Sodium in PDB 4en4: Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex

All present enzymatic activity of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex:
2.7.1.35;

The structure of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex, PDB code: 4en4 was solved by M.K.Safo, F.N.Musayev, A.K.Gandhi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.81 / 2.15
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.749, 115.221, 169.554, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.2

The structure of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex (pdb code 4en4). 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 the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex, PDB code: 4en4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex


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 the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:38.2 occ:1.00 O A:THR148 2.4 29.3 1.0 O3B A:ATP404 2.6 44.8 1.0 O A:HOH518 2.6 27.4 1.0 OG1 A:THR186 2.7 31.4 1.0 O2G A:ATP404 2.8 59.4 1.0 OD1 A:ASP113 3.1 40.1 1.0 PG A:ATP404 3.2 69.0 1.0 C A:THR148 3.5 29.1 1.0 N A:ASN150 3.5 31.2 1.0 C A:PRO149 3.5 31.9 1.0 CA A:PRO149 3.7 29.4 1.0 O3G A:ATP404 3.7 55.8 1.0 PB A:ATP404 3.7 32.4 1.0 CG2 A:THR186 3.8 22.9 1.0 CB A:THR186 3.8 34.2 1.0 O2B A:ATP404 3.8 33.4 1.0 OE1 A:GLU153 3.9 40.1 1.0 CG A:ASP113 3.9 46.3 1.0 OD2 A:ASP113 4.0 41.0 1.0 N A:PRO149 4.1 32.1 1.0 O A:PRO149 4.1 35.5 1.0 OG1 A:THR148 4.2 30.9 1.0 CA A:ASN150 4.2 34.7 1.0 CB A:ASN150 4.4 34.2 1.0 CB A:THR148 4.6 31.1 1.0 O3A A:ATP404 4.6 35.9 1.0 O1G A:ATP404 4.6 65.3 1.0 CA A:THR148 4.7 31.1 1.0 O1B A:ATP404 4.9 27.7 1.0 CD A:GLU153 5.0 37.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex


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 the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:35.9 occ:1.00 O B:THR148 2.4 28.7 1.0 O B:HOH507 2.5 25.1 1.0 OG1 B:THR186 2.5 26.5 1.0 O3B B:ATP404 2.6 38.6 1.0 O1G B:ATP404 2.7 48.3 1.0 PG B:ATP404 3.2 56.4 1.0 OD2 B:ASP113 3.5 37.6 1.0 CG2 B:THR186 3.5 25.7 1.0 CB B:THR186 3.5 25.2 1.0 C B:THR148 3.6 32.3 1.0 PB B:ATP404 3.6 26.0 1.0 C B:PRO149 3.7 31.4 1.0 O2G B:ATP404 3.7 45.2 1.0 O1B B:ATP404 3.7 31.4 1.0 N B:ASN150 3.7 27.0 1.0 CA B:PRO149 4.0 26.1 1.0 OE1 B:GLU153 4.0 26.2 1.0 OG1 B:THR148 4.0 31.1 1.0 O B:PRO149 4.0 26.5 1.0 CG B:ASP113 4.2 27.0 1.0 OD1 B:ASP113 4.2 20.4 1.0 CB B:THR148 4.3 31.2 1.0 N B:PRO149 4.3 35.1 1.0 CA B:ASN150 4.3 29.5 1.0 CB B:ASN150 4.4 39.6 1.0 O3A B:ATP404 4.5 23.4 1.0 O3G B:ATP404 4.6 61.2 1.0 CA B:THR148 4.6 25.2 1.0 CA B:THR186 4.8 25.2 1.0 N B:THR186 4.9 21.5 1.0 O2B B:ATP404 4.9 22.7 1.0 CG B:ASN150 5.0 36.1 1.0

A.K.Gandhi, J.V.Desai, M.S.Ghatge, M.L.Di Salvo, S.Di Biase, R.Danso-Danquah, F.N.Musayev, R.Contestabile, V.Schirch, M.K.Safo. Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights Into Pyridoxal Kinase Inhibition. Plos One V. 7 40954 2012.
ISSN: ESSN 1932-6203
PubMed: 22879864
DOI: 10.1371/JOURNAL.PONE.0040954