Magnesium in PDB 9mhf: Cryo-Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L)

All present enzymatic activity of Cryo-Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L):
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) (pdb code 9mhf). 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), PDB code: 9mhf:
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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:40.9 occ:1.00 NZ A:LYS53 1.9 33.6 1.0 OD2 A:ASP166 2.0 29.1 1.0 O2A A:GTP2001 2.0 32.5 1.0 O A:HOH2101 2.1 22.9 1.0 O3B A:GTP2001 2.2 27.7 1.0 OD1 A:ASN153 2.7 26.5 1.0 O3G A:GTP2001 2.7 27.0 1.0 CG A:ASP166 2.8 22.6 1.0 PG A:GTP2001 2.8 23.3 1.0 O1B A:GTP2001 2.9 31.7 1.0 PB A:GTP2001 3.0 30.1 1.0 O2G A:GTP2001 3.0 39.2 1.0 PA A:GTP2001 3.0 21.8 1.0 CB A:ASP166 3.3 20.2 1.0 CE A:LYS53 3.3 22.9 1.0 O3A A:GTP2001 3.5 28.7 1.0 O1A A:GTP2001 3.5 24.6 1.0 OD1 A:ASP166 3.8 24.7 1.0 CG A:ASN153 3.8 20.8 1.0 O A:HOH2102 4.2 40.5 1.0 O1G A:GTP2001 4.2 33.2 1.0 ND2 A:ASN153 4.2 23.9 1.0 O2B A:GTP2001 4.4 26.8 1.0 O5' A:GTP2001 4.4 35.3 1.0 CD A:LYS53 4.6 27.1 1.0 CA A:ASP166 4.8 23.9 1.0 NH2 A:ARG103 4.9 20.1 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Reconstruction of PI3KC3-C1 in Complex with Human RAB1A(Q70L)


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) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:21.1 occ:1.00 OG E:SER25 1.8 19.8 1.0 O E:HOH1102 2.0 14.9 1.0 OG1 E:THR43 2.0 27.0 1.0 O E:HOH1101 2.1 18.4 1.0 OD2 E:ASP66 2.3 25.6 1.0 O2B E:GTP1000 2.5 20.4 1.0 O3G E:GTP1000 2.6 23.4 1.0 CB E:THR43 2.9 17.3 1.0 CG E:ASP66 3.0 19.6 1.0 OD1 E:ASP66 3.1 18.5 1.0 CB E:SER25 3.1 14.6 1.0 N E:SER25 3.5 16.2 1.0 CA E:SER25 3.6 14.2 1.0 CG2 E:THR43 3.7 16.0 1.0 PG E:GTP1000 3.8 16.9 1.0 PB E:GTP1000 3.9 12.5 1.0 O E:THR67 4.0 21.4 1.0 O2G E:GTP1000 4.0 21.2 1.0 CA E:THR43 4.1 14.5 1.0 N E:THR43 4.2 17.0 1.0 O E:HOH1105 4.3 24.1 1.0 C E:LYS24 4.4 16.0 1.0 O3B E:GTP1000 4.4 16.3 1.0 CB E:ASP66 4.4 17.3 1.0 O1B E:GTP1000 4.5 14.5 1.0 CB E:LYS24 4.5 14.4 1.0 O E:HOH1106 4.6 29.3 1.0 CE E:LYS24 4.9 10.6 1.0 C E:THR67 4.9 16.8 1.0 N E:THR67 5.0 16.4 1.0 O1A E:GTP1000 5.0 14.7 1.0 O1G E:GTP1000 5.0 15.8 1.0 O2A E:GTP1000 5.0 23.6 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.