Manganese in the structure of The Structure of Mitochondrial Pepck, Complex With Mn and Gdp (pdb 2fah)

The binding sites of Manganese atom in the structure of The Structure of Mitochondrial Pepck, Complex With Mn and Gdp (pdb code 2fah). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2fah structure was solved by T.HOLYOAK, S.M.SULLIVAN, T.NOWAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.8-2.1 Space group P1 a (A) 74.595 b (A) 90.852 c (A) 103.339 alpha (°) 64.23 beta (°) 73.74 gamma (°) 71.18 Rfactor (%) 18.7 Rfree (%) 23.4 Manganese Binding Sites: Manganese binding site 1 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2fah. 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: Lys263, A: His283, A: Ser305, A: Lys309, A: Asp330, A: Mla2001, A: Hoh2138, A: Hoh2139, A: Hoh2141, A: Hoh2203, conact list: Atom Atom Distance (A) Mn CE A:Lys263 3.32 Mn CD A:Lys263 4.59 Mn NZ A:Lys263 2.12 Mn NE2 A:His283 2.28 Mn ND1 A:His283 4.37 Mn CD2 A:His283 3.23 Mn CE1 A:His283 3.26 Mn CG A:His283 4.39 Mn CB A:Ser305 4.53 Mn OG A:Ser305 3.76 Mn CA A:Ser305 4.57 Mn CE A:Lys309 3.86 Mn NZ A:Lys309 3.91 Mn O A:Asp330 4.95 Mn CB A:Asp330 4.38 Mn OD2 A:Asp330 3.42 Mn OD1 A:Asp330 2.05 Mn CG A:Asp330 3.06 Mn CA A:Asp330 4.85 Mn O1B A:Mla2001 2.57 Mn C1 A:Mla2001 3.65 Mn C2 A:Mla2001 4.80 Mn O1A A:Mla2001 4.16 Mn O A:Hoh2138 1.99 Mn O A:Hoh2139 4.03 Mn O A:Hoh2141 3.90 Mn O A:Hoh2203 4.23 interactive model: Manganese binding site 2 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2fah. 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: Thr310, A: Asp329, A: Phe352, A: Gly353, A: Val354, A: Arg424, A: Gdp2000, A: Hoh2050, A: Hoh2139, A: Hoh2141, A: Hoh2203, conact list: Atom Atom Distance (A) Mn CB A:Thr310 3.91 Mn CG2 A:Thr310 4.74 Mn OG1 A:Thr310 3.08 Mn OD2 A:Asp329 4.76 Mn O A:Phe352 3.96 Mn C A:Phe352 4.57 Mn O A:Gly353 4.80 Mn N A:Gly353 4.39 Mn C A:Gly353 3.57 Mn CA A:Gly353 3.25 Mn O A:Val354 4.93 Mn N A:Val354 2.92 Mn CB A:Val354 3.90 Mn CG2 A:Val354 3.78 Mn C A:Val354 4.99 Mn CA A:Val354 3.98 Mn CZ A:Arg424 4.80 Mn NH1 A:Arg424 3.91 Mn O3B A:Gdp2000 4.92 Mn PA A:Gdp2000 3.82 Mn O2A A:Gdp2000 2.64 Mn O1B A:Gdp2000 2.93 Mn PB A:Gdp2000 3.44 Mn O5' A:Gdp2000 4.99 Mn O2B A:Gdp2000 3.11 Mn O3A A:Gdp2000 3.87 Mn O1A A:Gdp2000 4.70 Mn O A:Hoh2050 3.61 Mn O A:Hoh2139 3.75 Mn O A:Hoh2141 3.91 Mn O A:Hoh2203 4.51 interactive model: Manganese binding site 3 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2fah. 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: Lys263, B: His283, B: Ser305, B: Lys309, B: Asp330, B: Phe504, B: Mla3001, B: Hoh6037, B: Hoh6054, B: Hoh6100, B: Hoh6218, conact list: Atom Atom Distance (A) Mn CE B:Lys263 3.13 Mn CD B:Lys263 4.39 Mn NZ B:Lys263 2.01 Mn NE2 B:His283 2.30 Mn ND1 B:His283 4.37 Mn CD2 B:His283 3.23 Mn CE1 B:His283 3.28 Mn CG B:His283 4.38 Mn CB B:Ser305 4.45 Mn OG B:Ser305 3.67 Mn CA B:Ser305 4.60 Mn CE B:Lys309 4.13 Mn NZ B:Lys309 4.16 Mn CB B:Asp330 4.49 Mn OD2 B:Asp330 3.46 Mn OD1 B:Asp330 2.16 Mn CG B:Asp330 3.15 Mn CA B:Asp330 4.98 Mn CE2 B:Phe504 4.86 Mn CZ B:Phe504 4.80 Mn O1B B:Mla3001 4.94 Mn O3B B:Mla3001 4.37 Mn C3 B:Mla3001 3.72 Mn O3A B:Mla3001 2.60 Mn C2 B:Mla3001 4.70 Mn O B:Hoh6037 4.29 Mn O B:Hoh6054 1.94 Mn O B:Hoh6100 4.30 Mn O B:Hoh6218 4.39 interactive model: Manganese binding site 4 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2fah. 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: Thr310, B: Phe352, B: Gly353, B: Val354, B: Arg424, B: Gdp3000, B: Hoh6037, B: Hoh6068, B: Hoh6100, conact list: Atom Atom Distance (A) Mn CB B:Thr310 4.04 Mn CG2 B:Thr310 4.82 Mn OG1 B:Thr310 3.26 Mn O B:Phe352 4.11 Mn C B:Phe352 4.67 Mn O B:Gly353 4.62 Mn N B:Gly353 4.40 Mn C B:Gly353 3.40 Mn CA B:Gly353 3.19 Mn O B:Val354 4.61 Mn N B:Val354 2.67 Mn CB B:Val354 3.59 Mn CG2 B:Val354 3.50 Mn C B:Val354 4.67 Mn CA B:Val354 3.69 Mn CZ B:Arg424 4.57 Mn NH1 B:Arg424 3.71 Mn O3B B:Gdp3000 4.99 Mn PA B:Gdp3000 3.66 Mn O2A B:Gdp3000 2.50 Mn O1B B:Gdp3000 3.10 Mn PB B:Gdp3000 3.50 Mn C5' B:Gdp3000 4.96 Mn O5' B:Gdp3000 4.79 Mn O2B B:Gdp3000 3.22 Mn O3A B:Gdp3000 3.81 Mn O1A B:Gdp3000 4.58 Mn O B:Hoh6037 3.94 Mn O B:Hoh6068 3.37 Mn O B:Hoh6100 4.11 interactive model: Manganese binding site 5 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2fah. 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: Lys263, C: His283, C: Ser305, C: Lys309, C: Asp330, C: Phe504, C: Mla4003, C: Hoh6005, C: Hoh6207, C: Hoh6273, C: Hoh6282, conact list: Atom Atom Distance (A) Mn CE C:Lys263 3.08 Mn CD C:Lys263 4.37 Mn NZ C:Lys263 1.97 Mn NE2 C:His283 2.20 Mn ND1 C:His283 4.29 Mn CD2 C:His283 3.08 Mn CE1 C:His283 3.23 Mn CG C:His283 4.25 Mn CB C:Ser305 4.77 Mn OG C:Ser305 4.12 Mn CA C:Ser305 4.83 Mn CE C:Lys309 3.89 Mn CE C:Lys309 4.85 Mn NZ C:Lys309 4.23 Mn NZ C:Lys309 3.81 Mn O C:Asp330 4.91 Mn CB C:Asp330 4.37 Mn OD2 C:Asp330 3.23 Mn OD1 C:Asp330 2.09 Mn CG C:Asp330 2.99 Mn CA C:Asp330 4.89 Mn CE2 C:Phe504 4.86 Mn CZ C:Phe504 4.80 Mn O1B C:Mla4003 3.40 Mn O3B C:Mla4003 4.57 Mn C1 C:Mla4003 2.76 Mn C3 C:Mla4003 3.41 Mn O3A C:Mla4003 2.49 Mn C2 C:Mla4003 3.62 Mn O1A C:Mla4003 2.01 Mn O C:Hoh6005 2.31 Mn O C:Hoh6207 4.33 Mn O C:Hoh6273 4.15 Mn O C:Hoh6282 4.53 interactive model: Manganese binding site 6 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 2fah. 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: Thr310, C: Phe352, C: Gly353, C: Val354, C: Arg424, C: Gdp4000, C: Mla4003, C: Hoh6005, C: Hoh6124, C: Hoh6273, C: Hoh6282, C: Hoh6321, conact list: Atom Atom Distance (A) Mn N C:Thr310 4.98 Mn CB C:Thr310 4.06 Mn CG2 C:Thr310 4.97 Mn OG1 C:Thr310 3.24 Mn O C:Phe352 4.31 Mn C C:Phe352 4.96 Mn N C:Gly353 4.80 Mn C C:Gly353 3.92 Mn CA C:Gly353 3.68 Mn N C:Val354 3.16 Mn CB C:Val354 3.88 Mn CG2 C:Val354 3.65 Mn CA C:Val354 4.13 Mn CZ C:Arg424 4.80 Mn NH1 C:Arg424 3.97 Mn O3B C:Gdp4000 4.61 Mn PA C:Gdp4000 3.61 Mn O2A C:Gdp4000 2.60 Mn O1B C:Gdp4000 2.68 Mn PB C:Gdp4000 3.16 Mn O5' C:Gdp4000 4.80 Mn O2B C:Gdp4000 2.72 Mn O3A C:Gdp4000 3.69 Mn O1A C:Gdp4000 4.52 Mn O1B C:Mla4003 4.20 Mn O C:Hoh6005 4.77 Mn O C:Hoh6124 3.82 Mn O C:Hoh6273 4.16 Mn O C:Hoh6282 3.85 Mn O C:Hoh6321 2.25 interactive model: Manganese binding site 7 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 2fah. 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: Lys263, D: His283, D: Ser305, D: Lys309, D: Asp330, D: Phe504, D: Mla5001, D: Hoh6134, D: Hoh6201, D: Hoh6202, conact list: Atom Atom Distance (A) Mn CE D:Lys263 3.19 Mn CD D:Lys263 4.43 Mn NZ D:Lys263 2.05 Mn NE2 D:His283 2.15 Mn ND1 D:His283 4.19 Mn CD2 D:His283 3.14 Mn CE1 D:His283 3.08 Mn CG D:His283 4.26 Mn N D:Ser305 4.85 Mn CB D:Ser305 4.30 Mn OG D:Ser305 3.49 Mn CA D:Ser305 4.43 Mn CE D:Lys309 4.10 Mn NZ D:Lys309 3.86 Mn CB D:Asp330 4.66 Mn OD2 D:Asp330 3.60 Mn OD1 D:Asp330 2.31 Mn CG D:Asp330 3.31 Mn CE2 D:Phe504 4.77 Mn CZ D:Phe504 4.71 Mn O3B D:Mla5001 4.42 Mn C3 D:Mla5001 3.74 Mn O3A D:Mla5001 2.55 Mn C2 D:Mla5001 4.77 Mn O D:Hoh6134 4.25 Mn O D:Hoh6201 3.96 Mn O D:Hoh6202 1.93 interactive model: Manganese binding site 8 out of 8 in 2fah Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 2fah. 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: Thr310, D: Asp329, D: Phe352, D: Gly353, D: Val354, D: Arg424, D: Gdp5000, D: Hoh6033, D: Hoh6201, D: Hoh6236, conact list: Atom Atom Distance (A) Mn CB D:Thr310 3.91 Mn CG2 D:Thr310 4.72 Mn OG1 D:Thr310 3.08 Mn OD2 D:Asp329 4.80 Mn O D:Phe352 4.03 Mn C D:Phe352 4.61 Mn O D:Gly353 4.75 Mn N D:Gly353 4.39 Mn C D:Gly353 3.53 Mn CA D:Gly353 3.23 Mn O D:Val354 4.84 Mn N D:Val354 2.87 Mn CB D:Val354 3.88 Mn CG2 D:Val354 3.74 Mn C D:Val354 4.93 Mn CA D:Val354 3.95 Mn CZ D:Arg424 4.83 Mn NH1 D:Arg424 3.86 Mn O3B D:Gdp5000 4.83 Mn PA D:Gdp5000 3.82 Mn O2A D:Gdp5000 4.65 Mn O1B D:Gdp5000 3.16 Mn PB D:Gdp5000 3.41 Mn O2B D:Gdp5000 2.85 Mn O3A D:Gdp5000 3.93 Mn O1A D:Gdp5000 2.60 Mn O D:Hoh6033 3.80 Mn O D:Hoh6201 4.14 Mn O D:Hoh6236 3.69 interactive model: