Magnesium in the structure of Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form (pdb 2v9p)

The binding sites of Magnesium atom in the structure of Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form (pdb code 2v9p). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2v9p structure was solved by C.M.SANDERS, O.V.KOVALEVSKIY, D.SIZOV, A.A.LEBEDEV, M.N.ISUPOV, A.A.ANTSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-3.0 Space group P212121 a (A) 135.111 b (A) 180.649 c (A) 187.533 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.9 Rfree (%) 27.1 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 2v9p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2v9p. 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: Lys439, A: Ser440, A: Asp478, A: Asp479, A: Thr521, B: Asp497, B: Arg538, A: Po41580, A: Po41581, conact list: Atom Atom Distance (A) Mg NZ A:Lys439 4.85 Mg N A:Ser440 4.59 Mg CB A:Ser440 3.61 Mg OG A:Ser440 2.45 Mg CA A:Ser440 4.66 Mg OD2 A:Asp478 4.89 Mg OD1 A:Asp478 4.94 Mg CB A:Asp479 4.67 Mg OD2 A:Asp479 3.00 Mg OD1 A:Asp479 4.62 Mg CG A:Asp479 3.91 Mg OG1 A:Thr521 4.87 Mg OD2 B:Asp497 4.33 Mg CZ B:Arg538 4.30 Mg NH2 B:Arg538 3.01 Mg NH1 B:Arg538 4.89 Mg O1 A:Po41580 4.05 Mg O2 A:Po41580 2.27 Mg P A:Po41580 3.49 Mg O4 A:Po41580 3.87 Mg O3 A:Po41580 4.73 Mg O1 A:Po41581 4.24 Mg O2 A:Po41581 3.65 Mg P A:Po41581 3.15 Mg O4 A:Po41581 1.78 Mg O3 A:Po41581 3.80 interactive model: Magnesium binding site 2 out of 6 in 2v9p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2v9p. 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: Lys439, B: Ser440, B: Asp478, B: Asp479, B: Thr521, C: Asp497, C: Arg538, B: Po41579, B: Po41580, conact list: Atom Atom Distance (A) Mg CE B:Lys439 4.94 Mg NZ B:Lys439 4.89 Mg N B:Ser440 4.12 Mg CB B:Ser440 3.28 Mg OG B:Ser440 2.20 Mg CA B:Ser440 4.26 Mg OD2 B:Asp478 4.59 Mg OD1 B:Asp478 4.79 Mg CG B:Asp478 4.96 Mg CB B:Asp479 4.90 Mg OD2 B:Asp479 2.75 Mg OD1 B:Asp479 3.87 Mg CG B:Asp479 3.61 Mg OG1 B:Thr521 4.36 Mg OD2 C:Asp497 3.99 Mg CZ C:Arg538 4.87 Mg NH2 C:Arg538 3.54 Mg O1 B:Po41579 3.72 Mg O2 B:Po41579 1.90 Mg P B:Po41579 3.26 Mg O4 B:Po41579 4.01 Mg O3 B:Po41579 4.34 Mg O1 B:Po41580 4.28 Mg O2 B:Po41580 3.62 Mg P B:Po41580 3.19 Mg O4 B:Po41580 1.82 Mg O3 B:Po41580 3.90 interactive model: Magnesium binding site 3 out of 6 in 2v9p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2v9p. 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: Ser440, C: Asp478, C: Asp479, C: Thr521, D: Asp497, D: Arg538, C: Po41579, C: Po41580, conact list: Atom Atom Distance (A) Mg N C:Ser440 4.22 Mg CB C:Ser440 3.24 Mg OG C:Ser440 2.20 Mg CA C:Ser440 4.29 Mg OD2 C:Asp478 4.47 Mg OD1 C:Asp478 4.58 Mg CG C:Asp478 4.77 Mg CB C:Asp479 4.83 Mg OD2 C:Asp479 2.78 Mg OD1 C:Asp479 4.08 Mg CG C:Asp479 3.68 Mg OG1 C:Thr521 4.44 Mg OD2 D:Asp497 4.18 Mg NH2 D:Arg538 3.75 Mg O1 C:Po41579 4.10 Mg O2 C:Po41579 1.95 Mg P C:Po41579 3.44 Mg O4 C:Po41579 4.30 Mg O3 C:Po41579 4.32 Mg O1 C:Po41580 3.99 Mg O2 C:Po41580 4.31 Mg P C:Po41580 3.33 Mg O4 C:Po41580 1.94 Mg O3 C:Po41580 4.08 interactive model: Magnesium binding site 4 out of 6 in 2v9p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2v9p. 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: Lys439, G: Ser440, G: Asp478, G: Asp479, G: Thr521, H: Asp497, H: Arg538, G: Po41579, G: Po41580, conact list: Atom Atom Distance (A) Mg NZ G:Lys439 4.53 Mg N G:Ser440 4.21 Mg CB G:Ser440 3.25 Mg OG G:Ser440 1.93 Mg CA G:Ser440 4.24 Mg OD2 G:Asp478 4.39 Mg OD1 G:Asp478 4.67 Mg CG G:Asp478 4.85 Mg CB G:Asp479 4.68 Mg OD2 G:Asp479 3.16 Mg OD1 G:Asp479 4.71 Mg CG G:Asp479 4.00 Mg OG1 G:Thr521 4.45 Mg OD2 H:Asp497 4.31 Mg CZ H:Arg538 4.60 Mg NH2 H:Arg538 3.33 Mg O1 G:Po41579 3.79 Mg O2 G:Po41579 2.14 Mg P G:Po41579 3.43 Mg O4 G:Po41579 4.11 Mg O3 G:Po41579 4.57 Mg O1 G:Po41580 4.42 Mg O2 G:Po41580 3.83 Mg P G:Po41580 3.40 Mg O4 G:Po41580 2.00 Mg O3 G:Po41580 4.11 interactive model: Magnesium binding site 5 out of 6 in 2v9p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2v9p. 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: Lys439, H: Ser440, H: Asp478, H: Asp479, H: Thr521, I: Asp497, I: Tyr499, I: Arg538, H: Po41579, H: Po41580, conact list: Atom Atom Distance (A) Mg CB H:Lys439 4.99 Mg NZ H:Lys439 4.70 Mg N H:Ser440 3.91 Mg CB H:Ser440 2.98 Mg OG H:Ser440 1.94 Mg CA H:Ser440 4.00 Mg OD2 H:Asp478 4.49 Mg OD1 H:Asp478 4.32 Mg CG H:Asp478 4.71 Mg OD2 H:Asp479 2.93 Mg OD1 H:Asp479 4.42 Mg CG H:Asp479 3.93 Mg CB H:Thr521 4.89 Mg OG1 H:Thr521 4.16 Mg OD2 I:Asp497 4.38 Mg CE2 I:Tyr499 4.95 Mg NH2 I:Arg538 3.89 Mg O1 H:Po41579 4.03 Mg O2 H:Po41579 2.06 Mg P H:Po41579 3.49 Mg O4 H:Po41579 4.20 Mg O3 H:Po41579 4.51 Mg O1 H:Po41580 4.59 Mg O2 H:Po41580 3.94 Mg P H:Po41580 3.46 Mg O4 H:Po41580 2.11 Mg O3 H:Po41580 4.03 interactive model: Magnesium binding site 6 out of 6 in 2v9p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2v9p. 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: I: Lys439, I: Ser440, I: Asp478, I: Asp479, I: Thr521, J: Asp497, J: Arg538, I: Po41580, I: Po41581, conact list: Atom Atom Distance (A) Mg NZ I:Lys439 4.87 Mg N I:Ser440 4.26 Mg CB I:Ser440 3.16 Mg OG I:Ser440 2.34 Mg CA I:Ser440 4.28 Mg OD2 I:Asp478 4.73 Mg OD1 I:Asp478 4.75 Mg CG I:Asp478 4.99 Mg OD2 I:Asp479 2.81 Mg OD1 I:Asp479 4.31 Mg CG I:Asp479 3.87 Mg OG1 I:Thr521 4.55 Mg OD2 J:Asp497 3.76 Mg CG J:Asp497 4.90 Mg NH2 J:Arg538 3.72 Mg O1 I:Po41580 3.92 Mg O2 I:Po41580 2.09 Mg P I:Po41580 3.46 Mg O4 I:Po41580 4.11 Mg O3 I:Po41580 4.55 Mg O1 I:Po41581 4.52 Mg O2 I:Po41581 3.91 Mg P I:Po41581 3.44 Mg O4 I:Po41581 2.06 Mg O3 I:Po41581 4.05 interactive model: