Magnesium in the structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex With A Coumarin-Based Inhibitor (pdb 3ly2)

The binding sites of Magnesium atom in the structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex With A Coumarin-Based Inhibitor (pdb code 3ly2). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3ly2 structure was solved by A.K.SHIAU, A.R.COYLE, J.H.HSIEN, L.M.STASZEWSKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.8-2.6 Space group C2221 a (A) 214.796 b (A) 233.964 c (A) 165.258 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3ly2. 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: His234, A: His274, A: Asp275, A: His278, A: Glu304, A: His307, A: Thr345, A: Asp392, A: Z721000, A: Zn1001, A: Hoh1004, A: Hoh1005, A: Hoh1006, A: Hoh1007, A: Hoh1008, A: Hoh1010, A: Hoh2071, conact list: Atom Atom Distance (A) Mg NE2 A:His234 4.81 Mg CD2 A:His234 4.78 Mg O A:His274 4.14 Mg NE2 A:His274 4.46 Mg CD2 A:His274 4.12 Mg C A:His274 4.99 Mg CB A:Asp275 4.40 Mg OD2 A:Asp275 3.25 Mg OD1 A:Asp275 2.10 Mg CG A:Asp275 3.00 Mg CA A:Asp275 4.78 Mg NE2 A:His278 4.92 Mg CD2 A:His278 4.55 Mg OE2 A:Glu304 4.04 Mg CD A:Glu304 4.97 Mg NE2 A:His307 4.02 Mg CD2 A:His307 4.32 Mg O A:Thr345 4.59 Mg CB A:Thr345 4.74 Mg OG1 A:Thr345 4.23 Mg OD1 A:Asp392 4.52 Mg N22 A:Z721000 3.99 Mg C23 A:Z721000 4.59 Mg C21 A:Z721000 4.32 Mg ZN A:Zn1001 3.87 Mg O A:Hoh1004 2.08 Mg O A:Hoh1005 2.11 Mg O A:Hoh1006 2.12 Mg O A:Hoh1007 2.11 Mg O A:Hoh1008 4.09 Mg O A:Hoh1010 2.11 Mg O A:Hoh2071 4.12 interactive model: Magnesium binding site 2 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3ly2. 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: His234, B: His274, B: Asp275, B: His278, B: Glu304, B: His307, B: Thr345, B: Asp392, B: Z721000, B: Zn1001, B: Hoh1004, B: Hoh1005, B: Hoh1006, B: Hoh1007, B: Hoh1008, B: Hoh1010, B: Hoh2051, B: Hoh2153, conact list: Atom Atom Distance (A) Mg NE2 B:His234 4.93 Mg O B:His274 4.17 Mg NE2 B:His274 4.64 Mg CD2 B:His274 4.15 Mg C B:His274 4.96 Mg CB B:Asp275 4.46 Mg OD2 B:Asp275 3.46 Mg OD1 B:Asp275 2.11 Mg CG B:Asp275 3.12 Mg CA B:Asp275 4.78 Mg CD2 B:His278 4.61 Mg OE2 B:Glu304 3.95 Mg CD B:Glu304 4.85 Mg CG B:Glu304 4.92 Mg NE2 B:His307 4.03 Mg CD2 B:His307 4.37 Mg O B:Thr345 4.49 Mg CB B:Thr345 4.67 Mg OG1 B:Thr345 4.15 Mg OD1 B:Asp392 4.52 Mg N22 B:Z721000 3.93 Mg C23 B:Z721000 4.58 Mg C21 B:Z721000 4.26 Mg ZN B:Zn1001 4.01 Mg O B:Hoh1004 2.11 Mg O B:Hoh1005 2.10 Mg O B:Hoh1006 2.08 Mg O B:Hoh1007 2.12 Mg O B:Hoh1008 4.25 Mg O B:Hoh1010 2.12 Mg O B:Hoh2051 4.18 Mg O B:Hoh2153 4.57 interactive model: Magnesium binding site 3 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3ly2. 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: His234, C: His274, C: Asp275, C: His278, C: Glu304, C: His307, C: Thr345, C: Asp392, C: Z721000, C: Zn1001, C: Hoh1004, C: Hoh1005, C: Hoh1006, C: Hoh1007, C: Hoh1008, C: Hoh1010, C: Hoh2367, conact list: Atom Atom Distance (A) Mg NE2 C:His234 4.73 Mg CD2 C:His234 4.70 Mg O C:His274 4.04 Mg NE2 C:His274 4.42 Mg CD2 C:His274 4.10 Mg C C:His274 4.93 Mg CB C:Asp275 4.44 Mg OD2 C:Asp275 3.35 Mg OD1 C:Asp275 2.11 Mg CG C:Asp275 3.06 Mg CA C:Asp275 4.80 Mg NE2 C:His278 4.80 Mg CD2 C:His278 4.55 Mg OE2 C:Glu304 4.06 Mg NE2 C:His307 4.17 Mg CD2 C:His307 4.47 Mg O C:Thr345 4.65 Mg CB C:Thr345 4.79 Mg OG1 C:Thr345 4.23 Mg OD1 C:Asp392 4.50 Mg N22 C:Z721000 3.82 Mg C23 C:Z721000 4.36 Mg C21 C:Z721000 4.27 Mg ZN C:Zn1001 3.90 Mg O C:Hoh1004 2.09 Mg O C:Hoh1005 2.14 Mg O C:Hoh1006 2.08 Mg O C:Hoh1007 2.12 Mg O C:Hoh1008 4.13 Mg O C:Hoh1010 2.13 Mg O C:Hoh2367 4.27 interactive model: Magnesium binding site 4 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3ly2. 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: His234, D: His274, D: Asp275, D: His278, D: Glu304, D: His307, D: Thr345, D: Asp392, D: Z721000, D: Zn1001, D: Hoh1004, D: Hoh1005, D: Hoh1006, D: Hoh1007, D: Hoh1008, D: Hoh1010, D: Hoh2384, D: Hoh2385, conact list: Atom Atom Distance (A) Mg NE2 D:His234 4.77 Mg CD2 D:His234 4.78 Mg O D:His274 4.15 Mg NE2 D:His274 4.58 Mg CD2 D:His274 4.20 Mg CB D:Asp275 4.45 Mg OD2 D:Asp275 3.33 Mg OD1 D:Asp275 2.10 Mg CG D:Asp275 3.06 Mg CA D:Asp275 4.86 Mg NE2 D:His278 4.97 Mg CD2 D:His278 4.65 Mg OE2 D:Glu304 4.09 Mg NE2 D:His307 4.29 Mg CD2 D:His307 4.50 Mg O D:Thr345 4.41 Mg CB D:Thr345 4.65 Mg OG1 D:Thr345 4.14 Mg OD1 D:Asp392 4.47 Mg N22 D:Z721000 3.85 Mg C23 D:Z721000 4.39 Mg C21 D:Z721000 4.25 Mg ZN D:Zn1001 3.81 Mg O D:Hoh1004 2.08 Mg O D:Hoh1005 2.11 Mg O D:Hoh1006 2.10 Mg O D:Hoh1007 2.11 Mg O D:Hoh1008 3.92 Mg O D:Hoh1010 2.10 Mg O D:Hoh2384 4.90 Mg O D:Hoh2385 4.19 interactive model: Magnesium binding site 5 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3ly2. 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: His234, E: His274, E: Asp275, E: His278, E: Glu304, E: His307, E: Thr345, E: Asp392, E: Z721000, E: Zn1001, E: Hoh1004, E: Hoh1005, E: Hoh1006, E: Hoh1007, E: Hoh1008, E: Hoh1010, E: Hoh2096, conact list: Atom Atom Distance (A) Mg NE2 E:His234 4.74 Mg CD2 E:His234 4.69 Mg O E:His274 4.05 Mg NE2 E:His274 4.42 Mg CD2 E:His274 4.10 Mg C E:His274 4.95 Mg CB E:Asp275 4.45 Mg OD2 E:Asp275 3.36 Mg OD1 E:Asp275 2.11 Mg CG E:Asp275 3.07 Mg CA E:Asp275 4.81 Mg NE2 E:His278 4.79 Mg CD2 E:His278 4.54 Mg OE2 E:Glu304 4.05 Mg CD E:Glu304 5.00 Mg NE2 E:His307 4.16 Mg CD2 E:His307 4.46 Mg O E:Thr345 4.62 Mg CB E:Thr345 4.79 Mg OG1 E:Thr345 4.21 Mg OD1 E:Asp392 4.50 Mg N22 E:Z721000 3.81 Mg C23 E:Z721000 4.35 Mg C21 E:Z721000 4.27 Mg ZN E:Zn1001 3.89 Mg O E:Hoh1004 2.07 Mg O E:Hoh1005 2.13 Mg O E:Hoh1006 2.10 Mg O E:Hoh1007 2.12 Mg O E:Hoh1008 4.15 Mg O E:Hoh1010 2.12 Mg O E:Hoh2096 4.26 interactive model: Magnesium binding site 6 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3ly2. 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: His234, F: His274, F: Asp275, F: His278, F: Glu304, F: His307, F: Thr345, F: Asp392, F: Z721000, F: Zn1001, F: Hoh1004, F: Hoh1005, F: Hoh1006, F: Hoh1007, F: Hoh1008, F: Hoh1010, F: Hoh2121, conact list: Atom Atom Distance (A) Mg NE2 F:His234 4.78 Mg CD2 F:His234 4.80 Mg O F:His274 4.19 Mg NE2 F:His274 4.58 Mg CD2 F:His274 4.20 Mg CB F:Asp275 4.45 Mg OD2 F:Asp275 3.33 Mg OD1 F:Asp275 2.10 Mg CG F:Asp275 3.06 Mg CA F:Asp275 4.86 Mg NE2 F:His278 4.97 Mg CD2 F:His278 4.65 Mg OE2 F:Glu304 4.10 Mg NE2 F:His307 4.28 Mg CD2 F:His307 4.49 Mg O F:Thr345 4.41 Mg CB F:Thr345 4.64 Mg OG1 F:Thr345 4.12 Mg OD1 F:Asp392 4.46 Mg N22 F:Z721000 3.84 Mg C23 F:Z721000 4.37 Mg C21 F:Z721000 4.25 Mg ZN F:Zn1001 3.79 Mg O F:Hoh1004 2.08 Mg O F:Hoh1005 2.11 Mg O F:Hoh1006 2.11 Mg O F:Hoh1007 2.11 Mg O F:Hoh1008 3.92 Mg O F:Hoh1010 2.10 Mg O F:Hoh2121 4.20 interactive model: Magnesium binding site 7 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3ly2. 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: His234, G: His274, G: Asp275, G: His278, G: Glu304, G: His307, G: Thr345, G: Asp392, G: Z721000, G: Zn1001, G: Hoh1004, G: Hoh1005, G: Hoh1006, G: Hoh1007, G: Hoh1008, G: Hoh1010, G: Hoh2126, G: Hoh2268, conact list: Atom Atom Distance (A) Mg NE2 G:His234 4.83 Mg CD2 G:His234 4.79 Mg O G:His274 4.01 Mg NE2 G:His274 4.55 Mg CD2 G:His274 4.17 Mg C G:His274 4.93 Mg CB G:Asp275 4.48 Mg OD2 G:Asp275 3.46 Mg OD1 G:Asp275 2.11 Mg CG G:Asp275 3.12 Mg CA G:Asp275 4.85 Mg NE2 G:His278 4.97 Mg CD2 G:His278 4.64 Mg OE2 G:Glu304 4.04 Mg CD G:Glu304 4.95 Mg NE2 G:His307 4.18 Mg CD2 G:His307 4.49 Mg O G:Thr345 4.65 Mg CB G:Thr345 4.62 Mg OG1 G:Thr345 4.20 Mg OD1 G:Asp392 4.46 Mg N22 G:Z721000 3.85 Mg C23 G:Z721000 4.52 Mg C21 G:Z721000 4.16 Mg ZN G:Zn1001 3.90 Mg O G:Hoh1004 2.10 Mg O G:Hoh1005 2.14 Mg O G:Hoh1006 2.10 Mg O G:Hoh1007 2.13 Mg O G:Hoh1008 4.10 Mg O G:Hoh1010 2.10 Mg O G:Hoh2126 4.16 Mg O G:Hoh2268 4.84 interactive model: Magnesium binding site 8 out of 8 in 3ly2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3ly2. 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: His234, H: His274, H: Asp275, H: His278, H: Glu304, H: His307, H: Thr345, H: Asp392, H: Z721000, H: Zn1001, H: Hoh1004, H: Hoh1005, H: Hoh1006, H: Hoh1007, H: Hoh1008, H: Hoh1010, conact list: Atom Atom Distance (A) Mg NE2 H:His234 4.83 Mg CD2 H:His234 4.78 Mg O H:His274 4.01 Mg NE2 H:His274 4.54 Mg CD2 H:His274 4.17 Mg C H:His274 4.92 Mg CB H:Asp275 4.47 Mg OD2 H:Asp275 3.43 Mg OD1 H:Asp275 2.11 Mg CG H:Asp275 3.11 Mg CA H:Asp275 4.84 Mg NE2 H:His278 4.97 Mg CD2 H:His278 4.64 Mg OE2 H:Glu304 4.04 Mg CD H:Glu304 4.97 Mg NE2 H:His307 4.16 Mg CD2 H:His307 4.46 Mg O H:Thr345 4.66 Mg CB H:Thr345 4.63 Mg OG1 H:Thr345 4.19 Mg OD1 H:Asp392 4.45 Mg N22 H:Z721000 3.88 Mg C23 H:Z721000 4.54 Mg C21 H:Z721000 4.16 Mg ZN H:Zn1001 3.89 Mg O H:Hoh1004 2.09 Mg O H:Hoh1005 2.14 Mg O H:Hoh1006 2.11 Mg O H:Hoh1007 2.13 Mg O H:Hoh1008 4.07 Mg O H:Hoh1010 2.13 interactive model: