Magnesium in the structure of The Crystal Structure Of The Human RAC3 in Complex With the Crib Domain of Human P21-Activated Kinase 4 (PAK4) (pdb 2ov2)

The binding sites of Magnesium atom in the structure of The Crystal Structure Of The Human RAC3 in Complex With the Crib Domain of Human P21-Activated Kinase 4 (PAK4) (pdb code 2ov2). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2ov2 structure was solved by E.UGOCHUKWU, X.YANG, J.M.ELKINS, N.BURGESS-BROWN, G.BUNKOCZI, J.E.D.DEBRECZENI, M.SUNDSTROM, C.H.ARROWSMITH, J.WEIGELT, A.EDWARDS, F.VON DELFT, S.KNAPP, D.A.DOYLE, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 62.1-2.1 Space group P1 a (A) 50.843 b (A) 73.859 c (A) 133.840 alpha (°) 88.58 beta (°) 87.76 gamma (°) 70.64 Rfactor (%) 17.2 Rfree (%) 22.5 Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2ov2. 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: Thr17, A: Ile33, A: Pro34, A: Thr35, A: Asp57, A: Thr58, A: Gcp200, A: Hoh1222, A: Hoh1250, A: Hoh1301, A: Hoh1311, conact list: Atom Atom Distance (A) Mg CB A:Lys16 4.92 Mg C A:Lys16 4.97 Mg N A:Thr17 3.88 Mg CB A:Thr17 3.15 Mg CG2 A:Thr17 4.23 Mg OG1 A:Thr17 2.12 Mg CA A:Thr17 4.06 Mg O A:Ile33 4.53 Mg C A:Pro34 4.69 Mg CA A:Pro34 4.85 Mg N A:Thr35 3.79 Mg CB A:Thr35 3.20 Mg CG2 A:Thr35 4.29 Mg OG1 A:Thr35 2.18 Mg CA A:Thr35 4.13 Mg OD2 A:Asp57 4.17 Mg OD1 A:Asp57 4.16 Mg CG A:Asp57 4.54 Mg O A:Thr58 4.73 Mg PG A:Gcp200 3.30 Mg O2G A:Gcp200 4.09 Mg PA A:Gcp200 4.50 Mg O2B A:Gcp200 2.04 Mg O3A A:Gcp200 4.34 Mg O3G A:Gcp200 4.43 Mg O2A A:Gcp200 4.06 Mg O1B A:Gcp200 4.40 Mg C3B A:Gcp200 3.56 Mg PB A:Gcp200 3.28 Mg O1G A:Gcp200 1.97 Mg O1A A:Gcp200 4.68 Mg O A:Hoh1222 2.20 Mg O A:Hoh1250 2.06 Mg O A:Hoh1301 4.11 Mg O A:Hoh1311 4.98 interactive model: Magnesium binding site 2 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2ov2. 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: Lys16, F: Thr17, F: Ile33, F: Pro34, F: Thr35, F: Asp57, F: Thr58, F: Gcp200, F: Hoh1302, F: Hoh1334, F: Hoh1361, conact list: Atom Atom Distance (A) Mg CB F:Lys16 4.93 Mg N F:Thr17 4.01 Mg CB F:Thr17 3.30 Mg CG2 F:Thr17 4.35 Mg OG1 F:Thr17 2.15 Mg CA F:Thr17 4.20 Mg O F:Ile33 4.70 Mg C F:Pro34 4.57 Mg CA F:Pro34 4.72 Mg N F:Thr35 3.76 Mg CB F:Thr35 3.12 Mg CG2 F:Thr35 4.24 Mg OG1 F:Thr35 2.19 Mg CA F:Thr35 4.07 Mg OD2 F:Asp57 3.96 Mg OD1 F:Asp57 4.17 Mg CG F:Asp57 4.45 Mg O F:Thr58 4.48 Mg PG F:Gcp200 3.21 Mg O2G F:Gcp200 1.91 Mg PA F:Gcp200 4.62 Mg O2B F:Gcp200 4.30 Mg O3A F:Gcp200 4.45 Mg O3G F:Gcp200 3.99 Mg O2A F:Gcp200 4.74 Mg O1B F:Gcp200 2.14 Mg C3B F:Gcp200 3.54 Mg PB F:Gcp200 3.30 Mg O1G F:Gcp200 4.40 Mg O1A F:Gcp200 4.26 Mg O F:Hoh1302 2.14 Mg O F:Hoh1334 2.04 Mg O F:Hoh1361 4.60 interactive model: Magnesium binding site 3 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2ov2. 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: Thr17, B: Ile33, B: Pro34, B: Thr35, B: Asp57, B: Thr58, B: Gcp200, B: Hoh1215, B: Hoh1220, B: Hoh1253, conact list: Atom Atom Distance (A) Mg CB B:Lys16 4.83 Mg C B:Lys16 4.96 Mg N B:Thr17 3.94 Mg CB B:Thr17 3.23 Mg CG2 B:Thr17 4.27 Mg OG1 B:Thr17 2.07 Mg CA B:Thr17 4.15 Mg O B:Ile33 4.63 Mg C B:Pro34 4.65 Mg CA B:Pro34 4.85 Mg N B:Thr35 3.74 Mg CB B:Thr35 3.05 Mg CG2 B:Thr35 4.19 Mg OG1 B:Thr35 2.10 Mg CA B:Thr35 4.01 Mg OD2 B:Asp57 4.18 Mg OD1 B:Asp57 4.09 Mg CG B:Asp57 4.48 Mg O B:Thr58 4.53 Mg PG B:Gcp200 3.24 Mg O2G B:Gcp200 4.42 Mg PA B:Gcp200 4.55 Mg O2B B:Gcp200 1.95 Mg O3A B:Gcp200 4.36 Mg O3G B:Gcp200 3.95 Mg O2A B:Gcp200 4.13 Mg O1B B:Gcp200 4.18 Mg C3B B:Gcp200 3.52 Mg PB B:Gcp200 3.19 Mg O1G B:Gcp200 2.02 Mg O1A B:Gcp200 4.61 Mg O B:Hoh1215 4.32 Mg O B:Hoh1220 2.28 Mg O B:Hoh1253 1.98 interactive model: Magnesium binding site 4 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2ov2. 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: Lys16, C: Thr17, C: Ile33, C: Pro34, C: Thr35, C: Asp57, C: Thr58, C: Gcp200, C: Hoh1308, C: Hoh1356, C: Hoh1360, conact list: Atom Atom Distance (A) Mg CB C:Lys16 4.83 Mg CE C:Lys16 4.85 Mg C C:Lys16 4.85 Mg N C:Thr17 3.84 Mg CB C:Thr17 3.13 Mg CG2 C:Thr17 4.18 Mg OG1 C:Thr17 2.01 Mg CA C:Thr17 4.04 Mg O C:Ile33 4.74 Mg C C:Pro34 4.74 Mg N C:Thr35 3.78 Mg CB C:Thr35 3.06 Mg CG2 C:Thr35 4.10 Mg OG1 C:Thr35 2.00 Mg CA C:Thr35 4.03 Mg OD2 C:Asp57 4.09 Mg OD1 C:Asp57 4.01 Mg CG C:Asp57 4.41 Mg O C:Thr58 4.49 Mg PG C:Gcp200 3.27 Mg O2G C:Gcp200 4.47 Mg PA C:Gcp200 4.63 Mg O2B C:Gcp200 4.38 Mg O3A C:Gcp200 4.36 Mg O3G C:Gcp200 2.03 Mg O2A C:Gcp200 4.73 Mg O1B C:Gcp200 2.09 Mg C3B C:Gcp200 3.56 Mg PB C:Gcp200 3.28 Mg O1G C:Gcp200 3.94 Mg O1A C:Gcp200 4.33 Mg O C:Hoh1308 2.12 Mg O C:Hoh1356 4.00 Mg O C:Hoh1360 2.17 interactive model: Magnesium binding site 5 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2ov2. 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: Lys16, G: Thr17, G: Ile33, G: Pro34, G: Thr35, G: Asp57, G: Thr58, G: Gcp200, G: Hoh236, G: Hoh249, G: Hoh252, G: Hoh269, conact list: Atom Atom Distance (A) Mg CB G:Lys16 4.94 Mg N G:Thr17 4.02 Mg CB G:Thr17 3.15 Mg CG2 G:Thr17 4.18 Mg OG1 G:Thr17 2.08 Mg CA G:Thr17 4.11 Mg O G:Ile33 4.59 Mg C G:Pro34 4.55 Mg CA G:Pro34 4.84 Mg N G:Thr35 3.65 Mg CB G:Thr35 3.05 Mg CG2 G:Thr35 4.19 Mg OG1 G:Thr35 1.98 Mg CA G:Thr35 3.93 Mg OD2 G:Asp57 4.03 Mg OD1 G:Asp57 3.89 Mg CG G:Asp57 4.33 Mg O G:Thr58 4.42 Mg PG G:Gcp200 3.38 Mg O2G G:Gcp200 4.49 Mg PA G:Gcp200 4.78 Mg O2B G:Gcp200 4.52 Mg O3A G:Gcp200 4.61 Mg O3G G:Gcp200 2.11 Mg O2A G:Gcp200 4.91 Mg O1B G:Gcp200 2.14 Mg C3B G:Gcp200 3.84 Mg PB G:Gcp200 3.49 Mg O1G G:Gcp200 4.13 Mg O1A G:Gcp200 4.31 Mg O G:Hoh236 2.05 Mg O G:Hoh249 2.15 Mg O G:Hoh252 4.91 Mg O G:Hoh269 4.08 interactive model: Magnesium binding site 6 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2ov2. 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: Thr17, D: Ile33, D: Pro34, D: Thr35, D: Asp57, D: Thr58, D: Gcp200, D: Hoh1317, D: Hoh1328, D: Hoh1374, conact list: Atom Atom Distance (A) Mg CB D:Lys16 4.80 Mg C D:Lys16 4.93 Mg N D:Thr17 3.86 Mg CB D:Thr17 3.12 Mg CG2 D:Thr17 4.22 Mg OG1 D:Thr17 2.14 Mg CA D:Thr17 4.07 Mg O D:Ile33 4.51 Mg C D:Pro34 4.67 Mg CA D:Pro34 4.85 Mg N D:Thr35 3.79 Mg CB D:Thr35 3.22 Mg CG2 D:Thr35 4.35 Mg OG1 D:Thr35 2.18 Mg CA D:Thr35 4.11 Mg OD2 D:Asp57 4.17 Mg OD1 D:Asp57 4.09 Mg CG D:Asp57 4.53 Mg O D:Thr58 4.59 Mg PG D:Gcp200 3.22 Mg O2G D:Gcp200 2.00 Mg PA D:Gcp200 4.36 Mg O2B D:Gcp200 4.23 Mg O3A D:Gcp200 4.24 Mg O3G D:Gcp200 4.35 Mg O2A D:Gcp200 4.47 Mg O1B D:Gcp200 1.96 Mg C3B D:Gcp200 3.41 Mg PB D:Gcp200 3.15 Mg O1G D:Gcp200 4.01 Mg O1A D:Gcp200 3.88 Mg O D:Hoh1317 2.23 Mg O D:Hoh1328 2.11 Mg O D:Hoh1374 4.28 interactive model: Magnesium binding site 7 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 2ov2. 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: Thr17, E: Ile33, E: Pro34, E: Thr35, E: Asp57, E: Thr58, E: Gcp200, E: Hoh1218, E: Hoh1242, E: Hoh1249, conact list: Atom Atom Distance (A) Mg CB E:Lys16 4.78 Mg C E:Lys16 4.93 Mg NZ E:Lys16 4.98 Mg N E:Thr17 3.86 Mg CB E:Thr17 3.13 Mg CG2 E:Thr17 4.21 Mg OG1 E:Thr17 2.07 Mg CA E:Thr17 4.06 Mg O E:Ile33 4.53 Mg C E:Pro34 4.63 Mg CA E:Pro34 4.79 Mg N E:Thr35 3.83 Mg CB E:Thr35 3.28 Mg CG2 E:Thr35 4.41 Mg OG1 E:Thr35 2.23 Mg CA E:Thr35 4.18 Mg OD2 E:Asp57 4.13 Mg OD1 E:Asp57 4.14 Mg CG E:Asp57 4.51 Mg O E:Thr58 4.54 Mg PG E:Gcp200 3.21 Mg O2G E:Gcp200 4.09 Mg PA E:Gcp200 4.52 Mg O2B E:Gcp200 4.35 Mg O3A E:Gcp200 4.32 Mg O3G E:Gcp200 1.91 Mg O2A E:Gcp200 4.73 Mg O1B E:Gcp200 2.09 Mg C3B E:Gcp200 3.55 Mg PB E:Gcp200 3.27 Mg O1G E:Gcp200 4.35 Mg O1A E:Gcp200 4.13 Mg O E:Hoh1218 4.17 Mg O E:Hoh1242 2.11 Mg O E:Hoh1249 2.12 interactive model: Magnesium binding site 8 out of 8 in 2ov2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 2ov2. 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: Lys16, H: Thr17, H: Ile33, H: Pro34, H: Thr35, H: Asp57, H: Thr58, H: Gcp200, H: Hoh217, H: Hoh263, conact list: Atom Atom Distance (A) Mg CB H:Lys16 4.82 Mg CE H:Lys16 5.00 Mg C H:Lys16 4.94 Mg N H:Thr17 3.91 Mg CB H:Thr17 3.24 Mg CG2 H:Thr17 4.34 Mg OG1 H:Thr17 2.22 Mg CA H:Thr17 4.13 Mg O H:Ile33 4.67 Mg C H:Pro34 4.62 Mg CA H:Pro34 4.80 Mg N H:Thr35 3.73 Mg CB H:Thr35 3.18 Mg CG2 H:Thr35 4.31 Mg OG1 H:Thr35 2.11 Mg CA H:Thr35 4.07 Mg OD2 H:Asp57 4.18 Mg OD1 H:Asp57 4.21 Mg CG H:Asp57 4.57 Mg O H:Thr58 4.61 Mg PG H:Gcp200 3.17 Mg O2G H:Gcp200 3.99 Mg PA H:Gcp200 4.54 Mg O2B H:Gcp200 1.88 Mg O3A H:Gcp200 4.34 Mg O3G H:Gcp200 4.33 Mg O2A H:Gcp200 4.76 Mg O1B H:Gcp200 4.25 Mg C3B H:Gcp200 3.46 Mg PB H:Gcp200 3.19 Mg O1G H:Gcp200 1.93 Mg O1A H:Gcp200 3.94 Mg O H:Hoh217 2.17 Mg O H:Hoh263 2.09 interactive model: