Potassium in the structure of Structure of the Mnme G-Domain in Complex With Gdp*ALF4-, MG2+ and K+ (pdb 2gj8)
The binding sites of Potassium atom in the structure of Structure of the Mnme G-Domain in Complex With Gdp*ALF4-, MG2+ and K+ (pdb code 2gj8). This binding sites where shown with 5.0 Angstroms radius around Potassium atom. The 2gj8 structure was solved by A.SCRIMA, A.WITTINGHOFER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 20.0-1.7 | Space group | P1211 | a (A) | 57.540 | b (A) | 70.227 | c (A) | 91.300 | alpha (°) | 90.00 | beta (°) | 95.51 | gamma (°) | 90.00 | Rfactor (%) | 20.5 | Rfree (%) | 25.6 |
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Potassium Binding Sites:Potassium binding site 1 out of 4 in 2gj8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Potassium in the PDB 2gj8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asn226, A: Thr245, A: Asp246, A: Ile247, A: Ala248, A: Gly249, A: Thr250, A: Alf601, A: Mg602, A: Gdp650, A: Hoh654, | conact list:
Atom | Atom | Distance (A) | K | N A:Asn226 | 4.55 | K | CB A:Asn226 | 4.75 | K | ND2 A:Asn226 | 4.74 | K | OD1 A:Asn226 | 2.66 | K | CG A:Asn226 | 3.86 | K | CA A:Asn226 | 4.39 | K | O A:Thr245 | 2.86 | K | N A:Thr245 | 4.33 | K | OG1 A:Thr245 | 4.43 | K | C A:Thr245 | 3.99 | K | CA A:Thr245 | 4.75 | K | N A:Asp246 | 4.93 | K | C A:Asp246 | 4.69 | K | O A:Ile247 | 2.75 | K | N A:Ile247 | 4.37 | K | C A:Ile247 | 3.71 | K | CA A:Ile247 | 4.63 | K | N A:Ala248 | 4.44 | K | C A:Ala248 | 4.93 | K | CA A:Ala248 | 4.46 | K | N A:Gly249 | 4.77 | K | N A:Thr250 | 4.41 | K | CB A:Thr250 | 3.74 | K | CG2 A:Thr250 | 4.82 | K | OG1 A:Thr250 | 3.35 | K | CA A:Thr250 | 4.73 | K | F4 A:Alf601 | 3.80 | K | F3 A:Alf601 | 4.39 | K | F2 A:Alf601 | 2.58 | K | AL A:Alf601 | 3.69 | K | MG A:Mg602 | 4.97 | K | O3B A:Gdp650 | 4.50 | K | PA A:Gdp650 | 3.77 | K | O2A A:Gdp650 | 2.79 | K | PB A:Gdp650 | 3.92 | K | C5' A:Gdp650 | 3.84 | K | O5' A:Gdp650 | 4.26 | K | O2B A:Gdp650 | 2.98 | K | O3A A:Gdp650 | 3.75 | K | O A:Hoh654 | 3.63 |
| interactive model:
| Potassium binding site 2 out of 4 in 2gj8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Potassium in the PDB 2gj8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asn226, B: Thr245, B: Asp246, B: Ile247, B: Ala248, B: Gly249, B: Thr250, B: Alf611, B: Mg612, B: Gdp651, B: Hoh655, | conact list:
Atom | Atom | Distance (A) | K | N B:Asn226 | 4.43 | K | CB B:Asn226 | 4.69 | K | ND2 B:Asn226 | 4.74 | K | OD1 B:Asn226 | 2.65 | K | CG B:Asn226 | 3.84 | K | CA B:Asn226 | 4.30 | K | O B:Thr245 | 2.82 | K | N B:Thr245 | 4.39 | K | OG1 B:Thr245 | 4.49 | K | C B:Thr245 | 3.91 | K | CA B:Thr245 | 4.74 | K | N B:Asp246 | 4.77 | K | C B:Asp246 | 4.56 | K | CA B:Asp246 | 4.79 | K | O B:Ile247 | 2.91 | K | N B:Ile247 | 4.22 | K | C B:Ile247 | 3.74 | K | CA B:Ile247 | 4.64 | K | N B:Ala248 | 4.42 | K | C B:Ala248 | 4.97 | K | CA B:Ala248 | 4.47 | K | N B:Gly249 | 4.80 | K | N B:Thr250 | 4.36 | K | CB B:Thr250 | 3.64 | K | CG2 B:Thr250 | 4.72 | K | OG1 B:Thr250 | 3.36 | K | CA B:Thr250 | 4.63 | K | F4 B:Alf611 | 2.46 | K | F2 B:Alf611 | 3.62 | K | AL B:Alf611 | 3.60 | K | F1 B:Alf611 | 4.37 | K | MG B:Mg612 | 4.78 | K | O3B B:Gdp651 | 4.54 | K | PA B:Gdp651 | 3.74 | K | O2A B:Gdp651 | 2.72 | K | PB B:Gdp651 | 3.81 | K | C5' B:Gdp651 | 3.84 | K | O5' B:Gdp651 | 4.27 | K | O2B B:Gdp651 | 2.91 | K | O3A B:Gdp651 | 3.56 | K | O B:Hoh655 | 3.69 |
| interactive model:
| Potassium binding site 3 out of 4 in 2gj8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Potassium in the PDB 2gj8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asn226, C: Thr245, C: Asp246, C: Ile247, C: Ala248, C: Gly249, C: Thr250, C: Alf621, C: Mg622, C: Gdp652, C: Hoh654, | conact list:
Atom | Atom | Distance (A) | K | N C:Asn226 | 4.46 | K | CB C:Asn226 | 4.77 | K | ND2 C:Asn226 | 4.73 | K | OD1 C:Asn226 | 2.70 | K | CG C:Asn226 | 3.88 | K | CA C:Asn226 | 4.40 | K | O C:Thr245 | 2.79 | K | N C:Thr245 | 4.39 | K | OG1 C:Thr245 | 4.40 | K | C C:Thr245 | 3.90 | K | CA C:Thr245 | 4.72 | K | N C:Asp246 | 4.79 | K | C C:Asp246 | 4.53 | K | CA C:Asp246 | 4.80 | K | O C:Ile247 | 2.88 | K | N C:Ile247 | 4.22 | K | C C:Ile247 | 3.71 | K | CA C:Ile247 | 4.57 | K | N C:Ala248 | 4.39 | K | C C:Ala248 | 4.92 | K | CA C:Ala248 | 4.46 | K | N C:Gly249 | 4.74 | K | N C:Thr250 | 4.39 | K | CB C:Thr250 | 3.68 | K | CG2 C:Thr250 | 4.76 | K | OG1 C:Thr250 | 3.30 | K | CA C:Thr250 | 4.69 | K | F4 C:Alf621 | 2.60 | K | F2 C:Alf621 | 3.68 | K | AL C:Alf621 | 3.60 | K | F1 C:Alf621 | 4.28 | K | MG C:Mg622 | 4.98 | K | O3B C:Gdp652 | 2.98 | K | PA C:Gdp652 | 3.84 | K | O2A C:Gdp652 | 2.93 | K | O1B C:Gdp652 | 4.55 | K | PB C:Gdp652 | 3.90 | K | C5' C:Gdp652 | 3.96 | K | O5' C:Gdp652 | 4.37 | K | O3A C:Gdp652 | 3.69 | K | O C:Hoh654 | 3.76 |
| interactive model:
| Potassium binding site 4 out of 4 in 2gj8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Potassium in the PDB 2gj8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asn226, D: Thr245, D: Asp246, D: Ile247, D: Ala248, D: Gly249, D: Thr250, D: Alf631, D: Mg632, D: Gdp653, D: Hoh658, | conact list:
Atom | Atom | Distance (A) | K | N D:Asn226 | 4.46 | K | CB D:Asn226 | 4.76 | K | ND2 D:Asn226 | 4.68 | K | OD1 D:Asn226 | 2.69 | K | CG D:Asn226 | 3.85 | K | CA D:Asn226 | 4.38 | K | O D:Thr245 | 2.75 | K | N D:Thr245 | 4.45 | K | OG1 D:Thr245 | 4.46 | K | C D:Thr245 | 3.91 | K | CA D:Thr245 | 4.75 | K | N D:Asp246 | 4.78 | K | C D:Asp246 | 4.51 | K | CA D:Asp246 | 4.71 | K | O D:Ile247 | 2.83 | K | N D:Ile247 | 4.23 | K | C D:Ile247 | 3.71 | K | CA D:Ile247 | 4.56 | K | N D:Ala248 | 4.42 | K | CA D:Ala248 | 4.47 | K | N D:Gly249 | 4.77 | K | N D:Thr250 | 4.44 | K | CB D:Thr250 | 3.78 | K | CG2 D:Thr250 | 4.83 | K | OG1 D:Thr250 | 3.31 | K | CA D:Thr250 | 4.76 | K | F4 D:Alf631 | 3.75 | K | F3 D:Alf631 | 4.33 | K | F2 D:Alf631 | 2.55 | K | AL D:Alf631 | 3.57 | K | MG D:Mg632 | 4.98 | K | O3B D:Gdp653 | 4.46 | K | PA D:Gdp653 | 3.77 | K | O2A D:Gdp653 | 2.94 | K | PB D:Gdp653 | 3.87 | K | C5' D:Gdp653 | 3.86 | K | C4' D:Gdp653 | 4.99 | K | O5' D:Gdp653 | 4.36 | K | O2B D:Gdp653 | 2.88 | K | O3A D:Gdp653 | 3.62 | K | O D:Hoh658 | 3.73 |
| interactive model:
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