Sodium in PDB 8p5i: Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51

All present enzymatic activity of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51:
2.7.11.1;

The structure of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51, PDB code: 8p5i was solved by T.Battista, M.S.Semrau, A.Heroux, G.Lolli, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.40 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.47, 109.54, 96.52, 90, 92.84, 90
R / Rfree (%)	16.6 / 18.9

The structure of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Sodium atom in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 (pdb code 8p5i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51, PDB code: 8p5i:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:53.1 occ:1.00 HE1 A:TRP205 2.4 19.6 1.0 HG21 A:THR209 2.6 27.1 0.5 HG23 A:THR209 2.7 27.1 0.5 O A:HOH555 2.8 36.1 1.0 O A:MET186 2.8 25.2 1.0 HG1 A:THR209 2.8 14.2 0.0 O A:HOH408 2.9 28.6 1.0 OG1 A:THR209 3.0 14.2 0.5 CG2 A:THR209 3.0 26.8 0.5 HH A:TYR233 3.1 22.9 0.0 NE1 A:TRP205 3.1 19.6 1.0 HG21 A:THR209 3.1 15.4 0.5 OH A:TYR233 3.3 22.9 1.0 HZ2 A:TRP205 3.3 20.4 1.0 HG22 A:THR209 3.4 15.4 0.5 HB A:THR209 3.5 28.9 0.5 HG2 A:PRO220 3.6 26.8 1.0 HA A:TYR187 3.6 21.1 1.0 CG2 A:THR209 3.6 14.8 0.5 HD2 A:PHE221 3.7 28.0 1.0 CE2 A:TRP205 3.8 18.7 1.0 C A:MET186 3.8 26.6 1.0 CB A:THR209 3.8 27.5 0.5 HG22 A:THR209 3.8 26.8 0.5 CB A:THR209 3.9 16.3 0.5 CZ2 A:TRP205 3.9 21.4 1.0 HD2 A:PRO220 4.0 27.8 1.0 CD1 A:TRP205 4.2 19.5 1.0 HD23 A:LEU229 4.3 30.6 1.0 HB2 A:PHE221 4.3 28.3 1.0 CG A:PRO220 4.3 26.3 1.0 HB A:THR209 4.4 16.2 0.5 CA A:TYR187 4.4 21.0 1.0 HD1 A:TRP205 4.4 19.0 1.0 HG3 A:PRO220 4.5 26.8 1.0 HG3 A:MET186 4.5 49.8 1.0 O A:MET188 4.5 20.3 1.0 HG23 A:THR209 4.5 15.4 0.5 N A:TYR187 4.5 22.0 1.0 OG1 A:THR209 4.5 39.3 0.5 HA A:MET186 4.6 29.7 1.0 CD2 A:PHE221 4.6 28.5 1.0 CD A:PRO220 4.6 27.8 1.0 H A:PHE221 4.6 30.2 1.0 CZ A:TYR233 4.7 24.3 1.0 C A:TYR187 4.7 20.1 1.0 CA A:MET186 4.9 29.4 1.0 HD22 A:LEU259 4.9 21.7 1.0 O A:TYR187 4.9 21.7 1.0 HA A:THR209 5.0 20.1 0.5 HD11 A:LEU229 5.0 29.7 1.0

Sodium binding site 2 out of 3 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:59.5 occ:1.00 HE1 B:TRP205 2.3 24.3 1.0 O B:MET186 2.6 27.4 1.0 HG21 B:THR209 2.7 26.9 0.5 O B:HOH414 2.7 38.6 1.0 HG23 B:THR209 2.7 26.9 0.5 NE1 B:TRP205 3.1 23.9 1.0 HG21 B:THR209 3.1 17.1 0.5 HG1 B:THR209 3.1 18.1 0.0 CG2 B:THR209 3.1 26.9 0.5 OG1 B:THR209 3.1 18.0 0.5 HH B:TYR233 3.2 30.8 0.0 HA B:TYR187 3.2 23.4 1.0 HG22 B:THR209 3.3 17.1 0.5 OH B:TYR233 3.3 30.8 1.0 O B:HOH504 3.4 41.4 1.0 HZ2 B:TRP205 3.4 26.0 1.0 CG2 B:THR209 3.5 16.4 0.5 HB B:THR209 3.5 28.1 0.5 C B:MET186 3.6 26.1 1.0 CE2 B:TRP205 3.8 24.6 1.0 CB B:THR209 3.8 26.6 0.5 O B:HOH484 3.9 42.9 1.0 CB B:THR209 3.9 18.2 0.5 HG22 B:THR209 3.9 26.7 0.5 CZ2 B:TRP205 4.0 26.5 1.0 CA B:TYR187 4.0 22.8 1.0 CD1 B:TRP205 4.1 24.1 1.0 HD23 B:LEU229 4.1 39.2 1.0 HG2 B:PRO220 4.1 31.5 1.0 HD2 B:PHE221 4.2 30.3 1.0 N B:TYR187 4.2 22.3 1.0 HB B:THR209 4.3 18.1 0.5 O B:MET188 4.3 26.4 1.0 HD1 B:TRP205 4.3 23.4 1.0 C B:TYR187 4.3 24.1 1.0 OG1 B:THR209 4.4 38.8 0.5 HD2 B:PRO220 4.4 33.1 1.0 HG23 B:THR209 4.4 17.0 0.5 HA B:MET186 4.5 28.4 1.0 CZ B:TYR233 4.6 33.7 1.0 N B:MET188 4.7 24.8 1.0 H B:MET188 4.7 25.0 1.0 O B:TYR187 4.7 23.4 1.0 CA B:MET186 4.7 27.1 1.0 CG B:PRO220 4.9 30.9 1.0 HG1 B:THR209 4.9 38.2 0.0 HG3 B:PRO220 4.9 31.5 1.0 HD11 B:LEU229 4.9 35.1 1.0 HB2 B:PHE221 5.0 35.1 1.0

Sodium binding site 3 out of 3 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Kinase Domain of Mutant Human ULK1 in Complex with Compound Xmd-17-51 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na304 b:41.0 occ:1.00 O D:MET188 2.6 22.3 1.0 OH D:TYR233 2.7 23.1 1.0 HE2 D:TYR233 2.9 24.4 1.0 HD23 D:LEU229 2.9 30.9 1.0 HE1 D:TRP205 3.0 19.0 1.0 O D:HOH501 3.0 43.1 1.0 O D:PRO185 3.1 27.7 1.0 HH D:TYR233 3.2 23.0 0.0 HD21 D:LEU229 3.3 30.9 1.0 O D:MET186 3.3 26.1 1.0 H D:MET188 3.4 22.7 1.0 C D:MET186 3.5 26.5 1.0 CZ D:TYR233 3.5 24.1 1.0 CD2 D:LEU229 3.5 31.7 1.0 CE2 D:TYR233 3.5 24.1 1.0 C D:MET188 3.6 23.4 1.0 N D:MET188 3.6 23.4 1.0 HA D:MET186 3.7 29.9 1.0 NE1 D:TRP205 3.7 18.9 1.0 HB2 D:MET188 3.8 25.5 1.0 N D:TYR187 4.0 24.1 1.0 C D:TYR187 4.1 21.1 1.0 CA D:MET188 4.1 22.2 1.0 HZ2 D:TRP205 4.1 19.8 1.0 HA D:TYR187 4.1 23.5 1.0 CA D:MET186 4.1 28.9 1.0 C D:PRO185 4.2 29.1 1.0 HD22 D:LEU229 4.2 31.0 1.0 HD11 D:LEU229 4.3 30.0 1.0 CA D:TYR187 4.3 24.3 1.0 HG D:LEU229 4.3 29.7 1.0 CB D:MET188 4.4 25.4 1.0 CG D:LEU229 4.5 28.9 1.0 CE2 D:TRP205 4.5 19.6 1.0 H D:TYR187 4.5 24.8 1.0 HG21 D:THR209 4.6 26.6 0.5 CD1 D:TRP205 4.6 18.3 1.0 CZ2 D:TRP205 4.6 19.9 1.0 O D:HOH534 4.7 38.9 1.0 O D:TYR187 4.7 20.7 1.0 N D:MET186 4.7 30.6 1.0 HD12 D:ILE193 4.7 31.1 1.0 HG23 D:ILE193 4.7 26.0 1.0 HD1 D:TRP205 4.7 18.7 1.0 N D:ALA189 4.8 20.7 1.0 HA D:ALA189 4.8 20.3 1.0 HB3 D:MET188 4.8 25.5 1.0 CE1 D:TYR233 4.9 23.7 1.0 CD2 D:TYR233 4.9 25.0 1.0 HD3 D:PRO190 4.9 22.3 1.0 CD1 D:LEU229 4.9 30.4 1.0

T.Battista, M.S.Semrau, G.Lolli, P.Storici. Crystal Structures of ULK1 in Complex with Kcgs Compounds To Be Published.