Manganese in the structure of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex With Sulfate and Manganese Ions. (pdb 1d8h)

The binding sites of Manganese atom in the structure of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex With Sulfate and Manganese Ions. (pdb code 1d8h). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1d8h structure was solved by C.D.LIMA, L.K.WANG, S.SHUMAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.0 Space group C121 a (A) 116.436 b (A) 118.723 c (A) 85.138 alpha (°) 90.00 beta (°) 108.06 gamma (°) 90.00 Rfactor (%) 22.9 Rfree (%) 31 Manganese Binding Sites: Manganese binding site 1 out of 3 in 1d8h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1d8h. 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: Glu305, A: Glu307, A: Lys409, A: Glu433, A: Asp471, A: Glu494, A: Glu496, A: So4601, A: Hoh620, A: Hoh629, A: Hoh705, A: Hoh767, conact list: Atom Atom Distance (A) Mn OE1 A:Glu305 4.22 Mn OE2 A:Glu305 2.82 Mn CD A:Glu305 3.52 Mn CG A:Glu305 3.88 Mn OE1 A:Glu307 4.20 Mn CB A:Glu307 4.81 Mn OE2 A:Glu307 2.63 Mn CD A:Glu307 3.61 Mn CG A:Glu307 4.84 Mn NZ A:Lys409 4.60 Mn OE1 A:Glu433 4.93 Mn OD1 A:Asp471 4.48 Mn OE2 A:Glu494 4.80 Mn CD A:Glu494 4.96 Mn OE1 A:Glu496 4.73 Mn OE2 A:Glu496 2.49 Mn CD A:Glu496 3.61 Mn CG A:Glu496 4.07 Mn S A:So4601 4.12 Mn O1 A:So4601 4.63 Mn O4 A:So4601 3.04 Mn O3 A:So4601 4.93 Mn O A:Hoh620 2.10 Mn O A:Hoh629 3.58 Mn O A:Hoh705 4.81 Mn O A:Hoh767 2.94 interactive model: Manganese binding site 2 out of 3 in 1d8h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1d8h. 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: Glu305, B: Glu307, B: Lys409, B: Asp471, B: Glu494, B: Glu496, B: So4602, B: Hoh618, B: Hoh641, B: Hoh652, B: Hoh713, conact list: Atom Atom Distance (A) Mn OE1 B:Glu305 4.04 Mn OE2 B:Glu305 2.66 Mn CD B:Glu305 3.28 Mn CG B:Glu305 3.89 Mn OE1 B:Glu307 4.12 Mn CB B:Glu307 4.78 Mn OE2 B:Glu307 2.25 Mn CD B:Glu307 3.46 Mn CG B:Glu307 4.61 Mn NZ B:Lys409 4.68 Mn OD1 B:Asp471 4.15 Mn OE1 B:Glu494 4.79 Mn OE2 B:Glu494 4.83 Mn CD B:Glu494 4.83 Mn OE1 B:Glu496 4.20 Mn OE2 B:Glu496 2.32 Mn CD B:Glu496 3.23 Mn CG B:Glu496 3.56 Mn S B:So4602 4.83 Mn O1 B:So4602 4.48 Mn O2 B:So4602 4.87 Mn O4 B:So4602 4.49 Mn O B:Hoh618 2.02 Mn O B:Hoh641 2.91 Mn O B:Hoh652 4.10 Mn O B:Hoh713 3.08 interactive model: Manganese binding site 3 out of 3 in 1d8h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1d8h. 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: Glu305, C: Glu307, C: Lys409, C: Asp471, C: Glu494, C: Glu496, C: So4603, C: Hoh614, C: Hoh630, C: Hoh763, C: Hoh778, conact list: Atom Atom Distance (A) Mn OE1 C:Glu305 4.14 Mn OE2 C:Glu305 2.81 Mn CD C:Glu305 3.35 Mn CG C:Glu305 3.93 Mn OE1 C:Glu307 3.40 Mn CB C:Glu307 4.88 Mn OE2 C:Glu307 2.53 Mn CD C:Glu307 3.31 Mn CG C:Glu307 4.70 Mn NZ C:Lys409 4.60 Mn OD1 C:Asp471 4.10 Mn OE1 C:Glu494 4.80 Mn OE2 C:Glu494 4.18 Mn CD C:Glu494 4.53 Mn OE1 C:Glu496 4.52 Mn OE2 C:Glu496 2.49 Mn CD C:Glu496 3.32 Mn CG C:Glu496 3.64 Mn S C:So4603 4.36 Mn O2 C:So4603 4.52 Mn O3 C:So4603 3.08 Mn O C:Hoh614 2.32 Mn O C:Hoh630 3.57 Mn O C:Hoh763 2.60 Mn O C:Hoh778 3.96 interactive model: