Sodium in PDB 3keu: Crystal Structure of Human Pl Kinase with Bound Plp and Atp

All present enzymatic activity of Crystal Structure of Human Pl Kinase with Bound Plp and Atp:
2.7.1.35;

The structure of Crystal Structure of Human Pl Kinase with Bound Plp and Atp, PDB code: 3keu was solved by M.K.Safo, A.K.Gandhi, F.N.Musayev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.98 / 2.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.202, 114.585, 169.414, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.6

The structure of Crystal Structure of Human Pl Kinase with Bound Plp and Atp also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp (pdb code 3keu). 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 Human Pl Kinase with Bound Plp and Atp, PDB code: 3keu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp


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 Human Pl Kinase with Bound Plp and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.1 occ:1.00 O A:THR148 2.4 28.2 1.0 OG1 A:THR186 2.5 30.6 1.0 O3B A:ATP407 2.6 46.5 1.0 O2G A:ATP407 2.6 46.9 1.0 O A:HOH656 2.6 35.9 1.0 PG A:ATP407 3.2 64.9 1.0 O2B A:ATP407 3.4 31.2 1.0 PB A:ATP407 3.5 34.6 1.0 OD1 A:ASP113 3.5 32.9 1.0 CB A:THR186 3.6 43.9 1.0 C A:THR148 3.6 30.8 1.0 CG2 A:THR186 3.7 29.7 1.0 N A:ASN150 3.7 33.0 1.0 C A:PRO149 3.8 37.4 1.0 O1G A:ATP407 3.9 32.6 1.0 CA A:PRO149 4.0 30.6 1.0 OE1 A:GLU153 4.1 29.4 1.0 O A:PRO149 4.2 41.5 1.0 OG1 A:THR148 4.3 27.8 1.0 CG A:ASP113 4.3 36.4 1.0 CA A:ASN150 4.3 28.7 1.0 CB A:ASN150 4.3 29.2 1.0 OD2 A:ASP113 4.3 37.0 1.0 CB A:THR148 4.3 30.3 1.0 O3A A:ATP407 4.3 42.4 1.0 N A:PRO149 4.3 37.5 1.0 O3G A:ATP407 4.5 54.9 1.0 CA A:THR148 4.6 33.2 1.0 O1B A:ATP407 4.7 26.0 1.0 CA A:THR186 4.8 35.3 1.0 CA A:GLY234 4.8 20.2 1.0 N A:THR186 4.8 38.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp


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 Human Pl Kinase with Bound Plp and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:35.2 occ:1.00 O B:THR148 2.3 26.6 1.0 OG1 B:THR186 2.5 29.3 1.0 O1G B:ATP409 2.5 36.7 1.0 O3B B:ATP409 2.6 35.7 1.0 O B:HOH796 2.6 26.4 1.0 PG B:ATP409 3.1 63.9 1.0 CG2 B:THR186 3.4 31.4 1.0 C B:THR148 3.4 34.9 1.0 CB B:THR186 3.4 37.5 1.0 OD2 B:ASP113 3.5 42.4 1.0 C B:PRO149 3.6 33.5 1.0 PB B:ATP409 3.6 32.8 1.0 N B:ASN150 3.6 25.8 1.0 O2B B:ATP409 3.7 30.2 1.0 CA B:PRO149 3.9 25.7 1.0 OG1 B:THR148 3.9 32.7 1.0 O3G B:ATP409 4.0 54.8 1.0 O B:PRO149 4.0 32.2 1.0 OE1 B:GLU153 4.0 28.9 1.0 CB B:THR148 4.1 30.4 1.0 CG B:ASP113 4.2 41.1 1.0 N B:PRO149 4.2 36.4 1.0 OD1 B:ASP113 4.2 31.0 1.0 CA B:ASN150 4.3 33.8 1.0 O2G B:ATP409 4.4 54.5 1.0 CA B:THR148 4.4 28.4 1.0 O3A B:ATP409 4.5 26.0 1.0 CB B:ASN150 4.5 36.3 1.0 CA B:THR186 4.7 26.1 1.0 N B:THR186 4.7 31.8 1.0 O1B B:ATP409 4.8 35.2 1.0

A.K.Gandhi, F.N.Musayev, M.K.Safo. Crystal Structure of Pl Kinase in Complex with Mgatp and Plp: Structural Basis of Severe Induced Mgatp Substrate Inhibition of the Enzyme To Be Published.