Manganese in the structure of Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 Cocrystallized With Manganese and Amp (pdb 2e6c)

The binding sites of Manganese atom in the structure of Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 Cocrystallized With Manganese and Amp (pdb code 2e6c). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2e6c structure was solved by W.IWASAKI, K.MIKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 46.6-2.0 Space group P3121 a (A) 132.599 b (A) 132.599 c (A) 130.783 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.8 Rfree (%) 24.9 Manganese Binding Sites: Manganese binding site 1 out of 4 in 2e6c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2e6c. 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: Asp8, A: Asp9, A: Asn96, A: Leu97, A: Thr110, C: Glu37, A: Hoh506, A: Hoh585, A: Hoh594, C: Hoh2436, conact list: Atom Atom Distance (A) Mn O A:Asp8 4.71 Mn CB A:Asp8 4.49 Mn OD2 A:Asp8 2.06 Mn C A:Asp8 4.41 Mn OD1 A:Asp8 3.36 Mn CG A:Asp8 3.07 Mn CA A:Asp8 4.90 Mn N A:Asp9 4.28 Mn CB A:Asp9 4.42 Mn OD2 A:Asp9 3.67 Mn OD1 A:Asp9 2.22 Mn CG A:Asp9 3.22 Mn CA A:Asp9 4.49 Mn CB A:Asn96 4.57 Mn ND2 A:Asn96 3.54 Mn OD1 A:Asn96 2.21 Mn CG A:Asn96 3.19 Mn O A:Leu97 4.76 Mn N A:Leu97 4.86 Mn OG1 A:Thr110 4.30 Mn OE1 C:Glu37 2.22 Mn OE2 C:Glu37 3.61 Mn CD C:Glu37 3.12 Mn CG C:Glu37 4.23 Mn O A:Hoh506 4.33 Mn O A:Hoh585 4.96 Mn O A:Hoh594 2.51 Mn O C:Hoh2436 3.89 interactive model: Manganese binding site 2 out of 4 in 2e6c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2e6c. 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: Asp8, B: Asp9, B: Asn96, B: Leu97, B: Thr110, B: Hoh1519, conact list: Atom Atom Distance (A) Mn O B:Asp8 4.69 Mn CB B:Asp8 4.65 Mn OD2 B:Asp8 2.49 Mn C B:Asp8 4.45 Mn OD1 B:Asp8 3.39 Mn CG B:Asp8 3.27 Mn N B:Asp9 4.31 Mn CB B:Asp9 4.46 Mn OD2 B:Asp9 2.31 Mn OD1 B:Asp9 3.83 Mn CG B:Asp9 3.32 Mn CA B:Asp9 4.43 Mn CB B:Asn96 4.53 Mn ND2 B:Asn96 3.53 Mn OD1 B:Asn96 2.15 Mn CG B:Asn96 3.16 Mn O B:Leu97 4.81 Mn OG1 B:Thr110 4.58 Mn O B:Hoh1519 4.23 interactive model: Manganese binding site 3 out of 4 in 2e6c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2e6c. 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: Glu37, C: Asp8, C: Asp9, C: Asn96, C: Leu97, C: Thr110, C: Hoh2408, C: Hoh2470, conact list: Atom Atom Distance (A) Mn OE1 A:Glu37 3.74 Mn OE2 A:Glu37 2.26 Mn CD A:Glu37 3.23 Mn CG A:Glu37 4.39 Mn O C:Asp8 4.57 Mn CB C:Asp8 4.49 Mn OD2 C:Asp8 2.07 Mn C C:Asp8 4.35 Mn OD1 C:Asp8 3.39 Mn CG C:Asp8 3.08 Mn CA C:Asp8 4.90 Mn N C:Asp9 4.28 Mn CB C:Asp9 4.40 Mn OD2 C:Asp9 3.62 Mn OD1 C:Asp9 2.23 Mn CG C:Asp9 3.19 Mn CA C:Asp9 4.48 Mn CB C:Asn96 4.50 Mn ND2 C:Asn96 3.46 Mn OD1 C:Asn96 2.15 Mn CG C:Asn96 3.12 Mn O C:Leu97 4.73 Mn N C:Leu97 4.77 Mn OG1 C:Thr110 4.33 Mn O C:Hoh2408 4.19 Mn O C:Hoh2470 2.16 interactive model: Manganese binding site 4 out of 4 in 2e6c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2e6c. 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: Asp8, D: Asp9, D: Asn96, D: Leu97, D: Thr110, D: Hoh3420, conact list: Atom Atom Distance (A) Mn O D:Asp8 4.81 Mn CB D:Asp8 3.75 Mn OD2 D:Asp8 3.10 Mn C D:Asp8 4.32 Mn CG D:Asp8 3.87 Mn CA D:Asp8 4.63 Mn N D:Asp9 4.10 Mn CB D:Asp9 4.43 Mn OD2 D:Asp9 2.22 Mn OD1 D:Asp9 3.72 Mn CG D:Asp9 3.24 Mn CA D:Asp9 4.46 Mn CB D:Asn96 4.60 Mn ND2 D:Asn96 3.69 Mn OD1 D:Asn96 2.23 Mn CG D:Asn96 3.27 Mn O D:Leu97 4.98 Mn N D:Leu97 4.95 Mn OG1 D:Thr110 4.51 Mn O D:Hoh3420 4.07 interactive model: