Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp, PDB code: 3keu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg400 b:40.5 occ:1.00 O1B A:ATP407 2.0 26.0 1.0 O2A A:ATP407 2.2 42.5 1.0 OD2 A:ASP118 2.2 42.6 1.0 O4 A:MPD512 2.3 62.0 1.0 O A:HOH792 2.4 45.8 1.0 O A:HOH806 2.4 39.6 1.0 C4 A:MPD512 3.0 77.5 1.0 PA A:ATP407 3.1 36.0 1.0 CG A:ASP118 3.2 40.1 1.0 C3 A:MPD512 3.3 73.8 1.0 PB A:ATP407 3.3 34.6 1.0 OD1 A:ASP118 3.4 37.5 1.0 O3A A:ATP407 3.6 42.4 1.0 OG A:SER187 4.0 37.4 1.0 O A:HOH849 4.0 39.8 1.0 O2B A:ATP407 4.0 31.2 1.0 O1A A:ATP407 4.2 33.5 1.0 O A:HOH791 4.2 49.0 1.0 ND2 A:ASN150 4.3 29.3 1.0 O5' A:ATP407 4.3 25.8 1.0 C5 A:MPD512 4.5 80.5 1.0 CB A:ASP118 4.5 49.4 1.0 O3G A:ATP407 4.5 54.9 1.0 C2 A:MPD512 4.5 68.1 1.0 C1 A:MPD512 4.6 51.0 1.0 O3B A:ATP407 4.6 46.5 1.0 O A:HOH928 4.9 54.6 1.0 CB A:SER187 5.0 26.7 1.0 CB A:ASN150 5.0 29.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg401 b:57.1 occ:1.00 OD1 A:ASP235 2.5 26.7 1.0 O4P A:PLP500 2.5 72.5 0.5 O2P A:PLP500 2.9 81.7 0.5 O1G A:ATP407 2.9 32.6 1.0 P A:PLP500 3.0 58.0 0.5 CG A:ASP235 3.2 24.1 1.0 C5A A:PLP500 3.3 66.0 0.5 OD2 A:ASP235 3.4 28.2 1.0 O1P A:PLP500 3.5 60.2 0.5 CG2 A:VAL115 4.0 36.0 1.0 C5 A:PLP500 4.0 82.1 0.5 N A:ASP235 4.0 24.6 1.0 OD2 A:ASP113 4.1 37.0 1.0 O A:HOH918 4.1 39.2 1.0 O A:HOH786 4.2 34.2 1.0 PG A:ATP407 4.3 64.9 1.0 CG1 A:VAL115 4.4 32.5 1.0 CB A:ASP235 4.4 29.6 1.0 C6 A:PLP500 4.5 86.3 0.5 CA A:ASP235 4.5 23.4 1.0 O3P A:PLP500 4.6 62.5 0.5 C A:GLY234 4.6 30.4 1.0 O3G A:ATP407 4.6 54.9 1.0 O4 A:MPD508 4.7 45.9 0.5 CA A:GLY234 4.7 20.2 1.0 CB A:TYR84 4.8 25.4 1.0 C4 A:PLP500 4.8 84.0 0.5 CB A:VAL115 4.8 43.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Pl Kinase with Bound Plp and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:38.0 occ:1.00 O2A B:ATP409 2.1 33.6 1.0 O1B B:ATP409 2.1 35.2 1.0 OD2 B:ASP118 2.2 39.9 1.0 O B:HOH797 2.3 33.4 1.0 O B:HOH798 2.4 35.7 1.0 O4 B:MPD514 2.5 65.5 1.0 PA B:ATP409 3.1 35.7 1.0 CG B:ASP118 3.2 40.5 1.0 PB B:ATP409 3.4 32.8 1.0 C4 B:MPD514 3.4 72.5 1.0 O3A B:ATP409 3.5 26.0 1.0 OD1 B:ASP118 3.6 38.6 1.0 O2 B:MPD514 3.7 53.4 1.0 O B:HOH767 3.9 34.4 1.0 OG B:SER187 3.9 31.5 1.0 O2B B:ATP409 4.0 30.2 1.0 C1 B:MPD514 4.1 45.9 1.0 O1A B:ATP409 4.2 32.4 1.0 O B:HOH884 4.2 54.1 1.0 O5' B:ATP409 4.2 28.0 1.0 C2 B:MPD514 4.3 59.5 1.0 C5 B:MPD514 4.4 80.4 1.0 C3 B:MPD514 4.5 50.4 1.0 CB B:ASP118 4.5 38.3 1.0 ND2 B:ASN150 4.5 37.2 1.0 O2G B:ATP409 4.6 54.5 1.0 O3B B:ATP409 4.7 35.7 1.0 O B:HOH795 4.7 59.8 1.0 CB B:SER187 4.8 23.7 1.0 O B:HOH885 5.0 64.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Pl Kinase with Bound Plp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Pl Kinase with Bound Plp and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:52.7 occ:1.00 OD1 B:ASP235 2.6 27.4 1.0 O4P B:PLP500 2.7 54.9 0.5 O3G B:ATP409 3.1 54.8 1.0 O1P B:PLP500 3.3 48.3 0.5 CG B:ASP235 3.4 32.7 1.0 P B:PLP500 3.4 24.3 0.5 CG2 B:VAL115 3.6 23.9 1.0 O3P B:PLP500 3.7 48.3 0.5 OD2 B:ASP235 3.7 33.8 1.0 C5A B:PLP500 3.7 38.8 0.5 O B:HOH660 3.8 23.0 1.0 O B:HOH730 3.9 40.2 1.0 C5 B:PLP500 3.9 63.6 0.5 C6 B:PLP500 4.1 73.3 0.5 OD1 B:ASP113 4.1 31.0 1.0 CB B:TYR84 4.3 28.8 1.0 O4 B:MPD508 4.3 54.3 0.5 N B:ASP235 4.4 31.7 1.0 CG1 B:VAL115 4.4 30.4 1.0 PG B:ATP409 4.5 63.9 1.0 N B:TYR84 4.6 32.3 1.0 CB B:VAL115 4.6 39.7 1.0 CB B:ASP235 4.7 34.6 1.0 C4 B:PLP500 4.8 70.8 0.5 CA B:ASP235 4.8 33.9 1.0 O2P B:PLP500 4.9 43.3 0.5 C B:GLY234 4.9 34.3 1.0 O2G B:ATP409 4.9 54.5 1.0 CA B:TYR84 4.9 33.4 1.0 N1 B:PLP500 5.0 75.9 0.5

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.