Manganese in the structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex With Oxalate and Gtp (pdb 3mof)

The binding sites of Manganese atom in the structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex With Oxalate and Gtp (pdb code 3mof). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3mof structure was solved by T.A.JOHNSON, T.HOLYOAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.2-1.8 Space group P1211 a (A) 61.983 b (A) 119.601 c (A) 87.068 alpha (°) 90.00 beta (°) 106.87 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 22.8 Manganese Binding Sites: Manganese binding site 1 out of 5 in 3mof Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3mof. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys290, A: Thr291, A: Asp310, A: Asp311, A: Phe333, A: Gly334, A: Arg405, A: Gtp900, A: Mn700, A: Oxl1000, A: Hoh631, A: Hoh794, A: Hoh802, A: Hoh856, conact list: Atom Atom Distance (A) Mn CB A:Lys290 4.91 Mn N A:Thr291 4.04 Mn CB A:Thr291 3.35 Mn CG2 A:Thr291 4.47 Mn OG1 A:Thr291 2.22 Mn CA A:Thr291 4.22 Mn O A:Asp310 4.18 Mn CB A:Asp310 4.93 Mn OD2 A:Asp310 3.51 Mn C A:Asp310 4.95 Mn OD1 A:Asp310 4.74 Mn CG A:Asp310 4.19 Mn CB A:Asp311 4.86 Mn OD1 A:Asp311 4.27 Mn CG A:Asp311 4.92 Mn O A:Phe333 4.67 Mn CA A:Gly334 4.62 Mn NH1 A:Arg405 4.48 Mn PG A:Gtp900 3.45 Mn PG A:Gtp900 3.03 Mn O3B A:Gtp900 3.43 Mn O3B A:Gtp900 3.86 Mn O2G A:Gtp900 4.69 Mn O2G A:Gtp900 2.97 Mn PA A:Gtp900 4.46 Mn O2B A:Gtp900 1.94 Mn O2B A:Gtp900 4.46 Mn O3A A:Gtp900 4.15 Mn O3G A:Gtp900 4.05 Mn O3G A:Gtp900 4.25 Mn O2A A:Gtp900 4.76 Mn O1B A:Gtp900 4.27 Mn O1B A:Gtp900 2.63 Mn PB A:Gtp900 3.13 Mn PB A:Gtp900 3.72 Mn O1G A:Gtp900 2.39 Mn O1G A:Gtp900 2.03 Mn O1A A:Gtp900 3.92 Mn O1A A:Gtp900 4.62 Mn MN A:Mn700 0.00 Mn MN A:Mn700 1.27 Mn O3 A:Oxl1000 4.82 Mn O A:Hoh631 4.04 Mn O A:Hoh794 2.57 Mn O A:Hoh802 1.90 Mn O A:Hoh856 2.14 interactive model: Manganese binding site 2 out of 5 in 3mof Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3mof. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Thr291, A: Asp310, A: Phe333, A: Gly334, A: Val335, A: Arg405, A: Gtp900, A: Mn700, A: Hoh631, A: Hoh703, A: Hoh794, A: Hoh802, A: Hoh856, conact list: Atom Atom Distance (A) Mn N A:Thr291 4.30 Mn CB A:Thr291 3.40 Mn CG2 A:Thr291 4.50 Mn OG1 A:Thr291 2.70 Mn CA A:Thr291 4.47 Mn OD2 A:Asp310 4.35 Mn O A:Phe333 4.63 Mn C A:Gly334 4.69 Mn CA A:Gly334 4.15 Mn N A:Val335 4.08 Mn CB A:Val335 4.81 Mn CG2 A:Val335 4.42 Mn NH1 A:Arg405 4.01 Mn PG A:Gtp900 3.34 Mn PG A:Gtp900 2.74 Mn O3B A:Gtp900 3.02 Mn O3B A:Gtp900 3.30 Mn O2G A:Gtp900 4.31 Mn O2G A:Gtp900 3.28 Mn PA A:Gtp900 3.63 Mn PA A:Gtp900 4.36 Mn O2B A:Gtp900 2.05 Mn O2B A:Gtp900 4.29 Mn O3A A:Gtp900 3.49 Mn O3A A:Gtp900 4.22 Mn O3G A:Gtp900 4.35 Mn O3G A:Gtp900 3.92 Mn O2A A:Gtp900 4.24 Mn O1B A:Gtp900 4.29 Mn O1B A:Gtp900 2.05 Mn PB A:Gtp900 2.88 Mn PB A:Gtp900 3.18 Mn O1G A:Gtp900 2.41 Mn O1G A:Gtp900 1.43 Mn O1A A:Gtp900 2.84 Mn O1A A:Gtp900 3.45 Mn MN A:Mn700 1.27 Mn MN A:Mn700 0.00 Mn O A:Hoh631 4.66 Mn O A:Hoh703 4.19 Mn O A:Hoh794 1.42 Mn O A:Hoh802 3.07 Mn O A:Hoh856 2.86 interactive model: Manganese binding site 3 out of 5 in 3mof Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3mof. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys244, A: His264, A: Ser286, A: Lys290, A: Asp311, A: Gtp900, A: Oxl1000, A: Hoh631, A: Hoh802, conact list: Atom Atom Distance (A) Mn CE A:Lys244 3.35 Mn CD A:Lys244 4.76 Mn NZ A:Lys244 2.35 Mn NE2 A:His264 2.30 Mn ND1 A:His264 4.36 Mn CD2 A:His264 3.27 Mn CE1 A:His264 3.26 Mn CG A:His264 4.40 Mn CB A:Ser286 4.93 Mn OG A:Ser286 4.30 Mn OG A:Ser286 4.44 Mn CA A:Ser286 4.87 Mn CA A:Ser286 4.89 Mn CE A:Lys290 4.23 Mn NZ A:Lys290 4.00 Mn CB A:Asp311 4.40 Mn OD2 A:Asp311 3.20 Mn OD1 A:Asp311 2.13 Mn CG A:Asp311 2.98 Mn PG A:Gtp900 3.25 Mn PG A:Gtp900 3.81 Mn O3B A:Gtp900 4.65 Mn O3B A:Gtp900 4.93 Mn O2G A:Gtp900 3.89 Mn O2G A:Gtp900 2.78 Mn O3G A:Gtp900 2.09 Mn O3G A:Gtp900 3.68 Mn O1G A:Gtp900 3.54 Mn O1G A:Gtp900 4.76 Mn O2 A:Oxl1000 2.20 Mn C1 A:Oxl1000 2.78 Mn O1 A:Oxl1000 3.98 Mn O3 A:Oxl1000 2.00 Mn O4 A:Oxl1000 4.10 Mn C2 A:Oxl1000 2.86 Mn O A:Hoh631 4.32 Mn O A:Hoh802 4.21 interactive model: Manganese binding site 4 out of 5 in 3mof Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3mof. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Lys244, B: His264, B: Ser286, B: Lys290, B: Asp311, B: Gtp1000, B: Oxl1200, B: Hoh667, B: Hoh705, conact list: Atom Atom Distance (A) Mn CE B:Lys244 3.36 Mn CD B:Lys244 4.75 Mn NZ B:Lys244 2.46 Mn NE2 B:His264 2.31 Mn ND1 B:His264 4.36 Mn CD2 B:His264 3.29 Mn CE1 B:His264 3.25 Mn CG B:His264 4.42 Mn OG B:Ser286 4.18 Mn CE B:Lys290 4.18 Mn NZ B:Lys290 3.88 Mn CB B:Asp311 4.48 Mn OD2 B:Asp311 3.26 Mn OD1 B:Asp311 2.14 Mn CG B:Asp311 3.05 Mn PG B:Gtp1000 3.32 Mn O3B B:Gtp1000 4.69 Mn O2G B:Gtp1000 3.79 Mn O3G B:Gtp1000 2.22 Mn O1G B:Gtp1000 3.76 Mn O2 B:Oxl1200 4.05 Mn C1 B:Oxl1200 2.79 Mn O1 B:Oxl1200 4.01 Mn O3 B:Oxl1200 2.01 Mn O4 B:Oxl1200 2.23 Mn C2 B:Oxl1200 2.83 Mn O B:Hoh667 4.21 Mn O B:Hoh705 4.28 interactive model: Manganese binding site 5 out of 5 in 3mof Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3mof. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Lys290, B: Thr291, B: Asp310, B: Asp311, B: Phe333, B: Gly334, B: Val335, B: Arg405, B: Gtp1000, B: Oxl1200, B: Hoh667, B: Hoh704, B: Hoh705, B: Hoh716, B: Hoh820, conact list: Atom Atom Distance (A) Mn CB B:Lys290 4.94 Mn N B:Thr291 4.10 Mn CB B:Thr291 3.30 Mn CG2 B:Thr291 4.37 Mn OG1 B:Thr291 2.24 Mn CA B:Thr291 4.28 Mn O B:Asp310 4.38 Mn OD2 B:Asp310 3.74 Mn CG B:Asp310 4.52 Mn OD1 B:Asp311 4.65 Mn O B:Phe333 4.76 Mn CA B:Gly334 4.49 Mn N B:Val335 4.76 Mn NH1 B:Arg405 4.30 Mn PG B:Gtp1000 3.28 Mn O3B B:Gtp1000 3.50 Mn O2G B:Gtp1000 2.22 Mn PA B:Gtp1000 4.74 Mn O2B B:Gtp1000 2.18 Mn O3A B:Gtp1000 4.37 Mn O3G B:Gtp1000 3.99 Mn O2A B:Gtp1000 4.05 Mn O1B B:Gtp1000 4.43 Mn PB B:Gtp1000 3.32 Mn O1G B:Gtp1000 4.51 Mn O3 B:Oxl1200 4.95 Mn O B:Hoh667 2.13 Mn O B:Hoh704 4.67 Mn O B:Hoh705 4.10 Mn O B:Hoh716 2.13 Mn O B:Hoh820 2.24 interactive model: