Manganese in the structure of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex With (4R)-2-Methylpentane-2,4-Diol (pdb 3a9r)

The binding sites of Manganese atom in the structure of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex With (4R)-2-Methylpentane-2,4-Diol (pdb code 3a9r). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3a9r structure was solved by K.TAKEDA, H.YOSHIDA, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.8-1.8 Space group P21212 a (A) 144.751 b (A) 127.447 c (A) 110.885 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.8 Rfree (%) 20 Manganese Binding Sites: Manganese binding site 1 out of 6 in 3a9r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3a9r. 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: Glu342, A: Phe364, A: Asp366, A: Asn397, A: Ser398, A: Asn531, A: His532, A: Mrd601, conact list: Atom Atom Distance (A) Mn OE1 A:Glu342 2.90 Mn OE2 A:Glu342 3.71 Mn CD A:Glu342 3.61 Mn CG A:Glu342 4.92 Mn CE1 A:Phe364 4.64 Mn CB A:Asp366 4.48 Mn OD2 A:Asp366 2.44 Mn OD1 A:Asp366 2.84 Mn CG A:Asp366 2.99 Mn OD1 A:Asn397 3.60 Mn CG A:Asn397 4.82 Mn N A:Ser398 4.31 Mn CB A:Ser398 4.07 Mn OG A:Ser398 3.50 Mn CA A:Ser398 4.87 Mn OD1 A:Asn531 4.27 Mn NE2 A:His532 2.42 Mn ND1 A:His532 4.56 Mn CD2 A:His532 3.31 Mn CE1 A:His532 3.46 Mn CG A:His532 4.51 Mn C5 A:Mrd601 4.59 Mn C4 A:Mrd601 4.14 Mn C3 A:Mrd601 4.56 Mn O4 A:Mrd601 2.88 interactive model: Manganese binding site 2 out of 6 in 3a9r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3a9r. 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: Asp453, A: Phe454, A: Leu455, A: His492, A: Asp496, A: Pro501, A: Hoh802, A: Hoh803, A: Hoh804, A: Hoh805, A: Hoh806, A: Hoh903, A: Hoh907, A: Hoh933, A: Hoh1033, conact list: Atom Atom Distance (A) Mn CB A:Asp453 4.80 Mn OD2 A:Asp453 3.56 Mn C A:Asp453 4.76 Mn OD1 A:Asp453 2.46 Mn CG A:Asp453 3.38 Mn O A:Phe454 4.34 Mn N A:Phe454 4.60 Mn C A:Phe454 4.48 Mn CA A:Phe454 4.71 Mn N A:Leu455 4.95 Mn CB A:Leu455 4.92 Mn NE2 A:His492 4.38 Mn OD2 A:Asp496 4.03 Mn CG A:Asp496 4.94 Mn O A:Pro501 4.38 Mn O A:Hoh802 1.94 Mn O A:Hoh803 2.29 Mn O A:Hoh804 1.96 Mn O A:Hoh805 2.14 Mn O A:Hoh806 1.85 Mn O A:Hoh903 4.40 Mn O A:Hoh907 4.09 Mn O A:Hoh933 4.45 Mn O A:Hoh1033 4.24 interactive model: Manganese binding site 3 out of 6 in 3a9r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3a9r. 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: Glu342, B: Phe364, B: Asp366, B: Asn397, B: Ser398, B: Asn531, B: His532, B: Mrd601, conact list: Atom Atom Distance (A) Mn OE1 B:Glu342 2.88 Mn OE2 B:Glu342 3.72 Mn CD B:Glu342 3.59 Mn CG B:Glu342 4.86 Mn CE1 B:Phe364 4.80 Mn CB B:Asp366 4.43 Mn OD2 B:Asp366 2.44 Mn OD1 B:Asp366 2.81 Mn CG B:Asp366 2.95 Mn OD1 B:Asn397 3.69 Mn CG B:Asn397 4.91 Mn N B:Ser398 4.37 Mn CB B:Ser398 4.12 Mn OG B:Ser398 3.65 Mn CA B:Ser398 4.92 Mn OD1 B:Asn531 4.14 Mn NE2 B:His532 2.30 Mn ND1 B:His532 4.43 Mn CD2 B:His532 3.25 Mn CE1 B:His532 3.31 Mn CG B:His532 4.42 Mn C5 B:Mrd601 4.40 Mn C4 B:Mrd601 4.08 Mn C3 B:Mrd601 4.57 Mn O4 B:Mrd601 2.88 interactive model: Manganese binding site 4 out of 6 in 3a9r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3a9r. 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: Asp453, B: Phe454, B: Leu455, B: His492, B: Asp496, B: Pro501, B: Hoh734, B: Hoh802, B: Hoh803, B: Hoh804, B: Hoh805, B: Hoh806, B: Hoh912, B: Hoh1019, B: Hoh1091, conact list: Atom Atom Distance (A) Mn CB B:Asp453 4.95 Mn OD2 B:Asp453 3.67 Mn C B:Asp453 4.83 Mn OD1 B:Asp453 2.63 Mn CG B:Asp453 3.53 Mn O B:Phe454 4.35 Mn N B:Phe454 4.63 Mn C B:Phe454 4.45 Mn CA B:Phe454 4.71 Mn N B:Leu455 4.88 Mn CB B:Leu455 4.84 Mn NE2 B:His492 4.24 Mn OD2 B:Asp496 3.97 Mn CG B:Asp496 4.88 Mn O B:Pro501 4.44 Mn O B:Hoh734 4.33 Mn O B:Hoh802 1.88 Mn O B:Hoh803 2.77 Mn O B:Hoh804 1.90 Mn O B:Hoh805 2.10 Mn O B:Hoh806 1.85 Mn O B:Hoh912 4.07 Mn O B:Hoh1019 4.32 Mn O B:Hoh1091 4.49 interactive model: Manganese binding site 5 out of 6 in 3a9r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3a9r. 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: Thr341, C: Glu342, C: Phe364, C: Asp366, C: Asn397, C: Ser398, C: Asn531, C: His532, C: Mrd601, conact list: Atom Atom Distance (A) Mn CG2 C:Thr341 4.98 Mn OE1 C:Glu342 2.73 Mn OE2 C:Glu342 3.71 Mn CD C:Glu342 3.48 Mn CG C:Glu342 4.69 Mn CE1 C:Phe364 4.49 Mn CB C:Asp366 4.52 Mn OD2 C:Asp366 2.31 Mn OD1 C:Asp366 3.13 Mn CG C:Asp366 3.07 Mn OD1 C:Asn397 3.70 Mn CG C:Asn397 4.93 Mn N C:Ser398 4.50 Mn CB C:Ser398 4.19 Mn OG C:Ser398 3.72 Mn OD1 C:Asn531 4.34 Mn NE2 C:His532 2.18 Mn ND1 C:His532 4.25 Mn CD2 C:His532 3.17 Mn CE1 C:His532 3.12 Mn CG C:His532 4.29 Mn C5 C:Mrd601 4.63 Mn C4 C:Mrd601 4.16 Mn C3 C:Mrd601 4.71 Mn O4 C:Mrd601 2.84 interactive model: Manganese binding site 6 out of 6 in 3a9r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3a9r. 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: Asp453, C: Phe454, C: Leu455, C: His492, C: Asp496, C: Pro501, C: Hoh751, C: Hoh789, C: Hoh802, C: Hoh803, C: Hoh804, C: Hoh805, C: Hoh806, C: Hoh899, C: Hoh1039, conact list: Atom Atom Distance (A) Mn CB C:Asp453 4.81 Mn OD2 C:Asp453 3.52 Mn C C:Asp453 4.76 Mn OD1 C:Asp453 2.49 Mn CG C:Asp453 3.38 Mn O C:Phe454 4.45 Mn N C:Phe454 4.63 Mn C C:Phe454 4.52 Mn CA C:Phe454 4.73 Mn N C:Leu455 4.94 Mn CB C:Leu455 4.91 Mn NE2 C:His492 4.43 Mn OD2 C:Asp496 4.25 Mn O C:Pro501 4.50 Mn O C:Hoh751 4.54 Mn O C:Hoh789 4.27 Mn O C:Hoh802 1.88 Mn O C:Hoh803 1.99 Mn O C:Hoh804 1.98 Mn O C:Hoh805 2.08 Mn O C:Hoh806 2.06 Mn O C:Hoh899 4.32 Mn O C:Hoh1039 4.14 interactive model: