Manganese in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329L in Complex With L-Rhamnose (pdb 3m0v)

The binding sites of Manganese atom in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329L in Complex With L-Rhamnose (pdb code 3m0v). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3m0v 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) 47.7-1.8 Space group P1211 a (A) 74.640 b (A) 104.489 c (A) 111.622 alpha (°) 90.00 beta (°) 106.15 gamma (°) 90.00 Rfactor (%) 18.3 Rfree (%) 21.6 Manganese Binding Sites: Manganese binding site 1 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3m0v. 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: Rns2001, A: Hoh492, A: Hoh570, conact list: Atom Atom Distance (A) Mn OE1 A:Glu219 3.31 Mn OE2 A:Glu219 2.17 Mn CD A:Glu219 3.09 Mn CG A:Glu219 4.50 Mn CD2 A:Leu252 4.99 Mn CB A:Asp254 3.80 Mn OD2 A:Asp254 2.20 Mn OD1 A:Asp254 4.38 Mn CG A:Asp254 3.30 Mn NE2 A:His257 4.07 Mn ND1 A:His257 4.78 Mn CE1 A:His257 3.81 Mn NE2 A:His281 4.17 Mn CB A:His281 3.67 Mn ND1 A:His281 2.15 Mn CD2 A:His281 4.31 Mn CE1 A:His281 3.00 Mn CG A:His281 3.25 Mn CB A:Asp327 3.72 Mn OD2 A:Asp327 2.13 Mn OD1 A:Asp327 4.31 Mn CG A:Asp327 3.22 Mn MN A:Mn502 4.02 Mn C5 A:Rns2001 4.82 Mn O2 A:Rns2001 2.24 Mn C4 A:Rns2001 4.12 Mn C1 A:Rns2001 4.44 Mn O1 A:Rns2001 4.92 Mn C3 A:Rns2001 3.26 Mn O3 A:Rns2001 2.44 Mn O4 A:Rns2001 3.82 Mn C2 A:Rns2001 3.02 Mn O A:Hoh492 4.77 Mn O A:Hoh570 4.05 interactive model: Manganese binding site 2 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3m0v. 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: Rns2001, A: Hoh492, A: Hoh570, conact list: Atom Atom Distance (A) Mn OE2 A:Glu219 4.71 Mn CE A:Lys221 3.87 Mn CD A:Lys221 4.49 Mn NZ A:Lys221 3.83 Mn OD2 A:Asp254 3.77 Mn OD1 A:Asp254 4.60 Mn CG A:Asp254 4.32 Mn NE2 A:His257 2.10 Mn ND1 A:His257 4.12 Mn CD2 A:His257 3.19 Mn CE1 A:His257 2.95 Mn CG A:His257 4.26 Mn CB A:Asp289 4.36 Mn OD2 A:Asp289 2.15 Mn OD1 A:Asp289 3.26 Mn CG A:Asp289 3.01 Mn OD2 A:Asp291 4.16 Mn OD1 A:Asp291 4.16 Mn CG A:Asp291 4.59 Mn OD2 A:Asp327 4.23 Mn NH2 B:Arg65 4.65 Mn CZ B:Phe66 4.92 Mn MN A:Mn501 4.02 Mn O2 A:Rns2001 2.17 Mn C4 A:Rns2001 4.63 Mn C1 A:Rns2001 2.81 Mn O1 A:Rns2001 2.13 Mn C3 A:Rns2001 4.28 Mn O3 A:Rns2001 4.88 Mn O4 A:Rns2001 4.00 Mn C2 A:Rns2001 2.92 Mn O A:Hoh492 2.10 Mn O A:Hoh570 1.91 interactive model: Manganese binding site 3 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3m0v. 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: Asp327, B: Mn504, B: Rns2002, B: Hoh477, conact list: Atom Atom Distance (A) Mn OE1 B:Glu219 3.35 Mn OE2 B:Glu219 2.12 Mn CD B:Glu219 3.08 Mn CG B:Glu219 4.47 Mn CB B:Asp254 3.74 Mn OD2 B:Asp254 2.17 Mn OD1 B:Asp254 4.34 Mn CG B:Asp254 3.26 Mn CA B:Asp254 5.00 Mn NE2 B:His257 4.14 Mn ND1 B:His257 4.82 Mn CE1 B:His257 3.90 Mn NE2 B:His281 3.97 Mn CB B:His281 3.63 Mn ND1 B:His281 1.98 Mn CD2 B:His281 4.15 Mn CE1 B:His281 2.78 Mn CG B:His281 3.12 Mn CB B:Asp327 3.78 Mn OD2 B:Asp327 2.09 Mn OD1 B:Asp327 4.27 Mn CG B:Asp327 3.22 Mn MN B:Mn504 4.00 Mn C5 B:Rns2002 4.88 Mn O2 B:Rns2002 2.31 Mn C4 B:Rns2002 4.24 Mn C1 B:Rns2002 4.57 Mn C3 B:Rns2002 3.37 Mn O3 B:Rns2002 2.50 Mn O4 B:Rns2002 3.98 Mn C2 B:Rns2002 3.18 Mn O B:Hoh477 3.96 interactive model: Manganese binding site 4 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3m0v. 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: Rns2002, B: Hoh477, B: Hoh527, conact list: Atom Atom Distance (A) Mn NH2 A:Arg65 4.74 Mn CZ A:Phe66 4.95 Mn OE2 B:Glu219 4.66 Mn CE B:Lys221 3.94 Mn CD B:Lys221 4.39 Mn NZ B:Lys221 3.97 Mn OD2 B:Asp254 3.77 Mn OD1 B:Asp254 4.47 Mn CG B:Asp254 4.25 Mn NE2 B:His257 2.03 Mn ND1 B:His257 4.04 Mn CD2 B:His257 3.16 Mn CE1 B:His257 2.86 Mn CG B:His257 4.21 Mn CB B:Asp289 4.41 Mn OD2 B:Asp289 2.17 Mn OD1 B:Asp289 3.24 Mn CG B:Asp289 3.03 Mn OD2 B:Asp291 4.18 Mn OD1 B:Asp291 4.18 Mn CG B:Asp291 4.61 Mn OD2 B:Asp327 4.23 Mn MN B:Mn503 4.00 Mn O2 B:Rns2002 2.13 Mn C4 B:Rns2002 4.65 Mn C1 B:Rns2002 2.87 Mn O1 B:Rns2002 2.23 Mn C3 B:Rns2002 4.28 Mn O3 B:Rns2002 4.82 Mn O4 B:Rns2002 3.96 Mn C2 B:Rns2002 2.95 Mn O B:Hoh477 2.04 Mn O B:Hoh527 2.25 interactive model: Manganese binding site 5 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3m0v. 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: Asp327, C: Mn506, C: Rns2003, C: Hoh472, C: Hoh526, conact list: Atom Atom Distance (A) Mn OE1 C:Glu219 3.35 Mn OE2 C:Glu219 2.17 Mn CD C:Glu219 3.11 Mn CG C:Glu219 4.50 Mn CB C:Asp254 3.81 Mn OD2 C:Asp254 2.20 Mn OD1 C:Asp254 4.38 Mn CG C:Asp254 3.31 Mn NE2 C:His257 4.12 Mn ND1 C:His257 4.87 Mn CE1 C:His257 3.92 Mn NE2 C:His281 4.11 Mn CB C:His281 3.67 Mn ND1 C:His281 2.11 Mn CD2 C:His281 4.27 Mn CE1 C:His281 2.94 Mn CG C:His281 3.22 Mn CB C:Asp327 3.75 Mn OD2 C:Asp327 1.96 Mn OD1 C:Asp327 4.14 Mn CG C:Asp327 3.12 Mn MN C:Mn506 4.02 Mn C5 C:Rns2003 4.78 Mn O2 C:Rns2003 2.24 Mn C4 C:Rns2003 4.10 Mn C1 C:Rns2003 4.44 Mn O1 C:Rns2003 4.96 Mn C3 C:Rns2003 3.20 Mn O3 C:Rns2003 2.32 Mn O4 C:Rns2003 3.85 Mn C2 C:Rns2003 3.03 Mn O C:Hoh472 4.84 Mn O C:Hoh526 3.79 interactive model: Manganese binding site 6 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3m0v. 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: Rns2003, C: Hoh472, C: Hoh526, conact list: Atom Atom Distance (A) Mn OE2 C:Glu219 4.73 Mn CE C:Lys221 3.97 Mn CD C:Lys221 4.39 Mn NZ C:Lys221 3.82 Mn OD2 C:Asp254 3.78 Mn OD1 C:Asp254 4.64 Mn CG C:Asp254 4.35 Mn NE2 C:His257 2.12 Mn ND1 C:His257 4.16 Mn CD2 C:His257 3.19 Mn CE1 C:His257 3.00 Mn CG C:His257 4.28 Mn CB C:Asp289 4.36 Mn OD2 C:Asp289 2.12 Mn OD1 C:Asp289 3.18 Mn CG C:Asp289 2.98 Mn OD2 C:Asp291 4.22 Mn OD1 C:Asp291 4.05 Mn CG C:Asp291 4.57 Mn OD2 C:Asp327 4.43 Mn NH1 D:Arg65 4.57 Mn CZ D:Phe66 4.92 Mn MN C:Mn505 4.02 Mn O2 C:Rns2003 2.09 Mn C4 C:Rns2003 4.55 Mn C1 C:Rns2003 2.73 Mn O1 C:Rns2003 2.10 Mn C3 C:Rns2003 4.19 Mn O3 C:Rns2003 4.76 Mn O4 C:Rns2003 3.93 Mn C2 C:Rns2003 2.84 Mn O C:Hoh472 2.23 Mn O C:Hoh526 2.10 interactive model: Manganese binding site 7 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3m0v. 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: Rns2004, D: Hoh442, conact list: Atom Atom Distance (A) Mn OE1 D:Glu219 3.38 Mn OE2 D:Glu219 2.12 Mn CD D:Glu219 3.08 Mn CG D:Glu219 4.46 Mn CD2 D:Leu252 5.00 Mn CB D:Asp254 3.79 Mn OD2 D:Asp254 2.20 Mn OD1 D:Asp254 4.37 Mn CG D:Asp254 3.30 Mn NE2 D:His257 4.13 Mn ND1 D:His257 4.93 Mn CE1 D:His257 3.98 Mn NE2 D:His281 4.24 Mn CB D:His281 3.68 Mn ND1 D:His281 2.20 Mn CD2 D:His281 4.37 Mn CE1 D:His281 3.07 Mn CG D:His281 3.29 Mn CB D:Asp327 3.74 Mn OD2 D:Asp327 2.03 Mn OD1 D:Asp327 4.23 Mn CG D:Asp327 3.17 Mn MN D:Mn508 4.04 Mn C5 D:Rns2004 4.67 Mn O2 D:Rns2004 2.22 Mn C4 D:Rns2004 4.07 Mn C1 D:Rns2004 4.48 Mn C3 D:Rns2004 3.24 Mn O3 D:Rns2004 2.37 Mn O4 D:Rns2004 3.82 Mn C2 D:Rns2004 3.09 Mn O D:Hoh442 3.85 interactive model: Manganese binding site 8 out of 8 in 3m0v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3m0v. 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: Rns2004, D: Hoh442, D: Hoh481, conact list: Atom Atom Distance (A) Mn NH2 C:Arg65 4.65 Mn CZ C:Phe66 4.98 Mn OE2 D:Glu219 4.67 Mn CE D:Lys221 4.07 Mn CD D:Lys221 4.46 Mn NZ D:Lys221 3.94 Mn OD2 D:Asp254 3.78 Mn OD1 D:Asp254 4.54 Mn CG D:Asp254 4.31 Mn NE2 D:His257 2.17 Mn ND1 D:His257 4.22 Mn CD2 D:His257 3.22 Mn CE1 D:His257 3.07 Mn CG D:His257 4.33 Mn CB D:Asp289 4.36 Mn OD2 D:Asp289 2.10 Mn OD1 D:Asp289 3.16 Mn CG D:Asp289 2.96 Mn OD2 D:Asp291 4.11 Mn OD1 D:Asp291 4.05 Mn CG D:Asp291 4.51 Mn OD2 D:Asp327 4.25 Mn MN D:Mn507 4.04 Mn O2 D:Rns2004 2.14 Mn C4 D:Rns2004 4.59 Mn C1 D:Rns2004 2.74 Mn O1 D:Rns2004 2.12 Mn C3 D:Rns2004 4.23 Mn O3 D:Rns2004 4.80 Mn O4 D:Rns2004 3.88 Mn C2 D:Rns2004 2.87 Mn O D:Hoh442 2.12 Mn O D:Hoh481 2.26 interactive model: