Manganese in the structure of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein (pdb 2jla)

The binding sites of Manganese atom in the structure of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein (pdb code 2jla). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2jla structure was solved by A.DAWSON, P.K.FYFE, W.N.HUNTER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 83.0-2.8 Space group P65 a (A) 95.830 b (A) 95.830 c (A) 463.170 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.9 Rfree (%) 23.3 Manganese Binding Sites: Manganese binding site 1 out of 5 in 2jla Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2jla. 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: Gly441, A: Asp442, A: Leu443, A: Val467, A: Asn469, A: Asn470, A: Gly471, A: Gly472, A: Gln473, A: Tpp1557, A: Hoh2098, conact list: Atom Atom Distance (A) Mn C A:Gly441 4.67 Mn CA A:Gly441 4.62 Mn N A:Asp442 3.82 Mn CB A:Asp442 4.32 Mn OD2 A:Asp442 3.49 Mn OD1 A:Asp442 1.99 Mn CG A:Asp442 3.05 Mn CA A:Asp442 4.58 Mn N A:Leu443 4.57 Mn O A:Val467 4.37 Mn N A:Asn469 4.29 Mn CB A:Asn469 4.55 Mn ND2 A:Asn469 3.71 Mn C A:Asn469 4.73 Mn OD1 A:Asn469 2.16 Mn CG A:Asn469 3.24 Mn CA A:Asn469 4.75 Mn N A:Asn470 4.77 Mn O A:Gly471 2.24 Mn N A:Gly471 4.11 Mn C A:Gly471 3.36 Mn CA A:Gly471 4.30 Mn N A:Gly472 4.21 Mn C A:Gly472 4.81 Mn CA A:Gly472 4.28 Mn N A:Gln473 4.19 Mn CB A:Gln473 4.87 Mn CG A:Gln473 4.62 Mn O3B A:Tpp1557 2.24 Mn PA A:Tpp1557 3.32 Mn O2A A:Tpp1557 4.35 Mn O1B A:Tpp1557 4.41 Mn PB A:Tpp1557 3.20 Mn O2B A:Tpp1557 4.23 Mn O7 A:Tpp1557 4.27 Mn O3A A:Tpp1557 3.39 Mn O1A A:Tpp1557 2.08 Mn O A:Hoh2098 2.24 interactive model: Manganese binding site 2 out of 5 in 2jla Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2jla. 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: Gly441, B: Asp442, B: Leu443, B: Val467, B: Asn469, B: Asn470, B: Gly471, B: Gly472, B: Gln473, B: Tpp1557, B: Hoh2099, conact list: Atom Atom Distance (A) Mn C B:Gly441 4.85 Mn CA B:Gly441 4.80 Mn N B:Asp442 3.96 Mn CB B:Asp442 4.36 Mn OD2 B:Asp442 3.44 Mn OD1 B:Asp442 2.14 Mn CG B:Asp442 3.08 Mn CA B:Asp442 4.68 Mn N B:Leu443 4.65 Mn O B:Val467 4.58 Mn O B:Asn469 4.90 Mn N B:Asn469 4.27 Mn CB B:Asn469 4.38 Mn ND2 B:Asn469 3.47 Mn C B:Asn469 4.58 Mn OD1 B:Asn469 2.02 Mn CG B:Asn469 3.04 Mn CA B:Asn469 4.62 Mn N B:Asn470 4.76 Mn C B:Asn470 4.88 Mn O B:Gly471 2.11 Mn N B:Gly471 3.90 Mn C B:Gly471 3.20 Mn CA B:Gly471 4.12 Mn N B:Gly472 4.05 Mn C B:Gly472 4.67 Mn CA B:Gly472 4.16 Mn N B:Gln473 4.05 Mn CB B:Gln473 4.84 Mn CG B:Gln473 4.61 Mn O3B B:Tpp1557 2.27 Mn PA B:Tpp1557 3.23 Mn O2A B:Tpp1557 4.21 Mn O1B B:Tpp1557 4.57 Mn PB B:Tpp1557 3.25 Mn O2B B:Tpp1557 4.18 Mn O7 B:Tpp1557 4.20 Mn O3A B:Tpp1557 3.44 Mn O1A B:Tpp1557 1.94 Mn O B:Hoh2099 2.20 interactive model: Manganese binding site 3 out of 5 in 2jla Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2jla. 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: Gly441, C: Asp442, C: Leu443, C: Val467, C: Asn469, C: Asn470, C: Gly471, C: Gly472, C: Gln473, C: Tpp1557, C: Hoh2085, C: Hoh2086, conact list: Atom Atom Distance (A) Mn C C:Gly441 4.71 Mn CA C:Gly441 4.63 Mn N C:Asp442 3.87 Mn CB C:Asp442 4.31 Mn OD2 C:Asp442 3.47 Mn OD1 C:Asp442 2.03 Mn CG C:Asp442 3.04 Mn CA C:Asp442 4.58 Mn N C:Leu443 4.48 Mn O C:Val467 4.40 Mn N C:Asn469 4.31 Mn CB C:Asn469 4.58 Mn ND2 C:Asn469 3.78 Mn C C:Asn469 4.72 Mn OD1 C:Asn469 2.17 Mn CG C:Asn469 3.28 Mn CA C:Asn469 4.77 Mn N C:Asn470 4.67 Mn C C:Asn470 4.95 Mn O C:Gly471 2.22 Mn N C:Gly471 3.88 Mn C C:Gly471 3.22 Mn CA C:Gly471 4.11 Mn N C:Gly472 4.06 Mn C C:Gly472 4.68 Mn CA C:Gly472 4.19 Mn N C:Gln473 4.06 Mn CB C:Gln473 4.83 Mn CG C:Gln473 4.54 Mn O3B C:Tpp1557 2.05 Mn PA C:Tpp1557 3.36 Mn O2A C:Tpp1557 4.39 Mn O1B C:Tpp1557 4.32 Mn PB C:Tpp1557 3.16 Mn O2B C:Tpp1557 4.21 Mn O7 C:Tpp1557 4.25 Mn O3A C:Tpp1557 3.50 Mn O1A C:Tpp1557 2.00 Mn O C:Hoh2085 4.16 Mn O C:Hoh2086 2.19 interactive model: Manganese binding site 4 out of 5 in 2jla Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2jla. 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: Lys507, C: His509, C: Ala520, C: Asp523, C: Hoh2087, conact list: Atom Atom Distance (A) Mn NZ C:Lys507 4.75 Mn NE2 C:His509 2.26 Mn ND1 C:His509 4.30 Mn CD2 C:His509 3.29 Mn CE1 C:His509 3.16 Mn CG C:His509 4.40 Mn O C:Ala520 4.59 Mn CA C:Ala520 4.74 Mn CB C:Asp523 3.37 Mn OD2 C:Asp523 2.31 Mn OD1 C:Asp523 4.36 Mn CG C:Asp523 3.20 Mn CA C:Asp523 4.79 Mn O C:Hoh2087 2.08 interactive model: Manganese binding site 5 out of 5 in 2jla Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2jla. 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: Gly441, D: Asp442, D: Leu443, D: Val467, D: Asn469, D: Asn470, D: Gly471, D: Gly472, D: Gln473, D: Tpp1557, D: Hoh2111, conact list: Atom Atom Distance (A) Mn C D:Gly441 4.79 Mn CA D:Gly441 4.74 Mn N D:Asp442 3.88 Mn CB D:Asp442 4.29 Mn OD2 D:Asp442 3.33 Mn OD1 D:Asp442 2.08 Mn CG D:Asp442 3.00 Mn CA D:Asp442 4.59 Mn N D:Leu443 4.54 Mn O D:Val467 4.45 Mn N D:Asn469 4.39 Mn CB D:Asn469 4.56 Mn ND2 D:Asn469 3.69 Mn C D:Asn469 4.70 Mn OD1 D:Asn469 2.17 Mn CG D:Asn469 3.24 Mn CA D:Asn469 4.77 Mn N D:Asn470 4.78 Mn C D:Asn470 4.96 Mn O D:Gly471 2.38 Mn N D:Gly471 3.97 Mn C D:Gly471 3.28 Mn CA D:Gly471 4.19 Mn N D:Gly472 4.03 Mn C D:Gly472 4.66 Mn CA D:Gly472 4.08 Mn N D:Gln473 4.10 Mn CB D:Gln473 4.93 Mn CG D:Gln473 4.56 Mn O3B D:Tpp1557 2.06 Mn PA D:Tpp1557 3.30 Mn O2A D:Tpp1557 4.37 Mn O1B D:Tpp1557 4.29 Mn PB D:Tpp1557 3.17 Mn O2B D:Tpp1557 4.29 Mn O7 D:Tpp1557 4.19 Mn O3A D:Tpp1557 3.38 Mn O1A D:Tpp1557 2.06 Mn O D:Hoh2111 2.29 interactive model: