Manganese in the structure of Structure of The 6-Phospho-Beta Glucosidase From Thermotoga Maritima At 2.55 Angstrom Resolution in the Tetragonal Form With Manganese, Nad+ and Glucose-6-Phosphate (pdb 1up6)

The binding sites of Manganese atom in the structure of Structure of The 6-Phospho-Beta Glucosidase From Thermotoga Maritima At 2.55 Angstrom Resolution in the Tetragonal Form With Manganese, Nad+ and Glucose-6-Phosphate (pdb code 1up6). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1up6 structure was solved by A.VARROT, V.L.YIP, S.G.WITHERS, G.J.DAVIES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.5 Space group P43212 a (A) 179.438 b (A) 179.438 c (A) 282.911 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 25 Manganese Binding Sites: Manganese binding site 1 out of 5 in 1up6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1up6. 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: Asn140, A: Cys162, A: Asn163, A: Val164, A: Asn191, A: His192, A: Nad1416, A: G6p1418, conact list: Atom Atom Distance (A) Mn ND2 A:Asn140 4.36 Mn CB A:Cys162 3.84 Mn SG A:Cys162 2.72 Mn C A:Cys162 4.34 Mn CA A:Cys162 3.97 Mn N A:Asn163 3.71 Mn CB A:Asn163 4.94 Mn ND2 A:Asn163 3.23 Mn CG A:Asn163 4.37 Mn CA A:Asn163 4.78 Mn N A:Val164 4.92 Mn CG1 A:Val164 4.56 Mn ND2 A:Asn191 4.68 Mn OD1 A:Asn191 4.92 Mn NE2 A:His192 2.83 Mn ND1 A:His192 4.59 Mn CD2 A:His192 3.91 Mn CE1 A:His192 3.42 Mn CG A:His192 4.86 Mn N7N A:Nad1416 3.38 Mn O7N A:Nad1416 2.25 Mn C7N A:Nad1416 2.90 Mn C2N A:Nad1416 4.78 Mn C3N A:Nad1416 3.89 Mn C4N A:Nad1416 4.41 Mn C1 A:G6p1418 4.37 Mn O3 A:G6p1418 2.21 Mn C2 A:G6p1418 2.99 Mn O2 A:G6p1418 2.24 Mn C4 A:G6p1418 4.32 Mn C3 A:G6p1418 2.90 Mn O4 A:G6p1418 4.80 interactive model: Manganese binding site 2 out of 5 in 1up6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1up6. 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: Asp36, A: Ile37, A: Asp38, A: Glu39, A: Mn1420, A: Hoh2135, A: Hoh2136, conact list: Atom Atom Distance (A) Mn O A:Asp36 4.48 Mn O A:Ile37 2.02 Mn C A:Ile37 3.15 Mn CA A:Ile37 4.11 Mn N A:Asp38 3.99 Mn C A:Asp38 4.27 Mn CA A:Asp38 4.08 Mn N A:Glu39 3.54 Mn CB A:Glu39 4.02 Mn CA A:Glu39 4.37 Mn MN A:Mn1420 2.47 Mn O A:Hoh2135 2.54 Mn O A:Hoh2136 3.40 interactive model: Manganese binding site 3 out of 5 in 1up6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1up6. 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: Ile37, A: Asp38, A: Glu39, A: Mn1419, A: Hoh2135, A: Hoh2136, conact list: Atom Atom Distance (A) Mn O A:Ile37 2.19 Mn CB A:Ile37 4.40 Mn C A:Ile37 3.23 Mn CG1 A:Ile37 4.99 Mn CA A:Ile37 4.24 Mn N A:Asp38 4.00 Mn CA A:Asp38 4.08 Mn N A:Glu39 4.79 Mn MN A:Mn1419 2.47 Mn O A:Hoh2135 4.70 Mn O A:Hoh2136 3.13 interactive model: Manganese binding site 4 out of 5 in 1up6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1up6. 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: Asn140, C: Cys162, C: Asn163, C: Val164, C: Asn191, C: His192, C: Nad1416, C: G6p1418, conact list: Atom Atom Distance (A) Mn ND2 C:Asn140 4.46 Mn OD1 C:Asn140 4.68 Mn CB C:Cys162 3.52 Mn SG C:Cys162 2.44 Mn C C:Cys162 4.38 Mn CA C:Cys162 3.89 Mn N C:Asn163 3.87 Mn ND2 C:Asn163 3.45 Mn CG C:Asn163 4.60 Mn CA C:Asn163 5.00 Mn N C:Val164 4.98 Mn CG1 C:Val164 4.44 Mn ND2 C:Asn191 4.19 Mn OD1 C:Asn191 4.77 Mn CG C:Asn191 4.93 Mn NE2 C:His192 2.55 Mn ND1 C:His192 4.20 Mn CD2 C:His192 3.64 Mn CE1 C:His192 3.06 Mn CG C:His192 4.51 Mn N7N C:Nad1416 2.98 Mn O7N C:Nad1416 2.39 Mn C7N C:Nad1416 2.82 Mn C2N C:Nad1416 4.87 Mn C3N C:Nad1416 4.02 Mn C4N C:Nad1416 4.69 Mn C1 C:G6p1418 4.38 Mn O1 C:G6p1418 4.87 Mn O3 C:G6p1418 2.48 Mn C2 C:G6p1418 3.03 Mn O2 C:G6p1418 2.12 Mn C4 C:G6p1418 4.60 Mn C3 C:G6p1418 3.19 interactive model: Manganese binding site 5 out of 5 in 1up6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 1up6. 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: G: Asn140, G: Cys162, G: Asn163, G: Val164, G: Asn191, G: His192, G: Nad1416, conact list: Atom Atom Distance (A) Mn ND2 G:Asn140 4.32 Mn OD1 G:Asn140 4.25 Mn CG G:Asn140 4.75 Mn CB G:Cys162 3.73 Mn SG G:Cys162 2.44 Mn C G:Cys162 4.52 Mn CA G:Cys162 3.98 Mn N G:Asn163 3.99 Mn ND2 G:Asn163 3.27 Mn CG G:Asn163 4.53 Mn CG1 G:Val164 4.47 Mn ND2 G:Asn191 4.17 Mn OD1 G:Asn191 4.94 Mn NE2 G:His192 2.45 Mn ND1 G:His192 4.29 Mn CD2 G:His192 3.53 Mn CE1 G:His192 3.14 Mn CG G:His192 4.51 Mn N7N G:Nad1416 2.98 Mn O7N G:Nad1416 2.37 Mn C7N G:Nad1416 2.86 Mn C2N G:Nad1416 4.87 Mn C3N G:Nad1416 4.10 Mn C4N G:Nad1416 4.90 interactive model: