Magnesium in the structure of The Crystal Structure of Avian Influenza Virus PA_N in Complex With Ump (pdb 3hw3)

The binding sites of Magnesium atom in the structure of The Crystal Structure of Avian Influenza Virus PA_N in Complex With Ump (pdb code 3hw3). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3hw3 structure was solved by C.ZHAO, Z.LOU, Y.GUO, M.MA, Y.CHEN, Z.RAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.9 Space group P1 a (A) 51.132 b (A) 59.695 c (A) 66.850 alpha (°) 96.28 beta (°) 96.65 gamma (°) 109.44 Rfactor (%) 21.8 Rfree (%) 27.6 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3hw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3hw3. 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: His41, A: Glu80, A: Leu106, A: Pro107, A: Asp108, A: Glu119, A: U5p257, A: Hoh1001, A: Hoh1002, A: Hoh1003, A: Hoh1004, A: Hoh1071, conact list: Atom Atom Distance (A) Mg NE2 A:His41 4.46 Mg CE1 A:His41 4.00 Mg OE1 A:Glu80 3.95 Mg CB A:Glu80 4.23 Mg OE2 A:Glu80 2.15 Mg CD A:Glu80 3.14 Mg CG A:Glu80 3.98 Mg CA A:Glu80 4.80 Mg O A:Leu106 4.19 Mg O A:Pro107 3.89 Mg C A:Pro107 4.15 Mg CA A:Pro107 4.99 Mg N A:Asp108 4.30 Mg CB A:Asp108 4.21 Mg OD2 A:Asp108 3.58 Mg OD1 A:Asp108 1.92 Mg CG A:Asp108 3.04 Mg CA A:Asp108 4.26 Mg OE2 A:Glu119 4.35 Mg P A:U5p257 3.37 Mg O3P A:U5p257 2.02 Mg O1P A:U5p257 4.02 Mg O5' A:U5p257 3.79 Mg O2P A:U5p257 4.54 Mg O A:Hoh1001 2.15 Mg O A:Hoh1002 2.12 Mg O A:Hoh1003 2.03 Mg O A:Hoh1004 4.41 Mg O A:Hoh1071 4.37 interactive model: Magnesium binding site 2 out of 4 in 3hw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3hw3. 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: His41, B: Glu80, B: Leu106, B: Pro107, B: Asp108, B: Glu119, B: Hoh294, B: Hoh443, B: Hoh1001, B: Hoh1002, B: Hoh1003, B: Hoh1004, B: Hoh1049, conact list: Atom Atom Distance (A) Mg NE2 B:His41 4.43 Mg ND1 B:His41 4.89 Mg CE1 B:His41 3.88 Mg OE1 B:Glu80 4.11 Mg CB B:Glu80 4.52 Mg OE2 B:Glu80 2.15 Mg CD B:Glu80 3.33 Mg CG B:Glu80 4.26 Mg O B:Leu106 4.28 Mg O B:Pro107 4.25 Mg C B:Pro107 4.42 Mg N B:Asp108 4.59 Mg CB B:Asp108 4.35 Mg OD2 B:Asp108 3.56 Mg OD1 B:Asp108 2.07 Mg CG B:Asp108 3.12 Mg CA B:Asp108 4.47 Mg OE1 B:Glu119 4.10 Mg OE2 B:Glu119 4.33 Mg CD B:Glu119 4.65 Mg O B:Hoh294 4.15 Mg O B:Hoh443 3.94 Mg O B:Hoh1001 2.09 Mg O B:Hoh1002 2.10 Mg O B:Hoh1003 2.17 Mg O B:Hoh1004 1.85 Mg O B:Hoh1049 4.22 interactive model: Magnesium binding site 3 out of 4 in 3hw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3hw3. 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: His41, C: Glu80, C: Leu106, C: Pro107, C: Asp108, C: Glu119, C: Hoh297, C: Hoh1001, C: Hoh1002, C: Hoh1003, C: Hoh1004, C: Hoh1022, conact list: Atom Atom Distance (A) Mg NE2 C:His41 4.54 Mg ND1 C:His41 4.90 Mg CE1 C:His41 3.92 Mg OE1 C:Glu80 3.91 Mg CB C:Glu80 4.20 Mg OE2 C:Glu80 2.12 Mg CD C:Glu80 3.18 Mg CG C:Glu80 4.07 Mg CA C:Glu80 4.78 Mg O C:Leu106 4.05 Mg O C:Pro107 4.09 Mg C C:Pro107 4.27 Mg N C:Asp108 4.43 Mg CB C:Asp108 4.29 Mg OD2 C:Asp108 3.61 Mg OD1 C:Asp108 2.00 Mg CG C:Asp108 3.09 Mg CA C:Asp108 4.35 Mg OE2 C:Glu119 4.36 Mg O C:Hoh297 3.87 Mg O C:Hoh1001 2.12 Mg O C:Hoh1002 2.15 Mg O C:Hoh1003 2.07 Mg O C:Hoh1004 2.12 Mg O C:Hoh1022 4.24 interactive model: Magnesium binding site 4 out of 4 in 3hw3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3hw3. 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: His41, D: Glu80, D: Leu106, D: Pro107, D: Asp108, D: Glu119, D: Hoh1001, D: Hoh1002, D: Hoh1003, D: Hoh1004, conact list: Atom Atom Distance (A) Mg NE2 D:His41 4.71 Mg CE1 D:His41 4.23 Mg OE1 D:Glu80 4.58 Mg CB D:Glu80 4.54 Mg OE2 D:Glu80 2.77 Mg CD D:Glu80 3.75 Mg CG D:Glu80 4.42 Mg O D:Leu106 4.00 Mg C D:Leu106 4.82 Mg O D:Pro107 3.81 Mg C D:Pro107 3.93 Mg CA D:Pro107 4.63 Mg N D:Asp108 4.13 Mg CB D:Asp108 4.07 Mg OD2 D:Asp108 3.42 Mg OD1 D:Asp108 1.87 Mg CG D:Asp108 2.92 Mg CA D:Asp108 4.10 Mg OE1 D:Glu119 3.67 Mg OE2 D:Glu119 4.62 Mg CD D:Glu119 4.54 Mg O D:Hoh1001 2.18 Mg O D:Hoh1002 2.19 Mg O D:Hoh1003 1.90 Mg O D:Hoh1004 2.75 interactive model: