Manganese in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex With D-Allose (pdb 3m0m)

The binding sites of Manganese atom in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex With D-Allose (pdb code 3m0m). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3m0m structure was solved by H.YOSHIDA, K.TAKEDA, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.1-1.4 Space group P1211 a (A) 74.625 b (A) 104.260 c (A) 111.447 alpha (°) 90.00 beta (°) 106.20 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 19.6 Manganese Binding Sites: Manganese binding site 1 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3m0m. 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: Glu219, A: Leu252, A: Asp254, A: His257, A: His281, A: Asp327, A: Mn502, A: Aos3001, A: Hoh470, A: Hoh1453, conact list: Atom Atom Distance (A) Mn OE1 A:Glu219 3.36 Mn OE2 A:Glu219 2.14 Mn CD A:Glu219 3.10 Mn CG A:Glu219 4.47 Mn CD2 A:Leu252 4.94 Mn CB A:Asp254 3.82 Mn OD2 A:Asp254 2.19 Mn OD1 A:Asp254 4.38 Mn CG A:Asp254 3.31 Mn NE2 A:His257 4.10 Mn ND1 A:His257 4.82 Mn CE1 A:His257 3.90 Mn NE2 A:His281 4.26 Mn CB A:His281 3.69 Mn ND1 A:His281 2.22 Mn CD2 A:His281 4.38 Mn CE1 A:His281 3.08 Mn CG A:His281 3.30 Mn CB A:Asp327 3.75 Mn OD2 A:Asp327 2.05 Mn OD1 A:Asp327 4.24 Mn CG A:Asp327 3.18 Mn MN A:Mn502 4.04 Mn O5 A:Aos3001 3.87 Mn C5 A:Aos3001 4.25 Mn O2 A:Aos3001 2.22 Mn C4 A:Aos3001 4.35 Mn C1 A:Aos3001 4.45 Mn O1 A:Aos3001 4.95 Mn C3 A:Aos3001 3.25 Mn O3 A:Aos3001 2.38 Mn C2 A:Aos3001 3.04 Mn O A:Hoh470 4.77 Mn O A:Hoh1453 3.99 interactive model: Manganese binding site 2 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3m0m. 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: Glu219, A: Lys221, A: Asp254, A: His257, A: Asp289, A: Asp291, A: Asp327, B: Arg65, B: Phe66, A: Mn501, A: Aos3001, A: Hoh470, A: Hoh1453, conact list: Atom Atom Distance (A) Mn OE2 A:Glu219 4.74 Mn CE A:Lys221 3.97 Mn CD A:Lys221 4.49 Mn NZ A:Lys221 3.80 Mn OD2 A:Asp254 3.80 Mn OD1 A:Asp254 4.65 Mn CG A:Asp254 4.38 Mn NE2 A:His257 2.16 Mn ND1 A:His257 4.20 Mn CD2 A:His257 3.24 Mn CE1 A:His257 3.03 Mn CG A:His257 4.32 Mn CB A:Asp289 4.40 Mn OD2 A:Asp289 2.16 Mn OD1 A:Asp289 3.33 Mn CG A:Asp289 3.05 Mn OD2 A:Asp291 4.08 Mn OD1 A:Asp291 4.14 Mn CG A:Asp291 4.54 Mn OD2 A:Asp327 4.25 Mn NH2 B:Arg65 4.54 Mn CZ B:Phe66 4.86 Mn MN A:Mn501 4.04 Mn O5 A:Aos3001 3.88 Mn O2 A:Aos3001 2.24 Mn C4 A:Aos3001 5.00 Mn C1 A:Aos3001 2.84 Mn O1 A:Aos3001 2.19 Mn C3 A:Aos3001 4.37 Mn O3 A:Aos3001 4.88 Mn C2 A:Aos3001 2.95 Mn O A:Hoh470 2.11 Mn O A:Hoh1453 2.00 interactive model: Manganese binding site 3 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3m0m. 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: Glu219, B: Leu252, B: Asp254, B: His257, B: His281, B: Asp327, B: Mn504, B: Aos3002, B: Hoh461, B: Hoh1454, conact list: Atom Atom Distance (A) Mn OE1 B:Glu219 3.39 Mn OE2 B:Glu219 2.12 Mn CD B:Glu219 3.10 Mn CG B:Glu219 4.47 Mn CD2 B:Leu252 4.93 Mn CB B:Asp254 3.80 Mn OD2 B:Asp254 2.17 Mn OD1 B:Asp254 4.36 Mn CG B:Asp254 3.29 Mn NE2 B:His257 4.15 Mn ND1 B:His257 4.83 Mn CE1 B:His257 3.91 Mn NE2 B:His281 4.18 Mn CB B:His281 3.64 Mn ND1 B:His281 2.15 Mn CD2 B:His281 4.31 Mn CE1 B:His281 3.01 Mn CG B:His281 3.23 Mn CB B:Asp327 3.75 Mn OD2 B:Asp327 2.03 Mn OD1 B:Asp327 4.22 Mn CG B:Asp327 3.17 Mn MN B:Mn504 4.04 Mn O5 B:Aos3002 3.90 Mn C5 B:Aos3002 4.23 Mn O2 B:Aos3002 2.27 Mn C4 B:Aos3002 4.34 Mn C1 B:Aos3002 4.52 Mn C3 B:Aos3002 3.26 Mn O3 B:Aos3002 2.33 Mn C2 B:Aos3002 3.13 Mn O B:Hoh461 3.93 Mn O B:Hoh1454 4.96 interactive model: Manganese binding site 4 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3m0m. 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: Arg65, A: Phe66, B: Glu219, B: Lys221, B: Asp254, B: His257, B: Asp289, B: Asp291, B: Asp327, B: Mn503, B: Aos3002, B: Hoh461, B: Hoh1454, conact list: Atom Atom Distance (A) Mn NH2 A:Arg65 4.56 Mn CZ A:Phe66 4.81 Mn OE2 B:Glu219 4.69 Mn CE B:Lys221 4.02 Mn CD B:Lys221 4.51 Mn NZ B:Lys221 3.93 Mn OD2 B:Asp254 3.82 Mn OD1 B:Asp254 4.64 Mn CG B:Asp254 4.37 Mn NE2 B:His257 2.18 Mn ND1 B:His257 4.21 Mn CD2 B:His257 3.26 Mn CE1 B:His257 3.04 Mn CG B:His257 4.35 Mn CB B:Asp289 4.43 Mn OD2 B:Asp289 2.18 Mn OD1 B:Asp289 3.33 Mn CG B:Asp289 3.08 Mn OD2 B:Asp291 4.08 Mn OD1 B:Asp291 4.17 Mn CG B:Asp291 4.56 Mn OD2 B:Asp327 4.20 Mn MN B:Mn503 4.04 Mn O5 B:Aos3002 3.82 Mn C5 B:Aos3002 4.98 Mn O2 B:Aos3002 2.19 Mn C1 B:Aos3002 2.92 Mn O1 B:Aos3002 2.29 Mn C3 B:Aos3002 4.37 Mn O3 B:Aos3002 4.82 Mn C2 B:Aos3002 2.97 Mn O B:Hoh461 1.99 Mn O B:Hoh1454 2.20 interactive model: Manganese binding site 5 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3m0m. 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: Glu219, C: Leu252, C: Asp254, C: His257, C: His281, C: Asp327, C: Mn506, C: Aos3003, C: Hoh1466, C: Hoh1483, conact list: Atom Atom Distance (A) Mn OE1 C:Glu219 3.41 Mn OE2 C:Glu219 2.21 Mn CD C:Glu219 3.16 Mn CG C:Glu219 4.54 Mn CD2 C:Leu252 4.99 Mn CB C:Asp254 3.83 Mn OD2 C:Asp254 2.16 Mn OD1 C:Asp254 4.35 Mn CG C:Asp254 3.29 Mn NE2 C:His257 4.10 Mn ND1 C:His257 4.83 Mn CE1 C:His257 3.91 Mn NE2 C:His281 4.21 Mn CB C:His281 3.69 Mn ND1 C:His281 2.19 Mn CD2 C:His281 4.35 Mn CE1 C:His281 3.03 Mn CG C:His281 3.28 Mn CB C:Asp327 3.70 Mn OD2 C:Asp327 1.99 Mn OD1 C:Asp327 4.18 Mn CG C:Asp327 3.12 Mn MN C:Mn506 4.02 Mn O5 C:Aos3003 3.86 Mn C5 C:Aos3003 4.22 Mn O2 C:Aos3003 2.20 Mn C4 C:Aos3003 4.34 Mn C1 C:Aos3003 4.47 Mn C3 C:Aos3003 3.26 Mn O3 C:Aos3003 2.36 Mn C2 C:Aos3003 3.08 Mn O C:Hoh1466 4.84 Mn O C:Hoh1483 3.98 interactive model: Manganese binding site 6 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3m0m. 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: Glu219, C: Lys221, C: Asp254, C: His257, C: Asp289, C: Asp291, C: Asp327, D: Arg65, D: Phe66, C: Mn505, C: Aos3003, C: Hoh1466, C: Hoh1483, conact list: Atom Atom Distance (A) Mn OE2 C:Glu219 4.81 Mn CE C:Lys221 4.05 Mn CD C:Lys221 4.45 Mn NZ C:Lys221 3.85 Mn OD2 C:Asp254 3.81 Mn OD1 C:Asp254 4.69 Mn CG C:Asp254 4.40 Mn NE2 C:His257 2.19 Mn ND1 C:His257 4.22 Mn CD2 C:His257 3.28 Mn CE1 C:His257 3.05 Mn CG C:His257 4.36 Mn CB C:Asp289 4.40 Mn OD2 C:Asp289 2.16 Mn OD1 C:Asp289 3.28 Mn CG C:Asp289 3.04 Mn OD2 C:Asp291 4.01 Mn OD1 C:Asp291 4.08 Mn CG C:Asp291 4.48 Mn OD2 C:Asp327 4.24 Mn NH1 D:Arg65 4.52 Mn CZ D:Phe66 4.83 Mn MN C:Mn505 4.02 Mn O5 C:Aos3003 3.82 Mn C5 C:Aos3003 4.97 Mn O2 C:Aos3003 2.20 Mn C4 C:Aos3003 4.96 Mn C1 C:Aos3003 2.83 Mn O1 C:Aos3003 2.23 Mn C3 C:Aos3003 4.34 Mn O3 C:Aos3003 4.82 Mn C2 C:Aos3003 2.93 Mn O C:Hoh1466 2.18 Mn O C:Hoh1483 1.97 interactive model: Manganese binding site 7 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3m0m. 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: Glu219, D: Leu252, D: Asp254, D: His257, D: His281, D: Asp327, D: Mn508, D: Aos3004, D: Hoh443, D: Hoh881, conact list: Atom Atom Distance (A) Mn OE1 D:Glu219 3.38 Mn OE2 D:Glu219 2.08 Mn CD D:Glu219 3.07 Mn CG D:Glu219 4.44 Mn CD2 D:Leu252 4.94 Mn CB D:Asp254 3.77 Mn OD2 D:Asp254 2.17 Mn OD1 D:Asp254 4.36 Mn CG D:Asp254 3.27 Mn NE2 D:His257 4.10 Mn ND1 D:His257 4.84 Mn CE1 D:His257 3.92 Mn NE2 D:His281 4.28 Mn CB D:His281 3.66 Mn ND1 D:His281 2.23 Mn CD2 D:His281 4.38 Mn CE1 D:His281 3.11 Mn CG D:His281 3.29 Mn CB D:Asp327 3.72 Mn OD2 D:Asp327 2.03 Mn OD1 D:Asp327 4.23 Mn CG D:Asp327 3.17 Mn MN D:Mn508 4.05 Mn O5 D:Aos3004 3.96 Mn C5 D:Aos3004 4.28 Mn O2 D:Aos3004 2.27 Mn C4 D:Aos3004 4.35 Mn C1 D:Aos3004 4.50 Mn C3 D:Aos3004 3.25 Mn O3 D:Aos3004 2.34 Mn C2 D:Aos3004 3.10 Mn O D:Hoh443 3.83 Mn O D:Hoh881 4.88 interactive model: Manganese binding site 8 out of 8 in 3m0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3m0m. 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: Arg65, C: Phe66, D: Glu219, D: Lys221, D: Asp254, D: His257, D: Asp289, D: Asp291, D: Asp327, D: Mn507, D: Aos3004, D: Hoh443, D: Hoh881, conact list: Atom Atom Distance (A) Mn NH2 C:Arg65 4.54 Mn CZ C:Phe66 4.83 Mn OE2 D:Glu219 4.73 Mn CE D:Lys221 4.09 Mn CD D:Lys221 4.46 Mn NZ D:Lys221 3.87 Mn OD2 D:Asp254 3.80 Mn OD1 D:Asp254 4.66 Mn CG D:Asp254 4.38 Mn NE2 D:His257 2.16 Mn ND1 D:His257 4.20 Mn CD2 D:His257 3.23 Mn CE1 D:His257 3.03 Mn CG D:His257 4.32 Mn CB D:Asp289 4.35 Mn OD2 D:Asp289 2.09 Mn OD1 D:Asp289 3.26 Mn CG D:Asp289 2.99 Mn OD2 D:Asp291 4.05 Mn OD1 D:Asp291 4.15 Mn CG D:Asp291 4.53 Mn OD2 D:Asp327 4.19 Mn MN D:Mn507 4.05 Mn O5 D:Aos3004 3.89 Mn O2 D:Aos3004 2.15 Mn C4 D:Aos3004 4.98 Mn C1 D:Aos3004 2.79 Mn O1 D:Aos3004 2.20 Mn C3 D:Aos3004 4.31 Mn O3 D:Aos3004 4.81 Mn C2 D:Aos3004 2.88 Mn O D:Hoh443 2.05 Mn O D:Hoh881 2.21 interactive model: