Magnesium in the structure of Human Pyruvate Kinase M2 (pdb 1t5a)

The binding sites of Magnesium atom in the structure of Human Pyruvate Kinase M2 (pdb code 1t5a). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1t5a structure was solved by J.D.DOMBRAUCKAS, B.D.SANTARSIERO, A.D.MESECAR, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.8 Space group P212121 a (A) 108.209 b (A) 145.006 c (A) 159.260 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.1 Rfree (%) 27.8 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1t5a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1t5a. 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: Phe244, A: Lys270, A: Glu272, A: Asp296, A: Oxl533, A: K701, A: Hoh729, A: Hoh734, conact list: Atom Atom Distance (A) Mg CZ A:Phe244 4.80 Mg CE1 A:Phe244 4.77 Mg NZ A:Lys270 4.01 Mg OE1 A:Glu272 4.37 Mg OE2 A:Glu272 2.41 Mg CD A:Glu272 3.63 Mg CG A:Glu272 4.64 Mg N A:Asp296 4.99 Mg CB A:Asp296 4.45 Mg OD2 A:Asp296 2.37 Mg OD1 A:Asp296 4.36 Mg CG A:Asp296 3.56 Mg O2 A:Oxl533 4.43 Mg C1 A:Oxl533 3.33 Mg O1 A:Oxl533 2.59 Mg O3 A:Oxl533 4.54 Mg O4 A:Oxl533 2.40 Mg C2 A:Oxl533 3.24 Mg K A:K701 4.45 Mg O A:Hoh729 2.65 Mg O A:Hoh734 3.70 interactive model: Magnesium binding site 2 out of 4 in 1t5a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1t5a. 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: Phe244, B: Lys270, B: Glu272, B: Asp296, B: Oxl533, B: K702, B: Hoh723, conact list: Atom Atom Distance (A) Mg CZ B:Phe244 4.72 Mg CE1 B:Phe244 4.60 Mg NZ B:Lys270 3.97 Mg OE1 B:Glu272 4.33 Mg OE2 B:Glu272 2.43 Mg CD B:Glu272 3.66 Mg CG B:Glu272 4.73 Mg CB B:Asp296 4.56 Mg OD2 B:Asp296 2.41 Mg OD1 B:Asp296 4.45 Mg CG B:Asp296 3.64 Mg O2 B:Oxl533 4.41 Mg C1 B:Oxl533 3.29 Mg O1 B:Oxl533 2.56 Mg O3 B:Oxl533 4.47 Mg O4 B:Oxl533 2.46 Mg C2 B:Oxl533 3.24 Mg K B:K702 4.60 Mg O B:Hoh723 3.58 interactive model: Magnesium binding site 3 out of 4 in 1t5a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1t5a. 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: Ser243, C: Phe244, C: Lys270, C: Glu272, C: Asp296, C: Oxl533, C: K703, C: Hoh725, conact list: Atom Atom Distance (A) Mg OG C:Ser243 4.68 Mg CD1 C:Phe244 4.99 Mg CZ C:Phe244 4.30 Mg CE1 C:Phe244 4.07 Mg CE C:Lys270 4.68 Mg NZ C:Lys270 3.67 Mg OE1 C:Glu272 3.79 Mg OE2 C:Glu272 2.10 Mg CD C:Glu272 3.25 Mg CG C:Glu272 4.46 Mg CB C:Asp296 4.61 Mg OD2 C:Asp296 2.43 Mg OD1 C:Asp296 4.50 Mg CG C:Asp296 3.69 Mg O2 C:Oxl533 2.47 Mg C1 C:Oxl533 3.43 Mg O1 C:Oxl533 4.63 Mg O3 C:Oxl533 2.74 Mg O4 C:Oxl533 4.53 Mg C2 C:Oxl533 3.33 Mg K C:K703 4.70 Mg O C:Hoh725 3.56 interactive model: Magnesium binding site 4 out of 4 in 1t5a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1t5a. 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: Phe244, D: Lys270, D: Glu272, D: Asp296, D: Oxl533, D: K704, D: Hoh719, conact list: Atom Atom Distance (A) Mg CZ D:Phe244 4.96 Mg CE1 D:Phe244 4.86 Mg NZ D:Lys270 4.17 Mg OE1 D:Glu272 4.76 Mg OE2 D:Glu272 2.87 Mg CD D:Glu272 4.10 Mg CB D:Asp296 4.81 Mg OD2 D:Asp296 2.60 Mg OD1 D:Asp296 4.51 Mg CG D:Asp296 3.80 Mg O2 D:Oxl533 4.40 Mg C1 D:Oxl533 3.19 Mg O1 D:Oxl533 2.51 Mg O3 D:Oxl533 4.28 Mg O4 D:Oxl533 2.64 Mg C2 D:Oxl533 3.25 Mg K D:K704 4.05 Mg O D:Hoh719 3.24 interactive model: