Magnesium in the structure of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed With Mg and Dipeptide L-Ile-L-Tyr (pdb 3jw7)

The binding sites of Magnesium atom in the structure of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed With Mg and Dipeptide L-Ile-L-Tyr (pdb code 3jw7). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3jw7 structure was solved by A.A.FEDOROV, E.V.FEDOROV, H.J.IMKER, A.SAKAI, J.A.GERLT, S.C.ALMO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-1.8 Space group C121 a (A) 194.918 b (A) 187.442 c (A) 91.894 alpha (°) 90.00 beta (°) 89.99 gamma (°) 90.00 Rfactor (%) 22.1 Rfree (%) 25.4 Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3jw7. 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: Lys159, A: Lys161, A: Asp189, A: Asn191, A: Glu215, A: Asp240, A: Glu241, A: Asn262, A: Lys264, A: Tyr356, A: Hoh360, A: Hoh369, A: Hoh648, conact list: Atom Atom Distance (A) Mg CE A:Lys159 4.33 Mg NZ A:Lys159 3.57 Mg NZ A:Lys161 4.09 Mg CB A:Asp189 4.57 Mg OD2 A:Asp189 2.32 Mg OD1 A:Asp189 3.55 Mg CG A:Asp189 3.25 Mg ND2 A:Asn191 3.99 Mg OD1 A:Asn191 4.97 Mg CG A:Asn191 4.80 Mg OE1 A:Glu215 3.82 Mg CB A:Glu215 4.31 Mg OE2 A:Glu215 2.33 Mg CD A:Glu215 3.21 Mg CG A:Glu215 4.15 Mg CB A:Asp240 3.70 Mg OD2 A:Asp240 2.34 Mg OD1 A:Asp240 4.43 Mg CG A:Asp240 3.33 Mg OE1 A:Glu241 4.43 Mg ND2 A:Asn262 4.14 Mg NZ A:Lys264 4.24 Mg O A:Tyr356 2.76 Mg C A:Tyr356 2.88 Mg CA A:Tyr356 4.38 Mg OXT A:Tyr356 2.34 Mg O A:Hoh360 2.43 Mg O A:Hoh369 4.84 Mg O A:Hoh648 4.21 interactive model: Magnesium binding site 2 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3jw7. 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: Lys159, B: Lys161, B: Asp189, B: Asn191, B: Glu215, B: Asp240, B: Glu241, B: Asn262, B: Lys264, B: Ile355, B: Tyr356, B: Hoh359, B: Hoh369, B: Hoh1322, conact list: Atom Atom Distance (A) Mg CE B:Lys159 4.33 Mg NZ B:Lys159 3.58 Mg NZ B:Lys161 4.03 Mg CB B:Asp189 4.57 Mg OD2 B:Asp189 2.30 Mg OD1 B:Asp189 3.53 Mg CG B:Asp189 3.24 Mg ND2 B:Asn191 3.97 Mg OD1 B:Asn191 4.95 Mg CG B:Asn191 4.78 Mg OE1 B:Glu215 3.88 Mg CB B:Glu215 4.38 Mg OE2 B:Glu215 2.28 Mg CD B:Glu215 3.17 Mg CG B:Glu215 4.01 Mg CB B:Asp240 3.69 Mg OD2 B:Asp240 2.32 Mg OD1 B:Asp240 4.42 Mg CG B:Asp240 3.31 Mg OE1 B:Glu241 4.35 Mg CD B:Glu241 5.00 Mg ND2 B:Asn262 4.25 Mg NZ B:Lys264 4.27 Mg O B:Ile355 4.94 Mg O B:Tyr356 2.72 Mg CB B:Tyr356 4.98 Mg C B:Tyr356 2.84 Mg CA B:Tyr356 4.34 Mg OXT B:Tyr356 2.30 Mg O B:Hoh359 2.41 Mg O B:Hoh369 4.76 Mg O B:Hoh1322 4.19 interactive model: Magnesium binding site 3 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3jw7. 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: C: Lys159, C: Lys161, C: Asp189, C: Asn191, C: Glu215, C: Asp240, C: Glu241, C: Asn262, C: Lys264, C: Tyr356, C: Hoh363, C: Hoh364, C: Hoh1430, conact list: Atom Atom Distance (A) Mg CE C:Lys159 4.26 Mg NZ C:Lys159 3.54 Mg NZ C:Lys161 4.06 Mg CB C:Asp189 4.55 Mg OD2 C:Asp189 2.32 Mg OD1 C:Asp189 3.53 Mg CG C:Asp189 3.24 Mg ND2 C:Asn191 4.08 Mg CG C:Asn191 4.91 Mg OE1 C:Glu215 3.69 Mg CB C:Glu215 4.22 Mg OE2 C:Glu215 2.24 Mg CD C:Glu215 2.99 Mg CG C:Glu215 3.77 Mg CB C:Asp240 3.59 Mg OD2 C:Asp240 2.31 Mg OD1 C:Asp240 4.38 Mg CG C:Asp240 3.27 Mg OE1 C:Glu241 4.26 Mg ND2 C:Asn262 4.15 Mg NZ C:Lys264 4.21 Mg O C:Tyr356 2.78 Mg C C:Tyr356 2.97 Mg CA C:Tyr356 4.46 Mg OXT C:Tyr356 2.51 Mg O C:Hoh363 2.40 Mg O C:Hoh364 4.90 Mg O C:Hoh1430 4.34 interactive model: Magnesium binding site 4 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3jw7. 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: D: Lys159, D: Lys161, D: Asp189, D: Asn191, D: Glu215, D: Asp240, D: Glu241, D: Asn262, D: Lys264, D: Tyr356, D: Hoh397, D: Hoh925, D: Hoh1007, conact list: Atom Atom Distance (A) Mg CE D:Lys159 4.23 Mg NZ D:Lys159 3.49 Mg NZ D:Lys161 4.13 Mg CB D:Asp189 4.57 Mg OD2 D:Asp189 2.36 Mg OD1 D:Asp189 3.58 Mg CG D:Asp189 3.27 Mg ND2 D:Asn191 4.15 Mg OD1 D:Asn191 5.00 Mg CG D:Asn191 4.88 Mg OE1 D:Glu215 3.63 Mg CB D:Glu215 4.17 Mg OE2 D:Glu215 2.09 Mg CD D:Glu215 2.93 Mg CG D:Glu215 3.78 Mg CB D:Asp240 3.64 Mg OD2 D:Asp240 2.32 Mg OD1 D:Asp240 4.36 Mg CG D:Asp240 3.28 Mg OE1 D:Glu241 4.37 Mg ND2 D:Asn262 4.11 Mg CG D:Asn262 5.00 Mg NZ D:Lys264 4.26 Mg O D:Tyr356 2.79 Mg C D:Tyr356 2.98 Mg CA D:Tyr356 4.48 Mg OXT D:Tyr356 2.51 Mg O D:Hoh397 4.95 Mg O D:Hoh925 2.44 Mg O D:Hoh1007 4.36 interactive model: Magnesium binding site 5 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3jw7. 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: E: Lys159, E: Lys161, E: Asp189, E: Asn191, E: Glu215, E: Asp240, E: Glu241, E: Asn262, E: Lys264, E: Ile355, E: Tyr356, E: Hoh368, E: Hoh387, E: Hoh1402, conact list: Atom Atom Distance (A) Mg CE E:Lys159 4.35 Mg NZ E:Lys159 3.61 Mg NZ E:Lys161 4.10 Mg CB E:Asp189 4.70 Mg OD2 E:Asp189 2.44 Mg OD1 E:Asp189 3.64 Mg CG E:Asp189 3.37 Mg ND2 E:Asn191 3.91 Mg OD1 E:Asn191 4.98 Mg CG E:Asn191 4.76 Mg OE1 E:Glu215 3.86 Mg CB E:Glu215 4.39 Mg OE2 E:Glu215 2.22 Mg CD E:Glu215 3.10 Mg CG E:Glu215 3.90 Mg CB E:Asp240 3.63 Mg OD2 E:Asp240 2.27 Mg OD1 E:Asp240 4.32 Mg CG E:Asp240 3.24 Mg OE1 E:Glu241 4.37 Mg CD E:Glu241 4.97 Mg ND2 E:Asn262 4.34 Mg NZ E:Lys264 4.06 Mg O E:Ile355 4.94 Mg O E:Tyr356 2.68 Mg CB E:Tyr356 4.93 Mg C E:Tyr356 2.81 Mg CA E:Tyr356 4.30 Mg OXT E:Tyr356 2.30 Mg O E:Hoh368 2.30 Mg O E:Hoh387 4.82 Mg O E:Hoh1402 4.06 interactive model: Magnesium binding site 6 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3jw7. 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: F: Lys159, F: Lys161, F: Asp189, F: Asn191, F: Glu215, F: Asp240, F: Glu241, F: Asn262, F: Lys264, F: Tyr356, F: Hoh390, F: Hoh393, F: Hoh660, conact list: Atom Atom Distance (A) Mg CE F:Lys159 4.40 Mg NZ F:Lys159 3.76 Mg NZ F:Lys161 4.25 Mg CB F:Asp189 4.66 Mg OD2 F:Asp189 2.40 Mg OD1 F:Asp189 3.64 Mg CG F:Asp189 3.34 Mg ND2 F:Asn191 4.09 Mg CG F:Asn191 4.89 Mg OE1 F:Glu215 3.78 Mg CB F:Glu215 4.35 Mg OE2 F:Glu215 2.22 Mg CD F:Glu215 3.05 Mg CG F:Glu215 3.86 Mg CB F:Asp240 3.54 Mg OD2 F:Asp240 2.21 Mg OD1 F:Asp240 4.22 Mg CG F:Asp240 3.15 Mg OE1 F:Glu241 4.25 Mg CD F:Glu241 4.93 Mg ND2 F:Asn262 4.24 Mg NZ F:Lys264 4.14 Mg O F:Tyr356 2.77 Mg C F:Tyr356 2.92 Mg CA F:Tyr356 4.42 Mg OXT F:Tyr356 2.41 Mg O F:Hoh390 4.90 Mg O F:Hoh393 2.22 Mg O F:Hoh660 4.19 interactive model: Magnesium binding site 7 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3jw7. 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: G: Lys159, G: Lys161, G: Asp189, G: Asn191, G: Glu215, G: Asp240, G: Glu241, G: Asn262, G: Lys264, G: Tyr356, G: Hoh384, G: Hoh406, G: Hoh2521, conact list: Atom Atom Distance (A) Mg CE G:Lys159 4.40 Mg NZ G:Lys159 3.77 Mg NZ G:Lys161 4.20 Mg CB G:Asp189 4.70 Mg OD2 G:Asp189 2.44 Mg OD1 G:Asp189 3.67 Mg CG G:Asp189 3.38 Mg ND2 G:Asn191 3.98 Mg CG G:Asn191 4.85 Mg OE1 G:Glu215 3.81 Mg CB G:Glu215 4.36 Mg OE2 G:Glu215 2.21 Mg CD G:Glu215 3.08 Mg CG G:Glu215 3.89 Mg CB G:Asp240 3.57 Mg OD2 G:Asp240 2.18 Mg OD1 G:Asp240 4.25 Mg CG G:Asp240 3.16 Mg OE1 G:Glu241 4.28 Mg CD G:Glu241 4.89 Mg ND2 G:Asn262 4.21 Mg NZ G:Lys264 4.10 Mg O G:Tyr356 2.82 Mg C G:Tyr356 2.94 Mg CA G:Tyr356 4.43 Mg OXT G:Tyr356 2.40 Mg O G:Hoh384 2.28 Mg O G:Hoh406 4.89 Mg O G:Hoh2521 4.20 interactive model: Magnesium binding site 8 out of 8 in 3jw7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3jw7. 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: H: Lys159, H: Lys161, H: Asp189, H: Asn191, H: Glu215, H: Asp240, H: Glu241, H: Asn262, H: Lys264, H: Ile355, H: Tyr356, H: Hoh359, H: Hoh417, H: Hoh1070, conact list: Atom Atom Distance (A) Mg CE H:Lys159 4.40 Mg NZ H:Lys159 3.58 Mg NZ H:Lys161 4.07 Mg CB H:Asp189 4.66 Mg OD2 H:Asp189 2.40 Mg OD1 H:Asp189 3.54 Mg CG H:Asp189 3.30 Mg ND2 H:Asn191 3.85 Mg OD1 H:Asn191 4.98 Mg CG H:Asn191 4.73 Mg OE1 H:Glu215 3.85 Mg CB H:Glu215 4.41 Mg OE2 H:Glu215 2.23 Mg CD H:Glu215 3.14 Mg CG H:Glu215 3.97 Mg CB H:Asp240 3.64 Mg OD2 H:Asp240 2.26 Mg OD1 H:Asp240 4.32 Mg CG H:Asp240 3.24 Mg OE1 H:Glu241 4.37 Mg CD H:Glu241 4.97 Mg ND2 H:Asn262 4.33 Mg NZ H:Lys264 4.15 Mg O H:Ile355 4.97 Mg O H:Tyr356 2.67 Mg CB H:Tyr356 4.96 Mg C H:Tyr356 2.82 Mg CA H:Tyr356 4.32 Mg OXT H:Tyr356 2.33 Mg O H:Hoh359 2.30 Mg O H:Hoh417 4.92 Mg O H:Hoh1070 4.06 interactive model: