Magnesium in the structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed With Nad+ and MN2+ (pdb 1cw3)

The binding sites of Magnesium atom in the structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed With Nad+ and MN2+ (pdb code 1cw3). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1cw3 structure was solved by L.NI, J.ZHOU, T.D.HURLEY, H.WEINER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 45.0-2.6 Space group P1211 a (A) 101.400 b (A) 176.300 c (A) 102.000 alpha (°) 90.00 beta (°) 94.70 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 24.2 Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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: Gln196, A: Thr197, A: Val345, A: Hoh1508, conact list: Atom Atom Distance (A) Mg CB A:Thr39 4.71 Mg OG1 A:Thr39 3.43 Mg C A:Thr39 4.65 Mg CA A:Thr39 4.88 Mg O A:Val40 2.67 Mg N A:Val40 3.92 Mg CB A:Val40 4.92 Mg C A:Val40 3.77 Mg CA A:Val40 4.33 Mg N A:Asn41 4.91 Mg CD A:Pro42 4.36 Mg O A:Asp109 2.76 Mg CB A:Asp109 4.75 Mg OD2 A:Asp109 4.69 Mg C A:Asp109 3.87 Mg OD1 A:Asp109 2.84 Mg CG A:Asp109 3.92 Mg CA A:Asp109 4.38 Mg O A:Gln196 2.21 Mg CB A:Gln196 4.44 Mg C A:Gln196 3.38 Mg CA A:Gln196 4.09 Mg N A:Thr197 4.44 Mg CG2 A:Thr197 4.36 Mg CA A:Thr197 4.69 Mg O A:Val345 4.40 Mg CG2 A:Val345 4.74 Mg O A:Hoh1508 2.81 interactive model: Magnesium binding site 2 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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: Hoh2508, B: Hoh2552, conact list: Atom Atom Distance (A) Mg O B:Thr39 4.87 Mg CB B:Thr39 4.00 Mg CG2 B:Thr39 4.91 Mg OG1 B:Thr39 2.68 Mg C B:Thr39 4.09 Mg CA B:Thr39 4.31 Mg O B:Val40 2.56 Mg N B:Val40 3.60 Mg C B:Val40 3.61 Mg CA B:Val40 4.14 Mg N B:Asn41 4.74 Mg CD B:Pro42 4.81 Mg CD1 B:Ile48 4.62 Mg O B:Asp109 2.86 Mg CB B:Asp109 4.20 Mg OD2 B:Asp109 3.98 Mg C B:Asp109 3.77 Mg OD1 B:Asp109 2.40 Mg CG B:Asp109 3.31 Mg CA B:Asp109 3.99 Mg N B:Asn110 5.00 Mg O B:Gln196 2.29 Mg C B:Gln196 3.49 Mg CA B:Gln196 4.39 Mg N B:Thr197 4.39 Mg CG2 B:Thr197 4.42 Mg CA B:Thr197 4.46 Mg O B:Hoh2508 2.61 Mg O B:Hoh2552 4.87 interactive model: Magnesium binding site 3 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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: Gln196, C: Thr197, C: Val345, C: Hoh3511, conact list: Atom Atom Distance (A) Mg O C:Thr39 4.88 Mg CB C:Thr39 4.29 Mg OG1 C:Thr39 3.07 Mg C C:Thr39 4.07 Mg CA C:Thr39 4.39 Mg O C:Val40 2.27 Mg N C:Val40 3.42 Mg CB C:Val40 4.61 Mg C C:Val40 3.33 Mg CA C:Val40 3.86 Mg N C:Asn41 4.49 Mg CA C:Asn41 4.94 Mg CD C:Pro42 4.41 Mg CD1 C:Ile48 4.78 Mg O C:Asp109 2.83 Mg CB C:Asp109 4.57 Mg OD2 C:Asp109 4.51 Mg C C:Asp109 3.86 Mg OD1 C:Asp109 2.60 Mg CG C:Asp109 3.72 Mg CA C:Asp109 4.20 Mg O C:Gln196 2.55 Mg C C:Gln196 3.75 Mg CA C:Gln196 4.51 Mg N C:Thr197 4.75 Mg CG2 C:Thr197 4.76 Mg CA C:Thr197 4.89 Mg O C:Val345 4.86 Mg O C:Hoh3511 2.38 interactive model: Magnesium binding site 4 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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, D: Hoh4568, conact list: Atom Atom Distance (A) Mg OG1 D:Thr39 3.81 Mg C D:Thr39 4.67 Mg O D:Val40 2.39 Mg N D:Val40 3.89 Mg CB D:Val40 4.73 Mg C D:Val40 3.51 Mg CA D:Val40 4.16 Mg N D:Asn41 4.62 Mg CA D:Asn41 4.97 Mg N D:Pro42 4.90 Mg CD D:Pro42 3.99 Mg CG D:Pro42 4.87 Mg O D:Asp109 2.58 Mg CB D:Asp109 4.73 Mg OD2 D:Asp109 4.87 Mg C D:Asp109 3.70 Mg OD1 D:Asp109 3.12 Mg CG D:Asp109 4.06 Mg CA D:Asp109 4.25 Mg N D:Asn110 4.83 Mg O D:Gln196 2.47 Mg CB D:Gln196 4.61 Mg C D:Gln196 3.63 Mg CA D:Gln196 4.32 Mg N D:Thr197 4.68 Mg CG2 D:Thr197 4.44 Mg CA D:Thr197 4.90 Mg O D:Val345 4.29 Mg CG2 D:Val345 4.77 Mg O D:Hoh4568 3.06 interactive model: Magnesium binding site 5 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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: Gln196, E: Thr197, E: Val345, E: Hoh9193, E: Hoh9219, conact list: Atom Atom Distance (A) Mg O E:Thr39 4.95 Mg CB E:Thr39 4.39 Mg OG1 E:Thr39 3.16 Mg C E:Thr39 4.19 Mg CA E:Thr39 4.50 Mg O E:Val40 2.40 Mg N E:Val40 3.60 Mg CB E:Val40 4.78 Mg C E:Val40 3.49 Mg CA E:Val40 4.03 Mg N E:Asn41 4.63 Mg CD E:Pro42 4.44 Mg CG E:Pro42 4.80 Mg CD1 E:Ile48 4.84 Mg O E:Asp109 2.78 Mg CB E:Asp109 4.50 Mg OD2 E:Asp109 4.47 Mg C E:Asp109 3.81 Mg OD1 E:Asp109 2.65 Mg CG E:Asp109 3.69 Mg CA E:Asp109 4.16 Mg O E:Gln196 2.41 Mg CB E:Gln196 4.96 Mg C E:Gln196 3.61 Mg CA E:Gln196 4.40 Mg N E:Thr197 4.61 Mg CG2 E:Thr197 4.50 Mg CA E:Thr197 4.74 Mg O E:Val345 4.86 Mg O E:Hoh9193 3.44 Mg O E:Hoh9219 2.47 interactive model: Magnesium binding site 6 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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: Val345, F: Hoh9248, F: Hoh9249, conact list: Atom Atom Distance (A) Mg CB F:Thr39 4.47 Mg OG1 F:Thr39 3.12 Mg C F:Thr39 4.53 Mg CA F:Thr39 4.79 Mg O F:Val40 2.63 Mg N F:Val40 3.95 Mg C F:Val40 3.75 Mg CA F:Val40 4.39 Mg N F:Asn41 4.82 Mg CD F:Pro42 4.46 Mg CD1 F:Ile48 4.72 Mg O F:Asp109 2.48 Mg CB F:Asp109 4.19 Mg OD2 F:Asp109 4.16 Mg C F:Asp109 3.48 Mg OD1 F:Asp109 2.46 Mg CG F:Asp109 3.39 Mg CA F:Asp109 3.85 Mg N F:Asn110 4.69 Mg O F:Gln196 2.28 Mg CB F:Gln196 4.85 Mg C F:Gln196 3.49 Mg CA F:Gln196 4.37 Mg N F:Thr197 4.43 Mg CG2 F:Thr197 4.29 Mg CA F:Thr197 4.49 Mg O F:Val345 4.98 Mg O F:Hoh9248 4.31 Mg O F:Hoh9249 4.02 interactive model: Magnesium binding site 7 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: Thr39, G: Val40, G: Asn41, G: Pro42, G: Asp109, G: Asn110, G: Gln196, G: Thr197, G: Val345, G: Hoh9290, G: Hoh9399, conact list: Atom Atom Distance (A) Mg CB G:Thr39 4.81 Mg OG1 G:Thr39 3.59 Mg C G:Thr39 4.53 Mg CA G:Thr39 4.85 Mg O G:Val40 2.49 Mg N G:Val40 3.81 Mg CB G:Val40 4.82 Mg C G:Val40 3.60 Mg CA G:Val40 4.18 Mg N G:Asn41 4.74 Mg CD G:Pro42 4.20 Mg O G:Asp109 2.71 Mg CB G:Asp109 4.73 Mg OD2 G:Asp109 4.71 Mg C G:Asp109 3.82 Mg OD1 G:Asp109 2.93 Mg CG G:Asp109 3.94 Mg CA G:Asp109 4.35 Mg N G:Asn110 4.95 Mg O G:Gln196 2.34 Mg CB G:Gln196 4.62 Mg C G:Gln196 3.52 Mg CA G:Gln196 4.24 Mg N G:Thr197 4.57 Mg CG2 G:Thr197 4.38 Mg CA G:Thr197 4.78 Mg O G:Val345 4.34 Mg CG2 G:Val345 4.90 Mg O G:Hoh9290 3.08 Mg O G:Hoh9399 4.97 interactive model: Magnesium binding site 8 out of 8 in 1cw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 1cw3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium 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: Gln196, H: Thr197, H: Pro198, H: Hoh8574, H: Hoh8604, conact list: Atom Atom Distance (A) Mg O H:Thr39 4.93 Mg CB H:Thr39 4.02 Mg CG2 H:Thr39 4.85 Mg OG1 H:Thr39 2.70 Mg C H:Thr39 4.12 Mg CA H:Thr39 4.35 Mg O H:Val40 2.59 Mg N H:Val40 3.59 Mg C H:Val40 3.63 Mg CA H:Val40 4.13 Mg N H:Asn41 4.77 Mg CD H:Pro42 4.79 Mg CD1 H:Ile48 4.54 Mg O H:Asp109 2.85 Mg CB H:Asp109 4.24 Mg OD2 H:Asp109 4.02 Mg C H:Asp109 3.77 Mg OD1 H:Asp109 2.63 Mg CG H:Asp109 3.40 Mg CA H:Asp109 3.98 Mg O H:Gln196 2.29 Mg C H:Gln196 3.49 Mg CA H:Gln196 4.39 Mg N H:Thr197 4.40 Mg CG2 H:Thr197 4.59 Mg CA H:Thr197 4.49 Mg CD H:Pro198 4.99 Mg O H:Hoh8574 3.34 Mg O H:Hoh8604 2.34 interactive model: