Magnesium in PDB 4g1n: PKM2 in Complex with An Activator

All present enzymatic activity of PKM2 in Complex with An Activator:
2.7.1.40;

The structure of PKM2 in Complex with An Activator, PDB code: 4g1n was solved by C.Kung, J.Hixon, L.Dang, B.Delabarre, K.C.Qian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.24 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.118, 94.141, 146.149, 90.00, 99.39, 90.00
R / Rfree (%)	21.1 / 26.6

The binding sites of Magnesium atom in the PKM2 in Complex with An Activator (pdb code 4g1n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PKM2 in Complex with An Activator, PDB code: 4g1n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the PKM2 in Complex with An Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PKM2 in Complex with An Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:47.8 occ:1.00 O A:HOH702 1.7 39.5 1.0 OD2 A:ASP296 2.0 41.6 1.0 O A:HOH701 2.1 29.4 1.0 O1 A:OXL601 2.2 61.1 1.0 OE2 A:GLU272 2.3 35.7 1.0 O4 A:OXL601 2.3 50.8 1.0 C1 A:OXL601 3.0 60.7 1.0 C2 A:OXL601 3.0 56.0 1.0 CG A:ASP296 3.1 42.2 1.0 CD A:GLU272 3.3 35.6 1.0 OE1 A:GLU272 3.6 34.1 1.0 CB A:ASP296 3.7 41.0 1.0 NZ A:LYS270 4.1 40.0 1.0 OD1 A:ASP296 4.2 43.9 1.0 CZ A:PHE244 4.2 44.9 1.0 O3 A:OXL601 4.2 64.9 1.0 O2 A:OXL601 4.2 53.5 1.0 N A:ASP296 4.4 33.6 1.0 CE1 A:PHE244 4.4 46.3 1.0 CG A:GLU272 4.6 37.4 1.0 CA A:ASP296 4.7 38.3 1.0 CE A:LYS270 4.7 38.1 1.0 CB A:GLU272 4.7 38.7 1.0 CE2 A:PHE244 4.9 38.2 1.0 CB A:ALA293 4.9 29.8 1.0

Magnesium binding site 2 out of 4 in the PKM2 in Complex with An Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PKM2 in Complex with An Activator within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:39.6 occ:1.00 O B:HOH701 1.9 32.1 1.0 OD2 B:ASP296 2.0 42.2 1.0 O B:HOH702 2.1 37.2 1.0 O3 B:OXL601 2.1 44.7 1.0 O4 B:OXL601 2.2 44.7 1.0 OE2 B:GLU272 2.2 32.5 1.0 C1 B:OXL601 2.8 47.2 1.0 C2 B:OXL601 2.9 49.1 1.0 CG B:ASP296 3.1 38.2 1.0 CD B:GLU272 3.3 33.5 1.0 CB B:ASP296 3.6 35.4 1.0 OE1 B:GLU272 3.7 37.8 1.0 O1 B:OXL601 4.0 39.4 1.0 O2 B:OXL601 4.1 49.0 1.0 OD1 B:ASP296 4.2 42.6 1.0 NZ B:LYS270 4.3 30.6 1.0 N B:ASP296 4.3 30.7 1.0 CZ B:PHE244 4.3 37.1 1.0 CA B:ASP296 4.6 31.8 1.0 CE1 B:PHE244 4.6 38.1 1.0 CG B:GLU272 4.6 31.9 1.0 CB B:GLU272 4.7 33.0 1.0 CE B:LYS270 4.7 29.8 1.0 CB B:ALA293 4.8 29.0 1.0

Magnesium binding site 3 out of 4 in the PKM2 in Complex with An Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PKM2 in Complex with An Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:50.6 occ:1.00 OD2 C:ASP296 1.9 41.5 1.0 O C:HOH701 2.1 35.6 1.0 O3 C:OXL601 2.2 49.6 1.0 OE2 C:GLU272 2.2 50.7 1.0 O2 C:OXL601 2.3 48.1 1.0 C1 C:OXL601 3.0 49.0 1.0 C2 C:OXL601 3.0 46.0 1.0 CG C:ASP296 3.1 45.9 1.0 CD C:GLU272 3.2 48.7 1.0 OE1 C:GLU272 3.6 47.2 1.0 CB C:ASP296 3.7 42.6 1.0 NZ C:LYS270 3.9 40.8 1.0 OD1 C:ASP296 4.1 48.9 1.0 O C:HOH702 4.2 33.6 1.0 O1 C:OXL601 4.2 47.0 1.0 CZ C:PHE244 4.2 54.2 1.0 O4 C:OXL601 4.3 45.8 1.0 CE1 C:PHE244 4.4 52.7 1.0 CE C:LYS270 4.5 37.9 1.0 CG C:GLU272 4.6 44.1 1.0 N C:ASP296 4.6 36.9 1.0 CA C:ASP296 4.8 40.8 1.0 CB C:GLU272 4.8 43.5 1.0 CE2 C:PHE244 4.9 52.0 1.0

Magnesium binding site 4 out of 4 in the PKM2 in Complex with An Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PKM2 in Complex with An Activator within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:45.8 occ:1.00 OD2 D:ASP296 1.9 39.8 1.0 O D:HOH702 2.0 38.8 1.0 O D:HOH701 2.1 41.2 1.0 O2 D:OXL601 2.2 54.0 1.0 OE2 D:GLU272 2.3 42.6 1.0 O1 D:OXL601 2.6 45.9 1.0 CG D:ASP296 3.1 34.8 1.0 C2 D:OXL601 3.1 51.0 1.0 C1 D:OXL601 3.2 49.0 1.0 CD D:GLU272 3.3 40.8 1.0 OE1 D:GLU272 3.6 37.9 1.0 CB D:ASP296 3.7 36.3 1.0 OD1 D:ASP296 4.1 42.2 1.0 CZ D:PHE244 4.1 50.0 1.0 CE1 D:PHE244 4.2 50.3 1.0 O4 D:OXL601 4.3 52.2 1.0 O3 D:OXL601 4.5 48.0 1.0 N D:ASP296 4.5 29.8 1.0 CG D:GLU272 4.6 40.5 1.0 NZ D:LYS270 4.7 43.7 1.0 CA D:ASP296 4.7 33.5 1.0 CB D:GLU272 4.8 41.5 1.0 CE2 D:PHE244 4.9 46.8 1.0 CE D:LYS270 5.0 40.4 1.0

C.Kung, J.Hixon, S.Choe, K.Marks, S.Gross, E.Murphy, B.Delabarre, G.Cianchetta, S.Sethumadhavan, X.Wang, S.Yan, Y.Gao, C.Fang, W.Wei, F.Jiang, S.Wang, K.Qian, J.Saunders, E.Driggers, H.K.Woo, K.Kunii, S.Murray, H.Yang, K.Yen, W.Liu, L.C.Cantley, M.G.Vander Heiden, S.M.Su, S.Jin, F.G.Salituro, L.Dang. Small Molecule Activation of PKM2 in Cancer Cells Induces Serine Auxotrophy. Chem.Biol. V. 19 1187 2012.
ISSN: ISSN 1074-5521
PubMed: 22999886
DOI: 10.1016/J.CHEMBIOL.2012.07.021