Magnesium in the structure of Crystal Structure Of The Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein (pdb 3k0f)

The binding sites of Magnesium atom in the structure of Crystal Structure Of The Phosphorylation-Site Double Mutant T426A/T432A of the Kaic Circadian Clock Protein (pdb code 3k0f). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3k0f structure was solved by R.PATTANAYEK, M.EGLI, S.PATTANAYEK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-3.0 Space group P212121 a (A) 132.927 b (A) 135.415 c (A) 205.618 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.9 Rfree (%) 28.8 Magnesium Binding Sites: Magnesium binding site 1 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3k0f. 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: Thr295, A: Glu318, A: Glu319, A: Asp378, B: Ala432, B: Arg459, A: Atp901, A: Hoh523, A: Hoh541, conact list: Atom Atom Distance (A) Mg CB A:Thr295 3.87 Mg CG2 A:Thr295 4.53 Mg OG1 A:Thr295 2.67 Mg OE1 A:Glu318 3.19 Mg OE2 A:Glu318 4.84 Mg CD A:Glu318 4.25 Mg OE2 A:Glu319 3.73 Mg CD A:Glu319 4.52 Mg CG A:Glu319 4.86 Mg OD2 A:Asp378 4.79 Mg OD1 A:Asp378 4.90 Mg CB B:Ala432 4.99 Mg CZ B:Arg459 4.15 Mg NE B:Arg459 3.98 Mg NH2 B:Arg459 3.45 Mg PG A:Atp901 2.30 Mg O3B A:Atp901 2.28 Mg O2G A:Atp901 2.34 Mg PA A:Atp901 4.30 Mg O2B A:Atp901 4.59 Mg O3A A:Atp901 3.14 Mg O3G A:Atp901 2.32 Mg O2A A:Atp901 4.18 Mg O1B A:Atp901 3.98 Mg PB A:Atp901 3.34 Mg O1G A:Atp901 3.78 Mg O A:Hoh523 3.08 Mg O A:Hoh541 4.33 interactive model: Magnesium binding site 2 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3k0f. 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: Lys52, A: Thr53, A: Asp145, A: Thr181, B: Arg226, A: Atp903, conact list: Atom Atom Distance (A) Mg CB A:Lys52 4.16 Mg CE A:Lys52 4.41 Mg CD A:Lys52 4.86 Mg C A:Lys52 4.78 Mg NZ A:Lys52 4.17 Mg N A:Thr53 3.74 Mg CB A:Thr53 3.63 Mg CG2 A:Thr53 4.60 Mg OG1 A:Thr53 2.26 Mg CA A:Thr53 4.11 Mg OD2 A:Asp145 3.35 Mg OD1 A:Asp145 3.86 Mg CG A:Asp145 4.00 Mg CG2 A:Thr181 4.19 Mg NH2 B:Arg226 4.74 Mg PG A:Atp903 3.01 Mg O3B A:Atp903 2.83 Mg O2G A:Atp903 2.24 Mg O3A A:Atp903 4.00 Mg O3G A:Atp903 4.31 Mg O1B A:Atp903 4.37 Mg PB A:Atp903 4.00 Mg O1G A:Atp903 3.82 interactive model: Magnesium binding site 3 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3k0f. 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: Lys294, B: Thr295, B: Glu318, B: Glu319, B: Asp378, B: Thr413, B: Thr415, C: Arg459, B: Atp901, conact list: Atom Atom Distance (A) Mg CB B:Lys294 4.79 Mg CE B:Lys294 4.17 Mg NZ B:Lys294 4.21 Mg N B:Thr295 4.28 Mg CB B:Thr295 3.87 Mg CG2 B:Thr295 4.72 Mg OG1 B:Thr295 2.45 Mg CA B:Thr295 4.54 Mg OE1 B:Glu318 2.87 Mg OE2 B:Glu318 4.81 Mg CD B:Glu318 4.11 Mg OE2 B:Glu319 4.74 Mg OD2 B:Asp378 4.76 Mg OD1 B:Asp378 4.07 Mg CG B:Asp378 4.68 Mg CG2 B:Thr413 4.53 Mg OG1 B:Thr415 4.72 Mg NH2 C:Arg459 4.48 Mg PG B:Atp901 2.84 Mg O3B B:Atp901 2.50 Mg O2G B:Atp901 2.25 Mg O3A B:Atp901 3.94 Mg O3G B:Atp901 3.67 Mg O1B B:Atp901 3.99 Mg PB B:Atp901 3.72 Mg O1G B:Atp901 4.10 interactive model: Magnesium binding site 4 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3k0f. 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: Thr295, C: Glu318, C: Glu319, C: Asp378, D: Arg459, C: Atp901, C: Hoh541, conact list: Atom Atom Distance (A) Mg N C:Thr295 4.58 Mg CB C:Thr295 3.59 Mg CG2 C:Thr295 4.48 Mg OG1 C:Thr295 2.55 Mg CA C:Thr295 4.68 Mg OE1 C:Glu318 3.50 Mg CD C:Glu318 4.74 Mg OE2 C:Glu319 4.14 Mg CD C:Glu319 4.93 Mg OD1 C:Asp378 4.55 Mg CZ D:Arg459 4.93 Mg NE D:Arg459 4.75 Mg NH2 D:Arg459 4.21 Mg PG C:Atp901 2.83 Mg O3B C:Atp901 2.40 Mg O2G C:Atp901 2.32 Mg PA C:Atp901 4.58 Mg O2B C:Atp901 4.73 Mg O3A C:Atp901 3.22 Mg O3G C:Atp901 3.63 Mg O2A C:Atp901 4.65 Mg O1B C:Atp901 3.62 Mg PB C:Atp901 3.32 Mg O1G C:Atp901 4.10 Mg O C:Hoh541 3.57 interactive model: Magnesium binding site 5 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3k0f. 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: Lys52, B: Thr53, B: Glu78, B: Asp145, B: Ser146, B: Thr181, C: Arg226, B: Atp903, conact list: Atom Atom Distance (A) Mg CB B:Lys52 4.64 Mg CE B:Lys52 4.79 Mg CD B:Lys52 4.88 Mg NZ B:Lys52 4.26 Mg N B:Thr53 4.38 Mg CB B:Thr53 4.08 Mg CG2 B:Thr53 4.95 Mg OG1 B:Thr53 2.67 Mg CA B:Thr53 4.64 Mg OE2 B:Glu78 4.56 Mg OD2 B:Asp145 3.40 Mg OD1 B:Asp145 3.83 Mg CG B:Asp145 4.01 Mg CB B:Ser146 4.98 Mg CG2 B:Thr181 4.28 Mg NH2 C:Arg226 4.77 Mg PG B:Atp903 3.14 Mg O3B B:Atp903 2.93 Mg O2G B:Atp903 2.36 Mg O3A B:Atp903 4.28 Mg O3G B:Atp903 4.41 Mg O1B B:Atp903 4.40 Mg PB B:Atp903 4.14 Mg O1G B:Atp903 3.95 interactive model: Magnesium binding site 6 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3k0f. 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: Thr295, D: Glu318, D: Glu319, E: Arg459, D: Atp901, D: Hoh524, conact list: Atom Atom Distance (A) Mg N D:Thr295 4.89 Mg CB D:Thr295 3.63 Mg CG2 D:Thr295 4.38 Mg OG1 D:Thr295 2.80 Mg CA D:Thr295 4.89 Mg OE1 D:Glu318 4.27 Mg OE2 D:Glu319 3.63 Mg CD D:Glu319 4.58 Mg CZ E:Arg459 4.48 Mg NE E:Arg459 4.07 Mg NH2 E:Arg459 3.93 Mg PG D:Atp901 2.45 Mg O3B D:Atp901 2.33 Mg O2G D:Atp901 2.30 Mg PA D:Atp901 4.16 Mg O2B D:Atp901 4.46 Mg O3A D:Atp901 2.91 Mg O3G D:Atp901 2.64 Mg O2A D:Atp901 4.17 Mg O1B D:Atp901 3.81 Mg PB D:Atp901 3.16 Mg O1G D:Atp901 3.92 Mg O D:Hoh524 3.07 interactive model: Magnesium binding site 7 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3k0f. 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: Lys52, C: Thr53, C: Glu78, C: Asp145, C: Thr181, D: Arg226, C: Atp903, conact list: Atom Atom Distance (A) Mg CB C:Lys52 4.91 Mg CE C:Lys52 4.68 Mg NZ C:Lys52 4.68 Mg N C:Thr53 4.34 Mg CB C:Thr53 3.87 Mg CG2 C:Thr53 4.59 Mg OG1 C:Thr53 2.44 Mg CA C:Thr53 4.51 Mg OE2 C:Glu78 4.07 Mg OD2 C:Asp145 3.47 Mg OD1 C:Asp145 3.70 Mg CG C:Asp145 3.94 Mg CG2 C:Thr181 4.58 Mg NH2 D:Arg226 4.91 Mg PG C:Atp903 3.13 Mg O3B C:Atp903 3.00 Mg O2G C:Atp903 2.26 Mg O3A C:Atp903 4.08 Mg O3G C:Atp903 4.40 Mg O1B C:Atp903 4.44 Mg PB C:Atp903 4.11 Mg O1G C:Atp903 3.94 interactive model: Magnesium binding site 8 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3k0f. 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: Thr295, E: Glu318, E: Glu319, F: Lys457, F: Arg459, E: Atp901, E: Hoh553, F: Hoh526, conact list: Atom Atom Distance (A) Mg N E:Thr295 4.91 Mg CB E:Thr295 3.65 Mg CG2 E:Thr295 4.38 Mg OG1 E:Thr295 2.85 Mg CA E:Thr295 4.89 Mg OE1 E:Glu318 3.94 Mg CD E:Glu318 4.91 Mg OE2 E:Glu319 3.67 Mg CD E:Glu319 4.48 Mg CG E:Glu319 4.89 Mg NZ F:Lys457 4.81 Mg CZ F:Arg459 4.44 Mg NE F:Arg459 4.09 Mg NH2 F:Arg459 3.95 Mg PG E:Atp901 2.42 Mg O3B E:Atp901 2.46 Mg O2G E:Atp901 2.34 Mg PA E:Atp901 4.02 Mg O5' E:Atp901 4.78 Mg O2B E:Atp901 4.55 Mg O3A E:Atp901 2.93 Mg O3G E:Atp901 2.40 Mg O2A E:Atp901 3.92 Mg O1B E:Atp901 4.01 Mg PB E:Atp901 3.31 Mg O1G E:Atp901 3.90 Mg O E:Hoh553 4.75 Mg O F:Hoh526 2.66 interactive model: Magnesium binding site 9 out of 9 in 3k0f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 3k0f. 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: Arg459, F: Thr295, F: Glu318, F: Glu319, F: Asp378, F: Atp901, F: Hoh523, conact list: Atom Atom Distance (A) Mg CZ A:Arg459 4.40 Mg NE A:Arg459 4.14 Mg NH2 A:Arg459 3.88 Mg N F:Thr295 4.93 Mg CB F:Thr295 3.59 Mg CG2 F:Thr295 4.23 Mg OG1 F:Thr295 2.59 Mg CA F:Thr295 4.84 Mg OE1 F:Glu318 3.75 Mg CD F:Glu318 4.70 Mg OE2 F:Glu319 4.25 Mg CD F:Glu319 4.84 Mg OD1 F:Asp378 5.00 Mg PG F:Atp901 2.38 Mg O3B F:Atp901 2.57 Mg O2G F:Atp901 2.32 Mg PA F:Atp901 4.24 Mg O2B F:Atp901 4.70 Mg O3A F:Atp901 3.20 Mg O3G F:Atp901 2.22 Mg O2A F:Atp901 4.01 Mg O1B F:Atp901 4.29 Mg PB F:Atp901 3.53 Mg O1G F:Atp901 3.86 Mg O F:Hoh523 4.54 interactive model: