Magnesium in the structure of Crystal Structure of Ketopantoate Hydroxymethyltransferase Complexed the Product Ketopantoate (pdb 1m3u)

The binding sites of Magnesium atom in the structure of Crystal Structure of Ketopantoate Hydroxymethyltransferase Complexed the Product Ketopantoate (pdb code 1m3u). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1m3u structure was solved by F.VON DELFT, T.INOUE, S.A.SALDANHA, H.H.OTTENHOF, V.DHANARAJ, M.WITTY, C.ABELL, A.G.SMITH, T.L.BLUNDELL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 100.0-1.8 Space group P1211 a (A) 86.074 b (A) 157.170 c (A) 100.181 alpha (°) 90.00 beta (°) 97.44 gamma (°) 90.00 Rfactor (%) 15.2 Rfree (%) 19.3 Magnesium Binding Sites: Magnesium binding site 1 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1m3u. 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: Leu42, A: Gly44, A: Asp45, A: Ser46, A: Asp84, A: Lys112, A: Glu114, A: His136, A: Kpl265, A: Hoh267, A: Hoh268, A: Hoh269, A: Hoh270, conact list: Atom Atom Distance (A) Mg CD2 A:Leu42 4.99 Mg C A:Gly44 4.53 Mg CA A:Gly44 4.44 Mg N A:Asp45 3.76 Mg CB A:Asp45 4.46 Mg OD2 A:Asp45 4.07 Mg C A:Asp45 4.64 Mg OD1 A:Asp45 2.48 Mg CG A:Asp45 3.47 Mg CA A:Asp45 4.40 Mg N A:Ser46 4.22 Mg CB A:Asp84 4.55 Mg OD2 A:Asp84 2.26 Mg OD1 A:Asp84 3.77 Mg CG A:Asp84 3.35 Mg CE A:Lys112 4.60 Mg NZ A:Lys112 3.38 Mg OE2 A:Glu114 4.07 Mg ND1 A:His136 4.80 Mg CE1 A:His136 4.61 Mg C6 A:Kpl265 3.04 Mg C5 A:Kpl265 3.03 Mg O2 A:Kpl265 2.36 Mg C4 A:Kpl265 4.65 Mg C4 A:Kpl265 4.74 Mg O1 A:Kpl265 3.78 Mg C3 A:Kpl265 4.96 Mg C3 A:Kpl265 4.87 Mg O3 A:Kpl265 2.22 Mg O4 A:Kpl265 4.25 Mg C2 A:Kpl265 4.37 Mg C2 A:Kpl265 4.40 Mg O A:Hoh267 2.47 Mg O A:Hoh268 2.52 Mg O A:Hoh269 3.42 Mg O A:Hoh270 4.75 interactive model: Magnesium binding site 2 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1m3u. 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: Gly44, B: Asp45, B: Ser46, B: Asp84, B: Lys112, B: Glu114, B: His136, B: Kpl265, B: Hoh267, B: Hoh268, B: Hoh269, B: Hoh270, conact list: Atom Atom Distance (A) Mg C B:Gly44 4.57 Mg CA B:Gly44 4.51 Mg N B:Asp45 3.73 Mg CB B:Asp45 4.38 Mg OD2 B:Asp45 4.03 Mg C B:Asp45 4.62 Mg OD1 B:Asp45 2.44 Mg CG B:Asp45 3.41 Mg CA B:Asp45 4.39 Mg N B:Ser46 4.21 Mg CB B:Asp84 4.45 Mg OD2 B:Asp84 2.18 Mg OD1 B:Asp84 3.75 Mg CG B:Asp84 3.29 Mg CE B:Lys112 4.74 Mg NZ B:Lys112 3.42 Mg OE2 B:Glu114 4.07 Mg ND1 B:His136 4.88 Mg CE1 B:His136 4.69 Mg C6 B:Kpl265 3.03 Mg C5 B:Kpl265 3.09 Mg O2 B:Kpl265 2.58 Mg C4 B:Kpl265 4.80 Mg C4 B:Kpl265 4.84 Mg O1 B:Kpl265 4.15 Mg C3 B:Kpl265 4.94 Mg O3 B:Kpl265 2.29 Mg O4 B:Kpl265 4.19 Mg C2 B:Kpl265 4.45 Mg C2 B:Kpl265 4.46 Mg O B:Hoh267 2.43 Mg O B:Hoh268 2.53 Mg O B:Hoh269 3.48 Mg O B:Hoh270 4.80 interactive model: Magnesium binding site 3 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1m3u. 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: Gly44, C: Asp45, C: Ser46, C: Asp84, C: Lys112, C: Glu114, C: His136, C: Kpl265, C: Hoh267, C: Hoh268, C: Hoh269, C: Hoh270, conact list: Atom Atom Distance (A) Mg C C:Gly44 4.42 Mg CA C:Gly44 4.37 Mg N C:Asp45 3.67 Mg CB C:Asp45 4.35 Mg OD2 C:Asp45 3.98 Mg C C:Asp45 4.48 Mg OD1 C:Asp45 2.38 Mg CG C:Asp45 3.36 Mg CA C:Asp45 4.30 Mg N C:Ser46 4.08 Mg CB C:Asp84 4.44 Mg OD2 C:Asp84 2.21 Mg OD1 C:Asp84 3.75 Mg CG C:Asp84 3.29 Mg CE C:Lys112 4.66 Mg NZ C:Lys112 3.47 Mg OE2 C:Glu114 4.02 Mg ND1 C:His136 4.87 Mg CE1 C:His136 4.72 Mg C6 C:Kpl265 3.05 Mg C5 C:Kpl265 3.16 Mg O2 C:Kpl265 2.63 Mg C4 C:Kpl265 4.66 Mg C4 C:Kpl265 4.86 Mg O1 C:Kpl265 3.80 Mg O3 C:Kpl265 2.22 Mg O4 C:Kpl265 4.24 Mg C2 C:Kpl265 4.54 Mg C2 C:Kpl265 4.55 Mg O C:Hoh267 2.41 Mg O C:Hoh268 2.53 Mg O C:Hoh269 3.61 Mg O C:Hoh270 4.82 interactive model: Magnesium binding site 4 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1m3u. 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: Leu42, D: Gly44, D: Asp45, D: Ser46, D: Asp84, D: Lys112, D: Glu114, D: His136, D: Kpl265, D: Hoh267, D: Hoh268, D: Hoh269, D: Hoh270, conact list: Atom Atom Distance (A) Mg CD2 D:Leu42 4.95 Mg C D:Gly44 4.40 Mg CA D:Gly44 4.30 Mg N D:Asp45 3.65 Mg CB D:Asp45 4.45 Mg OD2 D:Asp45 4.14 Mg C D:Asp45 4.60 Mg OD1 D:Asp45 2.55 Mg CG D:Asp45 3.51 Mg CA D:Asp45 4.37 Mg N D:Ser46 4.15 Mg CB D:Asp84 4.40 Mg OD2 D:Asp84 2.15 Mg OD1 D:Asp84 3.62 Mg CG D:Asp84 3.21 Mg CE D:Lys112 4.64 Mg NZ D:Lys112 3.36 Mg OE2 D:Glu114 4.08 Mg ND1 D:His136 4.86 Mg CE1 D:His136 4.73 Mg C6 D:Kpl265 3.02 Mg C5 D:Kpl265 3.13 Mg O2 D:Kpl265 2.55 Mg C4 D:Kpl265 4.78 Mg C4 D:Kpl265 5.00 Mg O1 D:Kpl265 4.01 Mg O3 D:Kpl265 2.22 Mg O4 D:Kpl265 4.21 Mg C2 D:Kpl265 4.50 Mg C2 D:Kpl265 4.53 Mg O D:Hoh267 2.52 Mg O D:Hoh268 2.54 Mg O D:Hoh269 3.56 Mg O D:Hoh270 4.78 interactive model: Magnesium binding site 5 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1m3u. 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: Leu42, E: Gly44, E: Asp45, E: Ser46, E: Asp84, E: Lys112, E: Glu114, E: His136, E: Kpl265, E: Hoh267, E: Hoh268, E: Hoh269, conact list: Atom Atom Distance (A) Mg CD2 E:Leu42 4.87 Mg C E:Gly44 4.42 Mg CA E:Gly44 4.33 Mg N E:Asp45 3.67 Mg CB E:Asp45 4.39 Mg OD2 E:Asp45 4.05 Mg C E:Asp45 4.46 Mg OD1 E:Asp45 2.40 Mg CG E:Asp45 3.42 Mg CA E:Asp45 4.29 Mg N E:Ser46 4.00 Mg CA E:Ser46 5.00 Mg CB E:Asp84 4.63 Mg OD2 E:Asp84 2.38 Mg OD1 E:Asp84 3.91 Mg CG E:Asp84 3.46 Mg CE E:Lys112 4.70 Mg NZ E:Lys112 3.59 Mg OE2 E:Glu114 4.38 Mg ND1 E:His136 4.97 Mg CE1 E:His136 4.78 Mg C6 E:Kpl265 2.99 Mg C5 E:Kpl265 3.05 Mg O2 E:Kpl265 2.51 Mg C4 E:Kpl265 4.51 Mg C4 E:Kpl265 4.74 Mg O1 E:Kpl265 4.00 Mg C3 E:Kpl265 4.94 Mg O3 E:Kpl265 2.16 Mg O4 E:Kpl265 4.18 Mg C2 E:Kpl265 4.38 Mg C2 E:Kpl265 4.41 Mg O E:Hoh267 2.77 Mg O E:Hoh268 2.58 Mg O E:Hoh269 3.58 interactive model: Magnesium binding site 6 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1m3u. 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: Leu42, F: Gly44, F: Asp45, F: Ser46, F: Asp84, F: Lys112, F: Glu114, F: His136, F: Kpl265, F: Hoh267, F: Hoh268, F: Hoh269, F: Hoh270, conact list: Atom Atom Distance (A) Mg CD2 F:Leu42 4.77 Mg C F:Gly44 4.45 Mg CA F:Gly44 4.34 Mg N F:Asp45 3.72 Mg CB F:Asp45 4.52 Mg OD2 F:Asp45 4.26 Mg C F:Asp45 4.63 Mg OD1 F:Asp45 2.57 Mg CG F:Asp45 3.60 Mg CA F:Asp45 4.42 Mg N F:Ser46 4.18 Mg CB F:Asp84 4.51 Mg OD2 F:Asp84 2.26 Mg OD1 F:Asp84 3.73 Mg CG F:Asp84 3.32 Mg CE F:Lys112 4.44 Mg NZ F:Lys112 3.33 Mg OE2 F:Glu114 4.14 Mg ND1 F:His136 4.83 Mg CE1 F:His136 4.67 Mg C6 F:Kpl265 2.99 Mg C5 F:Kpl265 3.01 Mg O2 F:Kpl265 2.43 Mg C4 F:Kpl265 4.55 Mg C4 F:Kpl265 4.77 Mg O1 F:Kpl265 4.10 Mg C3 F:Kpl265 4.97 Mg C3 F:Kpl265 4.89 Mg O3 F:Kpl265 2.25 Mg O4 F:Kpl265 4.18 Mg C2 F:Kpl265 4.35 Mg C2 F:Kpl265 4.38 Mg O F:Hoh267 2.53 Mg O F:Hoh268 2.66 Mg O F:Hoh269 3.55 Mg O F:Hoh270 4.80 interactive model: Magnesium binding site 7 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1m3u. 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: Gly44, G: Asp45, G: Ser46, G: Asp84, G: Lys112, G: Glu114, G: His136, G: Kpl265, G: Hoh267, G: Hoh268, G: Hoh269, G: Hoh270, conact list: Atom Atom Distance (A) Mg C G:Gly44 4.52 Mg CA G:Gly44 4.36 Mg N G:Asp45 3.78 Mg CB G:Asp45 4.62 Mg OD2 G:Asp45 4.31 Mg C G:Asp45 4.78 Mg OD1 G:Asp45 2.72 Mg CG G:Asp45 3.70 Mg CA G:Asp45 4.52 Mg N G:Ser46 4.28 Mg CB G:Asp84 4.56 Mg OD2 G:Asp84 2.20 Mg OD1 G:Asp84 3.68 Mg CG G:Asp84 3.30 Mg CE G:Lys112 4.52 Mg NZ G:Lys112 3.27 Mg OE2 G:Glu114 4.05 Mg ND1 G:His136 4.80 Mg CE1 G:His136 4.62 Mg C6 G:Kpl265 3.05 Mg C5 G:Kpl265 3.08 Mg O2 G:Kpl265 2.41 Mg C4 G:Kpl265 4.85 Mg O1 G:Kpl265 4.01 Mg C3 G:Kpl265 4.90 Mg C3 G:Kpl265 4.92 Mg O3 G:Kpl265 2.27 Mg O4 G:Kpl265 4.27 Mg C2 G:Kpl265 4.46 Mg C2 G:Kpl265 4.50 Mg O G:Hoh267 2.44 Mg O G:Hoh268 2.51 Mg O G:Hoh269 3.60 Mg O G:Hoh270 4.58 interactive model: Magnesium binding site 8 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 1m3u. 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: Leu42, H: Gly44, H: Asp45, H: Ser46, H: Asp84, H: Lys112, H: Glu114, H: His136, H: Kpl265, H: Hoh267, H: Hoh268, H: Hoh269, H: Hoh270, conact list: Atom Atom Distance (A) Mg CD2 H:Leu42 4.75 Mg C H:Gly44 4.37 Mg CA H:Gly44 4.26 Mg N H:Asp45 3.65 Mg CB H:Asp45 4.46 Mg OD2 H:Asp45 4.16 Mg C H:Asp45 4.57 Mg OD1 H:Asp45 2.48 Mg CG H:Asp45 3.51 Mg CA H:Asp45 4.35 Mg N H:Ser46 4.15 Mg CB H:Asp84 4.37 Mg OD2 H:Asp84 2.09 Mg OD1 H:Asp84 3.65 Mg CG H:Asp84 3.19 Mg CE H:Lys112 4.59 Mg NZ H:Lys112 3.40 Mg OE2 H:Glu114 4.31 Mg CE1 H:His136 4.86 Mg C6 H:Kpl265 2.89 Mg C5 H:Kpl265 2.98 Mg O2 H:Kpl265 2.43 Mg C4 H:Kpl265 4.57 Mg C4 H:Kpl265 4.90 Mg O1 H:Kpl265 4.02 Mg C3 H:Kpl265 4.99 Mg C3 H:Kpl265 4.87 Mg O3 H:Kpl265 2.11 Mg O4 H:Kpl265 4.07 Mg C2 H:Kpl265 4.34 Mg C2 H:Kpl265 4.40 Mg O H:Hoh267 2.67 Mg O H:Hoh268 2.62 Mg O H:Hoh269 3.51 Mg O H:Hoh270 4.86 interactive model: Magnesium binding site 9 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 1m3u. 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: I: Gly44, I: Asp45, I: Ser46, I: Asp84, I: Lys112, I: Glu114, I: His136, I: Kpl265, I: Hoh267, I: Hoh268, I: Hoh269, I: Hoh270, I: Hoh528, conact list: Atom Atom Distance (A) Mg C I:Gly44 4.44 Mg CA I:Gly44 4.37 Mg N I:Asp45 3.63 Mg CB I:Asp45 4.37 Mg OD2 I:Asp45 4.05 Mg C I:Asp45 4.58 Mg OD1 I:Asp45 2.46 Mg CG I:Asp45 3.43 Mg CA I:Asp45 4.32 Mg N I:Ser46 4.17 Mg CB I:Asp84 4.42 Mg OD2 I:Asp84 2.18 Mg OD1 I:Asp84 3.71 Mg CG I:Asp84 3.26 Mg CE I:Lys112 4.48 Mg NZ I:Lys112 3.25 Mg OE2 I:Glu114 3.94 Mg ND1 I:His136 4.76 Mg CE1 I:His136 4.61 Mg C6 I:Kpl265 3.02 Mg C5 I:Kpl265 3.07 Mg O2 I:Kpl265 2.53 Mg C4 I:Kpl265 4.64 Mg C4 I:Kpl265 4.79 Mg O1 I:Kpl265 3.99 Mg C3 I:Kpl265 4.93 Mg O3 I:Kpl265 2.25 Mg O4 I:Kpl265 4.20 Mg C2 I:Kpl265 4.45 Mg C2 I:Kpl265 4.45 Mg O I:Hoh267 2.35 Mg O I:Hoh268 2.43 Mg O I:Hoh269 3.46 Mg O I:Hoh270 4.74 Mg O I:Hoh528 4.82 interactive model: Magnesium binding site 10 out of 10 in 1m3u Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 1m3u. 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: J: Gly44, J: Asp45, J: Ser46, J: Asp84, J: Lys112, J: Glu114, J: His136, J: Kpl265, J: Hoh267, J: Hoh268, J: Hoh269, J: Hoh270, conact list: Atom Atom Distance (A) Mg C J:Gly44 4.48 Mg CA J:Gly44 4.33 Mg N J:Asp45 3.75 Mg CB J:Asp45 4.64 Mg OD2 J:Asp45 4.26 Mg C J:Asp45 4.84 Mg OD1 J:Asp45 2.78 Mg CG J:Asp45 3.70 Mg CA J:Asp45 4.56 Mg N J:Ser46 4.33 Mg CB J:Asp84 4.50 Mg OD2 J:Asp84 2.14 Mg OD1 J:Asp84 3.67 Mg CG J:Asp84 3.26 Mg CE J:Lys112 4.54 Mg NZ J:Lys112 3.34 Mg OE2 J:Glu114 4.16 Mg ND1 J:His136 4.78 Mg CE1 J:His136 4.63 Mg C6 J:Kpl265 3.07 Mg C5 J:Kpl265 3.08 Mg O2 J:Kpl265 2.39 Mg C4 J:Kpl265 4.80 Mg O1 J:Kpl265 3.95 Mg C3 J:Kpl265 5.00 Mg C3 J:Kpl265 4.91 Mg O3 J:Kpl265 2.30 Mg O4 J:Kpl265 4.28 Mg C2 J:Kpl265 4.47 Mg C2 J:Kpl265 4.50 Mg O J:Hoh267 2.48 Mg O J:Hoh268 2.70 Mg O J:Hoh269 3.79 Mg O J:Hoh270 4.93 interactive model: