Magnesium in the structure of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions (pdb 1m0w)

The binding sites of Magnesium atom in the structure of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions (pdb code 1m0w). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1m0w structure was solved by A.GOGOS, L.SHAPIRO, S.K.BURLEY, NEW YORK SGX RESEARCH CENTERFOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.8 Space group P1 a (A) 51.661 b (A) 52.006 c (A) 100.636 alpha (°) 82.08 beta (°) 86.77 gamma (°) 77.49 Rfactor (%) 17.2 Rfree (%) 19.6 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1m0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1m0w. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp130, A: Glu146, A: Asn148, A: Glu442, A: Arg467, A: Mg503, A: Anp504, A: 3gc501, A: Hoh2001, A: Hoh2517, A: Hoh2585, A: Hoh2603, A: Hoh2724, conact list: Atom Atom Distance (A) Mg OD1 A:Asp130 4.14 Mg OE1 A:Glu146 2.13 Mg OE2 A:Glu146 4.24 Mg CD A:Glu146 3.20 Mg CG A:Glu146 3.75 Mg OD1 A:Asn148 4.21 Mg OE1 A:Glu442 4.30 Mg CZ A:Arg467 4.83 Mg NH2 A:Arg467 3.94 Mg NH1 A:Arg467 4.75 Mg MG A:Mg503 4.06 Mg PG A:Anp504 3.59 Mg O2G A:Anp504 2.23 Mg PA A:Anp504 3.51 Mg PA A:Anp504 3.44 Mg O3' A:Anp504 4.28 Mg O3' A:Anp504 4.18 Mg O5' A:Anp504 4.55 Mg O5' A:Anp504 4.57 Mg O2B A:Anp504 4.37 Mg O3A A:Anp504 3.98 Mg O3A A:Anp504 3.62 Mg N3B A:Anp504 4.28 Mg N3B A:Anp504 4.60 Mg C3' A:Anp504 4.84 Mg C3' A:Anp504 4.83 Mg O3G A:Anp504 4.69 Mg O2A A:Anp504 2.14 Mg O2A A:Anp504 2.26 Mg O1B A:Anp504 4.23 Mg O1B A:Anp504 2.36 Mg PB A:Anp504 4.43 Mg PB A:Anp504 3.59 Mg C5' A:Anp504 4.47 Mg C5' A:Anp504 4.47 Mg O1G A:Anp504 4.14 Mg O1A A:Anp504 4.40 Mg O1A A:Anp504 4.36 Mg O3 A:3gc501 4.68 Mg O3 A:3gc501 4.61 Mg O A:Hoh2001 4.99 Mg O A:Hoh2517 2.19 Mg O A:Hoh2585 2.24 Mg O A:Hoh2603 2.17 Mg O A:Hoh2724 3.89 interactive model: Magnesium binding site 2 out of 4 in 1m0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1m0w. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu146, A: Asn148, A: Lys324, A: Glu386, A: Mg502, A: Anp504, A: Hoh2001, A: Hoh2038, A: Hoh2045, A: Hoh2233, A: Hoh2298, A: Hoh2517, A: Hoh2539, conact list: Atom Atom Distance (A) Mg OE1 A:Glu146 2.44 Mg CB A:Glu146 4.95 Mg OE2 A:Glu146 2.28 Mg CD A:Glu146 2.69 Mg CG A:Glu146 4.20 Mg OD1 A:Asn148 3.82 Mg CG A:Asn148 4.90 Mg CE A:Lys324 4.71 Mg NZ A:Lys324 4.02 Mg OE1 A:Glu386 2.39 Mg CB A:Glu386 4.26 Mg OE2 A:Glu386 4.00 Mg CD A:Glu386 3.18 Mg CG A:Glu386 3.78 Mg MG A:Mg502 4.06 Mg PG A:Anp504 3.14 Mg O2G A:Anp504 3.53 Mg PA A:Anp504 4.86 Mg PA A:Anp504 4.95 Mg O2B A:Anp504 4.47 Mg O2B A:Anp504 2.78 Mg O3A A:Anp504 4.37 Mg O3A A:Anp504 4.18 Mg N3B A:Anp504 3.43 Mg O3G A:Anp504 4.51 Mg O2A A:Anp504 4.58 Mg O2A A:Anp504 4.94 Mg O1B A:Anp504 2.24 Mg O1B A:Anp504 3.41 Mg PB A:Anp504 3.42 Mg PB A:Anp504 3.64 Mg O1G A:Anp504 2.19 Mg O1A A:Anp504 4.95 Mg O A:Hoh2001 2.34 Mg O A:Hoh2038 4.90 Mg O A:Hoh2045 3.79 Mg O A:Hoh2233 3.98 Mg O A:Hoh2298 4.94 Mg O A:Hoh2517 4.31 Mg O A:Hoh2539 4.77 interactive model: Magnesium binding site 3 out of 4 in 1m0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1m0w. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp1130, B: Val1145, B: Glu1146, B: Asn1148, B: Glu1442, B: Arg1467, B: Mg1503, B: Anp1504, B: 3gc1501, B: Hoh2559, B: Hoh2673, B: Hoh2674, conact list: Atom Atom Distance (A) Mg OD1 B:Asp1130 4.13 Mg CG1 B:Val1145 4.99 Mg OE1 B:Glu1146 2.17 Mg OE2 B:Glu1146 4.25 Mg CD B:Glu1146 3.22 Mg CG B:Glu1146 3.75 Mg OD1 B:Asn1148 4.28 Mg OE1 B:Glu1442 4.36 Mg CZ B:Arg1467 4.73 Mg NH2 B:Arg1467 3.89 Mg NH1 B:Arg1467 4.61 Mg MG B:Mg1503 4.27 Mg PG B:Anp1504 3.73 Mg O2G B:Anp1504 2.36 Mg PA B:Anp1504 3.45 Mg PA B:Anp1504 3.41 Mg O3' B:Anp1504 4.24 Mg O3' B:Anp1504 4.26 Mg O5' B:Anp1504 4.47 Mg O5' B:Anp1504 4.53 Mg O2B B:Anp1504 4.21 Mg O3A B:Anp1504 3.75 Mg O3A B:Anp1504 3.50 Mg N3B B:Anp1504 4.37 Mg N3B B:Anp1504 4.52 Mg C3' B:Anp1504 4.69 Mg C3' B:Anp1504 4.79 Mg O3G B:Anp1504 4.83 Mg O2A B:Anp1504 2.18 Mg O2A B:Anp1504 2.29 Mg O1B B:Anp1504 4.30 Mg O1B B:Anp1504 2.28 Mg PB B:Anp1504 4.42 Mg PB B:Anp1504 3.47 Mg C5' B:Anp1504 4.37 Mg C5' B:Anp1504 4.43 Mg O1G B:Anp1504 4.34 Mg O1A B:Anp1504 4.41 Mg O1A B:Anp1504 4.38 Mg O3 B:3gc1501 4.87 Mg O3 B:3gc1501 4.78 Mg O B:Hoh2559 2.19 Mg O B:Hoh2673 2.21 Mg O B:Hoh2674 2.18 interactive model: Magnesium binding site 4 out of 4 in 1m0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1m0w. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu1146, B: Asn1148, B: Lys1324, B: Glu1386, B: Mg1502, B: Anp1504, B: Hoh2244, B: Hoh2554, B: Hoh2674, B: Hoh2732, conact list: Atom Atom Distance (A) Mg OE1 B:Glu1146 2.66 Mg OE2 B:Glu1146 2.46 Mg CD B:Glu1146 2.91 Mg CG B:Glu1146 4.42 Mg OD1 B:Asn1148 3.96 Mg NZ B:Lys1324 3.84 Mg OE1 B:Glu1386 2.22 Mg CB B:Glu1386 3.96 Mg OE2 B:Glu1386 4.10 Mg CD B:Glu1386 3.25 Mg CG B:Glu1386 3.98 Mg MG B:Mg1502 4.27 Mg PG B:Anp1504 3.11 Mg O2G B:Anp1504 3.52 Mg PA B:Anp1504 4.99 Mg O2B B:Anp1504 4.44 Mg O2B B:Anp1504 2.80 Mg O3A B:Anp1504 4.32 Mg O3A B:Anp1504 4.29 Mg N3B B:Anp1504 3.19 Mg O3G B:Anp1504 4.52 Mg O2A B:Anp1504 4.84 Mg O1B B:Anp1504 2.24 Mg O1B B:Anp1504 3.74 Mg PB B:Anp1504 3.32 Mg PB B:Anp1504 3.80 Mg O1G B:Anp1504 2.22 Mg O B:Hoh2244 3.72 Mg O B:Hoh2554 3.89 Mg O B:Hoh2674 4.48 Mg O B:Hoh2732 2.33 interactive model: