Magnesium in the structure of Human K-Ras in Complex With A Gtp Analogue (pdb 3gft)

The binding sites of Magnesium atom in the structure of Human K-Ras in Complex With A Gtp Analogue (pdb code 3gft). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3gft structure was solved by Y.TONG, W.TEMPEL, L.SHEN, C.H.ARROWSMITH, A.M.EDWARDS, M.SUNDSTROM, J.WEIGELT, A.BOCHKAREV, H.PARK, STRUCTURALGENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.3 Space group P212121 a (A) 63.535 b (A) 118.275 c (A) 156.836 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 26.7 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 3gft Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3gft. 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: Lys16, A: Ser17, A: Asp33, A: Pro34, A: Thr35, A: Asp57, A: Thr58, A: Gnp201, A: Hoh401, A: Hoh402, A: Hoh435, conact list: Atom Atom Distance (A) Mg CB A:Lys16 4.71 Mg CE A:Lys16 4.99 Mg C A:Lys16 4.76 Mg N A:Ser17 3.77 Mg CB A:Ser17 3.09 Mg OG A:Ser17 2.04 Mg CA A:Ser17 3.91 Mg O A:Asp33 4.32 Mg C A:Pro34 4.82 Mg N A:Thr35 3.92 Mg CB A:Thr35 3.19 Mg CG2 A:Thr35 4.21 Mg OG1 A:Thr35 2.12 Mg CA A:Thr35 4.17 Mg OD2 A:Asp57 3.96 Mg OD1 A:Asp57 4.09 Mg CG A:Asp57 4.42 Mg O A:Thr58 4.32 Mg PG A:Gnp201 3.35 Mg O2G A:Gnp201 2.11 Mg PA A:Gnp201 4.52 Mg O2B A:Gnp201 4.26 Mg O3A A:Gnp201 4.20 Mg N3B A:Gnp201 3.52 Mg O3G A:Gnp201 4.49 Mg O2A A:Gnp201 4.32 Mg O1B A:Gnp201 2.01 Mg PB A:Gnp201 3.24 Mg O1G A:Gnp201 4.21 Mg O1A A:Gnp201 4.62 Mg O A:Hoh401 2.11 Mg O A:Hoh402 2.19 Mg O A:Hoh435 4.94 interactive model: Magnesium binding site 2 out of 6 in 3gft Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3gft. 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: Lys16, B: Ser17, B: Asp33, B: Pro34, B: Thr35, B: Asp57, B: Thr58, B: Gnp201, B: Hoh403, B: Hoh404, conact list: Atom Atom Distance (A) Mg CB B:Lys16 4.81 Mg N B:Ser17 3.97 Mg CB B:Ser17 3.18 Mg OG B:Ser17 2.18 Mg CA B:Ser17 4.10 Mg O B:Asp33 4.14 Mg C B:Pro34 4.72 Mg CA B:Pro34 4.89 Mg N B:Thr35 3.87 Mg CB B:Thr35 3.18 Mg CG2 B:Thr35 4.26 Mg OG1 B:Thr35 2.19 Mg CA B:Thr35 4.15 Mg OD2 B:Asp57 3.99 Mg OD1 B:Asp57 4.29 Mg CG B:Asp57 4.55 Mg O B:Thr58 4.49 Mg PG B:Gnp201 3.19 Mg O2G B:Gnp201 1.87 Mg PA B:Gnp201 4.50 Mg O2B B:Gnp201 4.25 Mg O3A B:Gnp201 4.21 Mg N3B B:Gnp201 3.47 Mg O3G B:Gnp201 4.26 Mg O2A B:Gnp201 4.19 Mg O1B B:Gnp201 1.99 Mg PB B:Gnp201 3.19 Mg O1G B:Gnp201 4.21 Mg O1A B:Gnp201 4.53 Mg O B:Hoh403 2.36 Mg O B:Hoh404 2.16 interactive model: Magnesium binding site 3 out of 6 in 3gft Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3gft. 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: Ser17, C: Asp33, C: Pro34, C: Thr35, C: Asp57, C: Thr58, C: Gnp201, C: Hoh405, conact list: Atom Atom Distance (A) Mg N C:Ser17 4.09 Mg CB C:Ser17 3.17 Mg OG C:Ser17 2.28 Mg CA C:Ser17 4.18 Mg O C:Asp33 4.38 Mg O C:Asp33 4.40 Mg C C:Pro34 4.62 Mg CA C:Pro34 4.80 Mg N C:Thr35 3.84 Mg CB C:Thr35 3.32 Mg CG2 C:Thr35 4.45 Mg OG1 C:Thr35 2.24 Mg CA C:Thr35 4.19 Mg OD2 C:Asp57 4.37 Mg OD1 C:Asp57 4.41 Mg CG C:Asp57 4.67 Mg O C:Thr58 4.51 Mg PG C:Gnp201 3.27 Mg O2G C:Gnp201 2.01 Mg PA C:Gnp201 4.51 Mg O2B C:Gnp201 4.26 Mg O3A C:Gnp201 4.21 Mg N3B C:Gnp201 3.45 Mg O3G C:Gnp201 4.40 Mg O2A C:Gnp201 4.26 Mg O1B C:Gnp201 2.02 Mg PB C:Gnp201 3.20 Mg O1G C:Gnp201 4.24 Mg O1A C:Gnp201 4.56 Mg O C:Hoh405 2.06 interactive model: Magnesium binding site 4 out of 6 in 3gft Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3gft. 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: Lys16, D: Ser17, D: Asp57, D: Thr58, D: Ala59, D: Gnp201, conact list: Atom Atom Distance (A) Mg CB D:Lys16 3.94 Mg CE D:Lys16 4.12 Mg CD D:Lys16 4.92 Mg C D:Lys16 4.53 Mg CG D:Lys16 4.96 Mg CA D:Lys16 4.72 Mg NZ D:Lys16 4.72 Mg N D:Ser17 3.85 Mg CB D:Ser17 3.88 Mg OG D:Ser17 2.76 Mg CA D:Ser17 4.30 Mg CB D:Asp57 4.84 Mg OD2 D:Asp57 3.14 Mg OD1 D:Asp57 3.12 Mg CG D:Asp57 3.45 Mg O D:Thr58 3.21 Mg C D:Thr58 4.31 Mg CA D:Ala59 4.93 Mg PG D:Gnp201 3.41 Mg O2G D:Gnp201 2.20 Mg O2B D:Gnp201 4.09 Mg O3A D:Gnp201 4.72 Mg N3B D:Gnp201 3.85 Mg O3G D:Gnp201 4.72 Mg O1B D:Gnp201 2.23 Mg PB D:Gnp201 3.44 Mg O1G D:Gnp201 3.94 interactive model: Magnesium binding site 5 out of 6 in 3gft Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3gft. 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: Lys16, E: Ser17, E: Asp33, E: Thr35, E: Asp57, E: Thr58, E: Gnp201, conact list: Atom Atom Distance (A) Mg CB E:Lys16 4.52 Mg CE E:Lys16 4.73 Mg C E:Lys16 4.79 Mg N E:Ser17 3.84 Mg CB E:Ser17 3.23 Mg OG E:Ser17 2.15 Mg CA E:Ser17 4.01 Mg O E:Asp33 4.58 Mg N E:Thr35 4.12 Mg CB E:Thr35 3.23 Mg CG2 E:Thr35 4.26 Mg OG1 E:Thr35 2.47 Mg CA E:Thr35 4.31 Mg OD2 E:Asp57 3.79 Mg OD1 E:Asp57 4.01 Mg CG E:Asp57 4.26 Mg O E:Thr58 4.07 Mg PG E:Gnp201 3.00 Mg O2G E:Gnp201 1.77 Mg PA E:Gnp201 4.72 Mg O2B E:Gnp201 4.23 Mg O3A E:Gnp201 4.38 Mg N3B E:Gnp201 3.48 Mg O3G E:Gnp201 4.28 Mg O2A E:Gnp201 4.61 Mg O1B E:Gnp201 2.10 Mg PB E:Gnp201 3.28 Mg O1G E:Gnp201 3.66 Mg O1A E:Gnp201 4.66 interactive model: Magnesium binding site 6 out of 6 in 3gft Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3gft. 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: Ser17, F: Asp57, F: Thr58, F: Gnp201, F: Hoh406, F: Hoh407, conact list: Atom Atom Distance (A) Mg N F:Ser17 4.24 Mg CB F:Ser17 3.30 Mg OG F:Ser17 2.25 Mg CA F:Ser17 4.31 Mg OD2 F:Asp57 4.20 Mg OD1 F:Asp57 4.48 Mg CG F:Asp57 4.76 Mg O F:Thr58 4.56 Mg PG F:Gnp201 3.26 Mg O2G F:Gnp201 1.91 Mg PA F:Gnp201 4.57 Mg O2B F:Gnp201 4.53 Mg O3A F:Gnp201 4.37 Mg N3B F:Gnp201 3.57 Mg O3G F:Gnp201 4.17 Mg O2A F:Gnp201 4.03 Mg O1B F:Gnp201 2.23 Mg PB F:Gnp201 3.43 Mg O1G F:Gnp201 4.39 Mg O1A F:Gnp201 4.72 Mg O F:Hoh406 2.47 Mg O F:Hoh407 1.95 interactive model: