Sodium in PDB 6ru8: Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide

All present enzymatic activity of Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide:
2.7.11.1; 2.7.11.26;

The structure of Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide, PDB code: 6ru8 was solved by A.Chaikuad, M.Tuppi, J.Gebel, C.H.Arrowsmith, A.M.Edwards, C.Bountra, V.Dotsch, 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)	48.84 / 1.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.727, 84.131, 89.287, 108.60, 105.83, 91.57
R / Rfree (%)	17.2 / 21.1

The binding sites of Sodium atom in the Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide (pdb code 6ru8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide, PDB code: 6ru8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide


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 Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:47.9 occ:1.00 OD1 A:ASN143 2.2 41.3 1.0 O A:HOH523 2.2 47.9 1.0 O A:TYR286 2.3 34.6 1.0 O A:HOH422 2.4 49.0 1.0 OD1 A:ASN291 2.5 32.6 1.0 CG A:ASN291 3.2 34.8 1.0 CG A:ASN143 3.3 37.8 1.0 O A:HOH468 3.4 49.6 1.0 C A:TYR286 3.4 33.6 1.0 ND2 A:ASN291 3.5 33.4 1.0 CD2 A:PHE288 3.8 29.2 1.0 ND2 A:ASN143 3.9 39.3 1.0 CB A:TYR286 4.1 39.6 1.0 CA A:VAL287 4.2 33.8 1.0 N A:VAL287 4.3 33.7 1.0 CE2 A:PHE288 4.3 30.1 1.0 CB A:ASN291 4.4 36.0 1.0 N A:PHE288 4.4 26.7 1.0 CA A:TYR286 4.4 36.6 1.0 CB A:ASN143 4.5 35.0 1.0 CA A:ASN143 4.7 32.3 1.0 O A:GLY142 4.8 32.7 1.0 O1 A:EDO303 4.8 43.5 1.0 C A:VAL287 4.9 33.2 1.0 CG A:PHE288 4.9 28.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide


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 Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:42.8 occ:1.00 OD1 B:ASN143 2.0 36.4 1.0 O B:TYR286 2.3 36.5 1.0 OD1 B:ASN291 2.6 33.4 1.0 O B:HOH528 3.0 55.5 1.0 CG B:ASN143 3.1 35.9 1.0 CG B:ASN291 3.3 31.8 1.0 C B:TYR286 3.4 34.5 1.0 ND2 B:ASN291 3.6 31.6 1.0 ND2 B:ASN143 3.7 35.2 1.0 CD2 B:PHE288 3.8 29.8 1.0 CB B:TYR286 4.0 41.2 1.0 CE2 B:PHE288 4.2 30.2 1.0 N B:VAL287 4.3 33.0 1.0 CB B:ASN143 4.3 31.5 1.0 CA B:VAL287 4.3 32.1 1.0 CA B:TYR286 4.4 38.9 1.0 N B:PHE288 4.5 27.8 1.0 CB B:ASN291 4.6 32.7 1.0 CA B:ASN143 4.6 29.3 1.0 O B:GLY142 4.7 33.4 1.0 CG B:PHE288 4.9 26.1 1.0

A.Chaikuad, M.Tuppi, J.Gebel, C.H.Arrowsmith, A.M.Edwards, C.Bountra, V.Dotsch, S.Knapp, Structural Genomics Consortium (Sgc). Crystal Structure of Casein Kinase I Delta (CK1D) in Complex with Triple Phosphorylated P63 PAD3P Peptide To Be Published.