: Hoh5703, D: Hoh5704, conact list: Atom Atom Distance (A) Na CB D:Thr39 4.47 Na OG1 D:Thr39 3.25 Na C D:Thr39 4.33 Na CA D:Thr39 4.69 Na O D:Val40 2.26 Na N D:Val40 3.59 Na CB D:Val40 4.80 Na C D:Val40 3.36 Na CA D:Val40 3.97 Na N D:Asn41 4.47 Na CA D:Asn41 4.86 Na CD D:Pro42 4.23 Na CD1 D:Ile48 4.57 Na O D:Asp109 2.49 Na CB D:Asp109 4.17 Na OD2 D:Asp109 4.33 Na C D:Asp109 3.46 Na OD1 D:Asp109 2.48 Na CG D:Asp109 3.47 Na CA D:Asp109 3.77 Na N D:Asn110 4.69 Na O D:Gln196 2.54 Na C D:Gln196 3.75 Na CA D:Gln196 4.57 Na N D:Thr197 4.72 Na CG2 D:Thr197 4.67 Na CA D:Thr197 4.81 Na O D:Val345 5.00 Na O D:Hoh5703 3.12 Na O D:Hoh5704 2.56 interactive model: Sodium binding site 5 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1o01. 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: Ile48, E: Asp109, E: Asn110, E: Gln196, E: Thr197, E: Hoh5683, E: Hoh5685, conact list: Atom Atom Distance (A) Na CB E:Thr39 4.30 Na OG1 E:Thr39 3.03 Na C E:Thr39 4.21 Na CA E:Thr39 4.55 Na O E:Val40 2.32 Na N E:Val40 3.58 Na CB E:Val40 4.84 Na C E:Val40 3.38 Na CA E:Val40 3.99 Na N E:Asn41 4.47 Na CA E:Asn41 4.86 Na CD E:Pro42 4.28 Na CD1 E:Ile48 4.61 Na O E:Asp109 2.52 Na CB E:Asp109 4.14 Na OD2 E:Asp109 4.28 Na C E:Asp109 3.46 Na OD1 E:Asp109 2.39 Na CG E:Asp109 3.41 Na CA E:Asp109 3.72 Na N E:Asn110 4.71 Na O E:Gln196 2.63 Na C E:Gln196 3.84 Na CA E:Gln196 4.66 Na N E:Thr197 4.81 Na CG2 E:Thr197 4.81 Na CA E:Thr197 4.88 Na O E:Hoh5683 3.22 Na O E:Hoh5685 2.79 interactive model: Sodium binding site 6 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1o01. 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: Ile48, F: Asp109, F: Asn110, F: Gln196, F: Thr197, F: Hoh2342, F: Hoh2343, F: Hoh2346, conact list: Atom Atom Distance (A) Na CB F:Thr39 4.39 Na CG2 F:Thr39 4.95 Na OG1 F:Thr39 3.13 Na C F:Thr39 4.42 Na CA F:Thr39 4.73 Na O F:Val40 2.39 Na N F:Val40 3.75 Na CB F:Val40 4.94 Na C F:Val40 3.53 Na CA F:Val40 4.15 Na N F:Asn41 4.63 Na CA F:Asn41 4.98 Na CD F:Pro42 4.30 Na CD1 F:Ile48 4.82 Na O F:Asp109 2.48 Na CB F:Asp109 4.18 Na OD2 F:Asp109 4.30 Na C F:Asp109 3.45 Na OD1 F:Asp109 2.44 Na CG F:Asp109 3.45 Na CA F:Asp109 3.78 Na N F:Asn110 4.66 Na O F:Gln196 2.46 Na CB F:Gln196 4.96 Na C F:Gln196 3.68 Na CA F:Gln196 4.53 Na N F:Thr197 4.62 Na CG2 F:Thr197 4.47 Na CA F:Thr197 4.69 Na O F:Hoh2342 2.55 Na O F:Hoh2343 4.75 Na O F:Hoh2346 3.28 interactive model: Sodium binding site 7 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1o01. 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, G: Hoh1792, conact list: Atom Atom Distance (A) Na CB G:Thr39 4.59 Na OG1 G:Thr39 3.36 Na C G:Thr39 4.39 Na CA G:Thr39 4.75 Na O G:Val40 2.27 Na N G:Val40 3.68 Na CB G:Val40 4.77 Na C G:Val40 3.40 Na CA G:Val40 4.03 Na N G:Asn41 4.52 Na CA G:Asn41 4.88 Na CD G:Pro42 4.17 Na CD1 G:Ile48 4.79 Na O G:Asp109 2.48 Na CB G:Asp109 4.23 Na OD2 G:Asp109 4.28 Na C G:Asp109 3.49 Na OD1 G:Asp109 2.30 Na CG G:Asp109 3.42 Na CA G:Asp109 3.87 Na N G:Asn110 4.69 Na O G:Gln196 2.55 Na CB G:Gln196 5.00 Na C G:Gln196 3.76 Na CA G:Gln196 4.56 Na N G:Thr197 4.75 Na CG2 G:Thr197 4.68 Na CA G:Thr197 4.87 Na O G:Val345 4.86 Na O G:Hoh1792 3.08 interactive model: Sodium binding site 8 out of 8 in 1o01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1o01. 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: Ile48, H: Asp109, H: Asn110, H: Gln196, H: Thr197, H: Hoh1834, H: Hoh1836, conact list: Atom Atom Distance (A) Na CB H:Thr39 4.44 Na OG1 H:Thr39 3.13 Na C H:Thr39 4.43 Na CA H:Thr39 4.73 Na O H:Val40 2.51 Na N H:Val40 3.86 Na C H:Val40 3.63 Na CA H:Val40 4.26 Na N H:Asn41 4.72 Na CD H:Pro42 4.32 Na CD1 H:Ile48 4.84 Na O H:Asp109 2.50 Na CB H:Asp109 4.06 Na OD2 H:Asp109 4.11 Na C H:Asp109 3.44 Na OD1 H:Asp109 2.30 Na CG H:Asp109 3.29 Na CA H:Asp109 3.76 Na N H:Asn110 4.64 Na O H:Gln196 2.35 Na CB H:Gln196 4.85 Na C H:Gln196 3.56 Na CA H:Gln196 4.38 Na N H:Thr197 4.54 Na CG2 H:Thr197 4.48 Na CA H:Thr197 4.64 Na O H:Hoh1834 3.24 Na O H:Hoh1836 2.70 interactive model: