Magnesium in PDB 9mhg: Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation

All present enzymatic activity of Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation:
2.7.1.137; 2.7.11.1; 3.6.5.2;

The binding sites of Magnesium atom in the Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation (pdb code 9mhg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation, PDB code: 9mhg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:47.0 occ:1.00 O2G A:GTP2001 1.5 40.2 1.0 O2A A:GTP2001 1.7 39.5 1.0 NZ A:LYS53 1.9 31.3 1.0 O1B A:GTP2001 2.0 36.8 1.0 OD2 A:ASP166 2.1 30.9 1.0 PG A:GTP2001 2.5 34.3 1.0 OD1 A:ASN153 2.6 36.5 1.0 PB A:GTP2001 2.8 29.1 1.0 PA A:GTP2001 2.8 38.1 1.0 O3B A:GTP2001 2.8 33.7 1.0 CG A:ASP166 2.9 31.4 1.0 O3A A:GTP2001 3.2 36.3 1.0 CE A:LYS53 3.3 26.7 1.0 O3G A:GTP2001 3.4 31.6 1.0 O1A A:GTP2001 3.4 38.6 1.0 CB A:ASP166 3.5 29.6 1.0 O1G A:GTP2001 3.7 41.0 1.0 OD1 A:ASP166 3.7 33.5 1.0 CG A:ASN153 3.8 30.5 1.0 O5' A:GTP2001 4.2 33.6 1.0 O2B A:GTP2001 4.2 31.3 1.0 ND2 A:ASN153 4.3 31.9 1.0 CD A:LYS53 4.5 29.2 1.0 NH2 A:ARG103 4.9 25.6 1.0

Magnesium binding site 2 out of 2 in the Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L), VPS34 Kinase Domain in the Inactive Conformation within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:51.0 occ:1.00 O3G E:GTP1000 1.5 54.2 1.0 O2B E:GTP1000 2.0 52.8 1.0 OG E:SER25 2.1 45.9 1.0 OG1 E:THR43 2.2 44.2 1.0 PG E:GTP1000 2.7 50.8 1.0 CB E:THR43 2.9 41.0 1.0 PB E:GTP1000 3.1 54.0 1.0 O2G E:GTP1000 3.2 53.5 1.0 O3B E:GTP1000 3.3 47.9 1.0 CB E:SER25 3.4 47.6 1.0 OD2 E:ASP66 3.4 53.9 1.0 N E:THR43 3.7 42.8 1.0 O2A E:GTP1000 3.9 54.3 1.0 CA E:THR43 3.9 39.9 1.0 O1G E:GTP1000 4.0 51.2 1.0 N E:SER25 4.0 50.4 1.0 CG2 E:THR43 4.0 40.7 1.0 O1B E:GTP1000 4.1 54.9 1.0 CG E:ASP66 4.2 51.6 1.0 O3A E:GTP1000 4.2 56.5 1.0 OD1 E:ASP66 4.2 51.1 1.0 CA E:SER25 4.3 48.7 1.0 PA E:GTP1000 4.4 54.8 1.0 O E:ILE41 4.4 49.5 1.0 O1A E:GTP1000 4.5 52.7 1.0 C E:SER42 4.9 43.5 1.0 CE E:LYS24 4.9 45.5 1.0 O E:THR67 4.9 46.6 1.0

A.S.I.Cook, M.Chen, T.N.Ngyuen, A.Claveras-Cabezudo, G.Khuu, S.Rao, S.N.Garcia, M.Yang, A.T.Iavarone, X.Ren, M.Lazarou, G.Hummer, J.H.Hurley. Structural Pathway For Class III Pi 3-Kinase Activation By the Myristoylated Gtpbinding Pseudokinase VPS15 To Be Published.