Manganese in the structure of Crystal Structure Analysis of Dahp Synthase in Complex With MN2+ and 2-Phosphoglycolate (pdb 1gg1)

The binding sites of Manganese atom in the structure of Crystal Structure Analysis of Dahp Synthase in Complex With MN2+ and 2-Phosphoglycolate (pdb code 1gg1). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1gg1 structure was solved by T.WAGNER, I.A.SHUMILIN, R.BAUERLE, R.H.KRETSINGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group C121 a (A) 210.357 b (A) 53.188 c (A) 149.392 alpha (°) 90.00 beta (°) 116.09 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 23.7 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1gg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1gg1. 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: Cys61, A: Arg92, A: Lys97, A: His268, A: Glu302, A: Asp326, A: Pga372, A: Hoh1435, A: Hoh1460, conact list: Atom Atom Distance (A) Mn O A:Cys61 4.86 Mn CB A:Cys61 3.80 Mn SG A:Cys61 2.79 Mn CA A:Cys61 4.39 Mn NH2 A:Arg92 4.24 Mn CE A:Lys97 4.86 Mn NZ A:Lys97 3.62 Mn NE2 A:His268 2.36 Mn ND1 A:His268 4.42 Mn CD2 A:His268 3.24 Mn CE1 A:His268 3.35 Mn CG A:His268 4.40 Mn OE1 A:Glu302 2.16 Mn OE2 A:Glu302 3.47 Mn CD A:Glu302 3.15 Mn CG A:Glu302 4.47 Mn CB A:Asp326 3.72 Mn OD2 A:Asp326 2.20 Mn OD1 A:Asp326 4.37 Mn CG A:Asp326 3.27 Mn O2 A:Pga372 2.41 Mn C1 A:Pga372 3.39 Mn O1 A:Pga372 4.26 Mn O1P A:Pga372 4.97 Mn C2 A:Pga372 3.91 Mn O A:Hoh1435 4.27 Mn O A:Hoh1460 4.50 interactive model: Manganese binding site 2 out of 4 in 1gg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1gg1. 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: Cys61, B: Arg92, B: Lys97, B: His268, B: Lys273, B: Glu302, B: Asp326, B: Pga372, B: Hoh2375, B: Hoh2384, B: Hoh2448, B: Hoh2553, B: Hoh2571, conact list: Atom Atom Distance (A) Mn O B:Cys61 4.82 Mn CB B:Cys61 3.72 Mn SG B:Cys61 2.67 Mn C B:Cys61 4.95 Mn CA B:Cys61 4.29 Mn CZ B:Arg92 4.97 Mn NH2 B:Arg92 4.17 Mn CE B:Lys97 4.72 Mn NZ B:Lys97 3.91 Mn NE2 B:His268 2.36 Mn ND1 B:His268 4.42 Mn CD2 B:His268 3.38 Mn CE1 B:His268 3.27 Mn CG B:His268 4.51 Mn NZ B:Lys273 4.86 Mn OE1 B:Glu302 3.49 Mn OE2 B:Glu302 1.97 Mn CD B:Glu302 3.03 Mn CG B:Glu302 4.29 Mn N B:Asp326 4.92 Mn CB B:Asp326 3.61 Mn OD2 B:Asp326 2.06 Mn OD1 B:Asp326 4.16 Mn CG B:Asp326 3.09 Mn CA B:Asp326 4.88 Mn O2 B:Pga372 2.45 Mn C1 B:Pga372 3.35 Mn O1 B:Pga372 4.29 Mn O1P B:Pga372 4.92 Mn C2 B:Pga372 3.76 Mn O B:Hoh2375 2.26 Mn O B:Hoh2384 4.63 Mn O B:Hoh2448 4.25 Mn O B:Hoh2553 4.72 Mn O B:Hoh2571 4.69 interactive model: Manganese binding site 3 out of 4 in 1gg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1gg1. 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: C: Cys61, C: Arg92, C: Lys97, C: His268, C: Glu302, C: Asp326, C: Pga372, C: Hoh3375, C: Hoh3376, C: Hoh3397, C: Hoh3442, conact list: Atom Atom Distance (A) Mn CB C:Cys61 3.72 Mn SG C:Cys61 2.79 Mn CA C:Cys61 4.33 Mn NH2 C:Arg92 4.41 Mn CE C:Lys97 4.69 Mn NZ C:Lys97 3.83 Mn NE2 C:His268 2.50 Mn ND1 C:His268 4.62 Mn CD2 C:His268 3.22 Mn CE1 C:His268 3.63 Mn CG C:His268 4.47 Mn OE1 C:Glu302 3.20 Mn OE2 C:Glu302 2.04 Mn CD C:Glu302 2.95 Mn CG C:Glu302 4.34 Mn CB C:Asp326 3.45 Mn OD2 C:Asp326 1.86 Mn OD1 C:Asp326 4.04 Mn CG C:Asp326 2.95 Mn CA C:Asp326 4.83 Mn O2 C:Pga372 2.27 Mn C1 C:Pga372 3.26 Mn O1 C:Pga372 4.13 Mn O1P C:Pga372 4.90 Mn C2 C:Pga372 3.82 Mn O C:Hoh3375 2.48 Mn O C:Hoh3376 4.57 Mn O C:Hoh3397 4.31 Mn O C:Hoh3442 4.59 interactive model: Manganese binding site 4 out of 4 in 1gg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1gg1. 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: D: Cys61, D: Arg92, D: Lys97, D: His268, D: Lys273, D: Glu302, D: Asp326, D: Pga372, D: Hoh4375, D: Hoh4394, D: Hoh4430, D: Hoh4534, D: Hoh4535, conact list: Atom Atom Distance (A) Mn O D:Cys61 4.78 Mn CB D:Cys61 3.72 Mn SG D:Cys61 2.64 Mn C D:Cys61 4.96 Mn CA D:Cys61 4.32 Mn NH2 D:Arg92 4.27 Mn CE D:Lys97 4.69 Mn NZ D:Lys97 3.87 Mn NE2 D:His268 2.35 Mn ND1 D:His268 4.45 Mn CD2 D:His268 3.21 Mn CE1 D:His268 3.39 Mn CG D:His268 4.40 Mn NZ D:Lys273 4.86 Mn OE1 D:Glu302 2.14 Mn OE2 D:Glu302 3.29 Mn CD D:Glu302 3.04 Mn CG D:Glu302 4.39 Mn N D:Asp326 4.96 Mn CB D:Asp326 3.64 Mn OD2 D:Asp326 2.13 Mn OD1 D:Asp326 4.24 Mn CG D:Asp326 3.17 Mn CA D:Asp326 4.91 Mn O2 D:Pga372 2.47 Mn C1 D:Pga372 3.42 Mn O1 D:Pga372 4.21 Mn C2 D:Pga372 4.01 Mn O D:Hoh4375 2.19 Mn O D:Hoh4394 4.40 Mn O D:Hoh4430 4.07 Mn O D:Hoh4534 4.50 Mn O D:Hoh4535 4.60 interactive model: