Sodium in PDB 6ft9: Crystal Structure of CLK1 in Complex with Inhibitor 16

All present enzymatic activity of Crystal Structure of CLK1 in Complex with Inhibitor 16:
2.7.12.1;

The structure of Crystal Structure of CLK1 in Complex with Inhibitor 16, PDB code: 6ft9 was solved by A.Chaikuad, A.Walter, F.Von Delft, C.Bountra, C.H.Arrowsmith, A.M.Edwards, C.Kunick, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.11 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.400, 116.301, 91.330, 90.00, 98.98, 90.00
R / Rfree (%)	16.6 / 20.2

The structure of Crystal Structure of CLK1 in Complex with Inhibitor 16 also contains other interesting chemical elements:

Bromine

(Br)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of CLK1 in Complex with Inhibitor 16 (pdb code 6ft9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of CLK1 in Complex with Inhibitor 16, PDB code: 6ft9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of CLK1 in Complex with Inhibitor 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of CLK1 in Complex with Inhibitor 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:34.5 occ:1.00 O A:ARG346 2.8 28.9 1.0 NE1 A:TRP363 3.0 25.2 1.0 O A:HIS344 3.0 28.0 1.0 CE1 A:HIS387 3.1 29.8 1.0 NE2 A:HIS387 3.1 35.0 1.0 N A:ARG346 3.5 27.0 1.0 CD2 A:PHE379 3.5 28.1 1.0 C A:HIS344 3.6 28.7 1.0 C A:ARG346 3.7 29.6 1.0 C A:TYR345 3.7 26.9 1.0 SG A:CYS367 3.7 26.0 1.0 CE2 A:PHE379 3.9 28.0 1.0 CD1 A:TRP363 3.9 25.4 1.0 CA A:TYR345 3.9 27.5 1.0 CE2 A:TRP363 4.0 26.2 1.0 CE A:MET391 4.0 30.7 1.0 N A:TYR345 4.0 28.1 1.0 O A:ARG343 4.1 36.1 1.0 CA A:ARG346 4.1 29.8 1.0 O A:TYR345 4.3 28.0 1.0 CZ2 A:TRP363 4.3 27.5 1.0 ND1 A:HIS387 4.4 34.7 1.0 CG A:PHE379 4.4 26.3 1.0 CD2 A:HIS387 4.5 33.0 1.0 CA A:HIS344 4.7 31.6 1.0 CB A:PHE379 4.7 29.1 1.0 CB A:ARG346 4.7 35.7 1.0 N A:ALA347 4.7 28.0 1.0 CZ A:PHE379 4.9 27.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of CLK1 in Complex with Inhibitor 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of CLK1 in Complex with Inhibitor 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:35.8 occ:1.00 NE1 B:TRP363 2.9 27.8 1.0 O B:ARG346 2.9 27.4 1.0 O B:HIS344 3.0 32.5 1.0 CE1 B:HIS387 3.1 28.4 1.0 NE2 B:HIS387 3.1 32.4 1.0 CD2 B:PHE379 3.5 27.5 1.0 N B:ARG346 3.5 26.7 1.0 SG B:CYS367 3.6 27.7 1.0 C B:HIS344 3.7 33.2 1.0 C B:TYR345 3.7 27.9 1.0 C B:ARG346 3.7 26.9 1.0 CE2 B:PHE379 3.7 28.3 1.0 CD1 B:TRP363 3.8 25.9 1.0 CA B:TYR345 3.9 26.2 1.0 CE2 B:TRP363 3.9 26.0 1.0 N B:TYR345 4.0 26.3 1.0 CE B:MET391 4.1 32.5 1.0 CA B:ARG346 4.2 29.5 1.0 O B:ARG343 4.2 38.7 1.0 CZ2 B:TRP363 4.3 28.0 1.0 O B:TYR345 4.3 29.2 1.0 CG B:PHE379 4.3 30.1 1.0 ND1 B:HIS387 4.4 31.7 1.0 CD2 B:HIS387 4.5 31.8 1.0 CA B:HIS344 4.8 38.0 1.0 N B:ALA347 4.8 25.8 1.0 CZ B:PHE379 4.8 29.2 1.0 CB B:ARG346 4.8 33.7 1.0 CB B:PHE379 4.8 31.4 1.0 CG B:TRP363 5.0 25.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of CLK1 in Complex with Inhibitor 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of CLK1 in Complex with Inhibitor 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:38.1 occ:1.00 O C:HIS344 2.7 45.7 1.0 NE1 C:TRP363 2.8 25.6 1.0 O C:ARG346 2.9 34.3 1.0 NE2 C:HIS387 3.1 37.6 1.0 CE1 C:HIS387 3.3 38.8 1.0 N C:ARG346 3.6 35.0 1.0 C C:TYR345 3.6 39.0 1.0 SG C:CYS367 3.6 28.8 1.0 C C:HIS344 3.7 53.2 1.0 CD2 C:PHE379 3.7 36.4 1.0 C C:ARG346 3.7 34.9 1.0 CD1 C:TRP363 3.7 24.4 1.0 CA C:TYR345 3.8 37.1 1.0 CE2 C:TRP363 3.8 26.1 1.0 CE2 C:PHE379 3.9 35.0 1.0 N C:TYR345 4.0 38.1 1.0 CE C:MET391 4.1 40.7 1.0 O C:TYR345 4.1 38.8 1.0 CZ2 C:TRP363 4.1 27.1 1.0 CA C:ARG346 4.2 40.4 1.0 CD2 C:HIS387 4.4 39.6 1.0 CG C:PHE379 4.5 38.5 1.0 ND1 C:HIS387 4.6 42.1 1.0 N C:ALA347 4.7 30.7 1.0 CZ C:PHE379 4.8 35.9 1.0 CB C:ARG346 4.9 47.3 1.0 CG C:TRP363 4.9 24.0 1.0 CA C:HIS344 4.9 60.2 1.0 CD2 C:TRP363 5.0 24.8 1.0 CB C:PHE379 5.0 41.0 1.0

A.Walter, A.Chaikuad, R.Helmer, N.Loaec, L.Preu, I.Ott, S.Knapp, L.Meijer, C.Kunick. Molecular Structures of CDC2-Like Kinases in Complex with A New Inhibitor Chemotype. Plos One V. 13 96761 2018.
ISSN: ESSN 1932-6203
PubMed: 29723265
DOI: 10.1371/JOURNAL.PONE.0196761