Manganese in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex With D-Psicose (pdb 3ito)

The binding sites of Manganese atom in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex With D-Psicose (pdb code 3ito). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3ito structure was solved by H.YOSHIDA, M.YAMAJI, T.ISHII, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.1-1.9 Space group P1211 a (A) 74.762 b (A) 104.732 c (A) 115.035 alpha (°) 90.00 beta (°) 108.24 gamma (°) 90.00 Rfactor (%) 17.6 Rfree (%) 21.1 Manganese Binding Sites: Manganese binding site 1 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3ito. 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: Asp254, A: His257, A: His281, A: Asn327, A: Mn502, A: Psv601, A: Hoh530, conact list: Atom Atom Distance (A) Mn OE1 A:Glu219 3.31 Mn OE2 A:Glu219 2.12 Mn CD A:Glu219 3.06 Mn CG A:Glu219 4.46 Mn CB A:Asp254 3.70 Mn OD2 A:Asp254 4.35 Mn OD1 A:Asp254 2.21 Mn CG A:Asp254 3.26 Mn CA A:Asp254 4.99 Mn NE2 A:His257 3.97 Mn ND1 A:His257 4.59 Mn CE1 A:His257 3.65 Mn NE2 A:His281 4.18 Mn CB A:His281 3.74 Mn ND1 A:His281 2.17 Mn CD2 A:His281 4.35 Mn CE1 A:His281 2.99 Mn CG A:His281 3.30 Mn CB A:Asn327 4.07 Mn ND2 A:Asn327 2.57 Mn OD1 A:Asn327 4.41 Mn CG A:Asn327 3.53 Mn MN A:Mn502 3.93 Mn O5 A:Psv601 3.90 Mn C5 A:Psv601 4.51 Mn O2 A:Psv601 2.09 Mn C4 A:Psv601 4.58 Mn C1 A:Psv601 4.41 Mn O1 A:Psv601 4.94 Mn C3 A:Psv601 3.42 Mn O3 A:Psv601 2.54 Mn O4 A:Psv601 4.98 Mn C2 A:Psv601 3.22 Mn O A:Hoh530 3.99 interactive model: Manganese binding site 2 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3ito. 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: Asn327, B: Arg65, A: Mn501, A: Psv601, A: Hoh487, A: Hoh530, conact list: Atom Atom Distance (A) Mn OE2 A:Glu219 4.75 Mn CE A:Lys221 4.24 Mn CD A:Lys221 4.57 Mn NZ A:Lys221 4.12 Mn OD2 A:Asp254 4.35 Mn OD1 A:Asp254 3.67 Mn CG A:Asp254 4.16 Mn NE2 A:His257 2.09 Mn ND1 A:His257 4.14 Mn CD2 A:His257 3.16 Mn CE1 A:His257 2.99 Mn CG A:His257 4.26 Mn CB A:Asp289 4.41 Mn OD2 A:Asp289 2.28 Mn OD1 A:Asp289 3.03 Mn CG A:Asp289 2.98 Mn OD2 A:Asp291 4.31 Mn OD1 A:Asp291 3.87 Mn CG A:Asp291 4.53 Mn ND2 A:Asn327 3.84 Mn NH2 B:Arg65 4.76 Mn MN A:Mn501 3.93 Mn O5 A:Psv601 3.43 Mn C5 A:Psv601 4.86 Mn O2 A:Psv601 2.43 Mn C1 A:Psv601 3.09 Mn O1 A:Psv601 2.29 Mn C3 A:Psv601 4.58 Mn O3 A:Psv601 4.98 Mn C2 A:Psv601 3.12 Mn O A:Hoh487 2.36 Mn O A:Hoh530 2.04 interactive model: Manganese binding site 3 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3ito. 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: Asp254, B: His257, B: His281, B: Asn327, B: Mn504, B: Psv602, B: Hoh1435, conact list: Atom Atom Distance (A) Mn OE1 B:Glu219 3.16 Mn OE2 B:Glu219 2.23 Mn CD B:Glu219 3.00 Mn CG B:Glu219 4.38 Mn CB B:Asp254 3.78 Mn OD2 B:Asp254 2.30 Mn OD1 B:Asp254 4.46 Mn CG B:Asp254 3.36 Mn NE2 B:His257 4.13 Mn ND1 B:His257 4.59 Mn CE1 B:His257 3.70 Mn CB B:His281 4.00 Mn ND1 B:His281 2.97 Mn CE1 B:His281 3.90 Mn CG B:His281 3.88 Mn CB B:Asn327 4.08 Mn ND2 B:Asn327 2.50 Mn OD1 B:Asn327 4.61 Mn CG B:Asn327 3.62 Mn MN B:Mn504 4.07 Mn O5 B:Psv602 4.13 Mn C5 B:Psv602 4.73 Mn O2 B:Psv602 2.31 Mn C4 B:Psv602 4.63 Mn C1 B:Psv602 4.55 Mn C3 B:Psv602 3.46 Mn O3 B:Psv602 2.49 Mn O4 B:Psv602 4.93 Mn C2 B:Psv602 3.39 Mn O B:Hoh1435 4.40 interactive model: Manganese binding site 4 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3ito. 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: Asn327, B: Mn503, B: Psv602, B: Hoh684, B: Hoh1435, conact list: Atom Atom Distance (A) Mn NH2 A:Arg65 4.94 Mn CZ A:Phe66 4.99 Mn OE2 B:Glu219 4.58 Mn CE B:Lys221 4.23 Mn CD B:Lys221 4.61 Mn NZ B:Lys221 3.98 Mn OD2 B:Asp254 3.74 Mn OD1 B:Asp254 4.43 Mn CG B:Asp254 4.24 Mn NE2 B:His257 2.03 Mn ND1 B:His257 4.03 Mn CD2 B:His257 3.16 Mn CE1 B:His257 2.85 Mn CG B:His257 4.21 Mn CB B:Asp289 4.61 Mn OD2 B:Asp289 3.23 Mn OD1 B:Asp289 2.41 Mn CG B:Asp289 3.17 Mn OD2 B:Asp291 4.27 Mn OD1 B:Asp291 3.83 Mn CG B:Asp291 4.49 Mn ND2 B:Asn327 3.98 Mn MN B:Mn503 4.07 Mn O5 B:Psv602 3.50 Mn C5 B:Psv602 4.92 Mn O2 B:Psv602 2.32 Mn C1 B:Psv602 3.01 Mn O1 B:Psv602 2.18 Mn C3 B:Psv602 4.49 Mn O3 B:Psv602 4.87 Mn C2 B:Psv602 3.07 Mn O B:Hoh684 2.39 Mn O B:Hoh1435 1.97 interactive model: Manganese binding site 5 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3ito. 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: Asp254, C: His257, C: His281, C: Asn327, C: Mn506, C: Psv603, C: Hoh1436, conact list: Atom Atom Distance (A) Mn OE1 C:Glu219 3.22 Mn OE2 C:Glu219 2.17 Mn CD C:Glu219 3.01 Mn CG C:Glu219 4.37 Mn CB C:Asp254 3.77 Mn OD2 C:Asp254 2.30 Mn OD1 C:Asp254 4.43 Mn CG C:Asp254 3.34 Mn NE2 C:His257 4.04 Mn ND1 C:His257 4.52 Mn CE1 C:His257 3.61 Mn NE2 C:His281 4.48 Mn CB C:His281 3.77 Mn ND1 C:His281 2.45 Mn CD2 C:His281 4.57 Mn CE1 C:His281 3.33 Mn CG C:His281 3.47 Mn CB C:Asn327 4.12 Mn ND2 C:Asn327 2.46 Mn OD1 C:Asn327 4.59 Mn CG C:Asn327 3.61 Mn MN C:Mn506 3.98 Mn O5 C:Psv603 4.06 Mn C5 C:Psv603 4.76 Mn O2 C:Psv603 2.16 Mn C4 C:Psv603 4.68 Mn C1 C:Psv603 4.43 Mn O1 C:Psv603 4.83 Mn C3 C:Psv603 3.44 Mn O3 C:Psv603 2.56 Mn C2 C:Psv603 3.29 Mn O C:Hoh1436 4.08 interactive model: Manganese binding site 6 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3ito. 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: Asn327, D: Arg65, C: Mn505, C: Psv603, C: Hoh1421, C: Hoh1436, conact list: Atom Atom Distance (A) Mn OE2 C:Glu219 4.56 Mn CE C:Lys221 4.30 Mn CD C:Lys221 4.61 Mn NZ C:Lys221 4.07 Mn OD2 C:Asp254 3.67 Mn OD1 C:Asp254 4.30 Mn CG C:Asp254 4.14 Mn NE2 C:His257 1.98 Mn ND1 C:His257 4.00 Mn CD2 C:His257 3.11 Mn CE1 C:His257 2.82 Mn CG C:His257 4.16 Mn CB C:Asp289 4.53 Mn OD2 C:Asp289 2.52 Mn OD1 C:Asp289 3.03 Mn CG C:Asp289 3.10 Mn OD2 C:Asp291 4.39 Mn OD1 C:Asp291 3.78 Mn CG C:Asp291 4.52 Mn ND2 C:Asn327 4.10 Mn NH1 D:Arg65 4.95 Mn MN C:Mn505 3.98 Mn O5 C:Psv603 3.64 Mn O2 C:Psv603 2.47 Mn C1 C:Psv603 3.16 Mn O1 C:Psv603 2.20 Mn C3 C:Psv603 4.65 Mn C2 C:Psv603 3.23 Mn O C:Hoh1421 2.43 Mn O C:Hoh1436 1.99 interactive model: Manganese binding site 7 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3ito. 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: Asn327, D: Mn508, D: Psv604, D: Hoh457, conact list: Atom Atom Distance (A) Mn OE1 D:Glu219 3.32 Mn OE2 D:Glu219 2.09 Mn CD D:Glu219 3.05 Mn CG D:Glu219 4.43 Mn CD2 D:Leu252 4.88 Mn CB D:Asp254 3.69 Mn OD2 D:Asp254 2.16 Mn OD1 D:Asp254 4.32 Mn CG D:Asp254 3.23 Mn CA D:Asp254 4.96 Mn NE2 D:His257 3.99 Mn ND1 D:His257 4.60 Mn CE1 D:His257 3.69 Mn NE2 D:His281 4.18 Mn CB D:His281 3.70 Mn ND1 D:His281 2.17 Mn CD2 D:His281 4.33 Mn CE1 D:His281 3.01 Mn CG D:His281 3.28 Mn CB D:Asn327 4.12 Mn ND2 D:Asn327 2.58 Mn OD1 D:Asn327 4.39 Mn CG D:Asn327 3.54 Mn MN D:Mn508 3.81 Mn O5 D:Psv604 3.81 Mn C5 D:Psv604 4.42 Mn O2 D:Psv604 2.04 Mn C4 D:Psv604 4.44 Mn C1 D:Psv604 4.35 Mn O1 D:Psv604 4.81 Mn C3 D:Psv604 3.32 Mn O3 D:Psv604 2.42 Mn O4 D:Psv604 4.79 Mn C2 D:Psv604 3.14 Mn O D:Hoh457 3.91 interactive model: Manganese binding site 8 out of 8 in 3ito Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3ito. 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, D: Glu219, D: Lys221, D: Asp254, D: His257, D: Asp289, D: Asp291, D: Asn327, D: Mn507, D: Psv604, D: Hoh457, D: Hoh536, conact list: Atom Atom Distance (A) Mn NH2 C:Arg65 4.83 Mn OE2 D:Glu219 4.65 Mn CE D:Lys221 4.29 Mn CD D:Lys221 4.68 Mn NZ D:Lys221 4.24 Mn OD2 D:Asp254 3.55 Mn OD1 D:Asp254 4.34 Mn CG D:Asp254 4.10 Mn NE2 D:His257 2.11 Mn ND1 D:His257 4.17 Mn CD2 D:His257 3.17 Mn CE1 D:His257 3.02 Mn CG D:His257 4.27 Mn CB D:Asp289 4.47 Mn OD2 D:Asp289 2.23 Mn OD1 D:Asp289 3.17 Mn CG D:Asp289 3.05 Mn OD2 D:Asp291 4.31 Mn OD1 D:Asp291 3.90 Mn CG D:Asp291 4.54 Mn ND2 D:Asn327 3.72 Mn CG D:Asn327 5.00 Mn MN D:Mn507 3.81 Mn O5 D:Psv604 3.46 Mn C5 D:Psv604 4.87 Mn O2 D:Psv604 2.35 Mn C1 D:Psv604 3.12 Mn O1 D:Psv604 2.27 Mn C3 D:Psv604 4.54 Mn O3 D:Psv604 4.89 Mn C2 D:Psv604 3.11 Mn O D:Hoh457 2.04 Mn O D:Hoh536 2.40 interactive model: