Magnesium in PDB 9c59: Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc

All present enzymatic activity of Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc:
3.6.5.2;

The binding sites of Magnesium atom in the Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc (pdb code 9c59). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc, PDB code: 9c59:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:241.1 occ:1.00 O2G A:GTP1001 1.9 258.6 1.0 O2B A:GTP1001 2.2 258.6 1.0 OG1 A:THR48 2.2 245.9 1.0 OG1 A:THR31 2.2 267.1 1.0 CB A:THR48 2.9 245.9 1.0 PG A:GTP1001 3.1 258.6 1.0 CB A:THR31 3.3 267.1 1.0 PB A:GTP1001 3.4 258.6 1.0 O3B A:GTP1001 3.5 258.6 1.0 O3G A:GTP1001 3.7 258.6 1.0 N A:THR48 3.7 245.9 1.0 CA A:THR48 3.8 245.9 1.0 CG2 A:THR48 4.0 245.9 1.0 OD2 A:ASP67 4.0 234.5 1.0 O2A A:GTP1001 4.2 258.6 1.0 N A:THR31 4.2 267.1 1.0 O A:ILE46 4.2 221.7 1.0 CG2 A:THR31 4.3 267.1 1.0 CA A:THR31 4.3 267.1 1.0 O1G A:GTP1001 4.4 258.6 1.0 O3A A:GTP1001 4.4 258.6 1.0 O1B A:GTP1001 4.4 258.6 1.0 PA A:GTP1001 4.6 258.6 1.0 C A:PRO47 4.7 244.7 1.0 O1A A:GTP1001 4.7 258.6 1.0 CE A:LYS30 4.8 260.8 1.0 NZ A:LYS30 4.9 260.8 1.0 CG A:ASP67 4.9 234.5 1.0 OD1 A:ASP67 5.0 234.5 1.0

Magnesium binding site 2 out of 4 in the Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1000 b:118.2 occ:1.00 OG1 C:THR31 1.8 113.6 1.0 O2G C:GTP1001 1.9 136.4 1.0 O2B C:GTP1001 2.2 136.4 1.0 CB C:THR31 2.9 113.6 1.0 PG C:GTP1001 3.1 136.4 1.0 OG1 C:THR48 3.2 100.1 1.0 CB C:THR48 3.2 100.1 1.0 PB C:GTP1001 3.4 136.4 1.0 O3B C:GTP1001 3.5 136.4 1.0 CG2 C:THR31 3.6 113.6 1.0 O3G C:GTP1001 3.6 136.4 1.0 OD2 C:ASP67 3.7 109.6 1.0 N C:THR48 4.0 100.1 1.0 CA C:THR31 4.1 113.6 1.0 O2A C:GTP1001 4.2 136.4 1.0 CG2 C:THR48 4.2 100.1 1.0 CA C:THR48 4.2 100.1 1.0 N C:THR31 4.2 113.6 1.0 OD1 C:ASP67 4.3 109.6 1.0 O1G C:GTP1001 4.4 136.4 1.0 O3A C:GTP1001 4.4 136.4 1.0 CG C:ASP67 4.4 109.6 1.0 O1B C:GTP1001 4.4 136.4 1.0 PA C:GTP1001 4.6 136.4 1.0 O1A C:GTP1001 4.7 136.4 1.0 O C:THR48 4.8 100.1 1.0 C C:THR48 5.0 100.1 1.0

Magnesium binding site 3 out of 4 in the Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1000 b:241.1 occ:1.00 O2G a:GTP1001 1.9 258.6 1.0 O2B a:GTP1001 2.2 258.6 1.0 OG1 a:THR48 2.2 245.9 1.0 OG1 a:THR31 2.2 267.1 1.0 CB a:THR48 2.9 245.9 1.0 PG a:GTP1001 3.1 258.6 1.0 CB a:THR31 3.3 267.1 1.0 PB a:GTP1001 3.4 258.6 1.0 O3B a:GTP1001 3.5 258.6 1.0 O3G a:GTP1001 3.7 258.6 1.0 N a:THR48 3.7 245.9 1.0 CA a:THR48 3.8 245.9 1.0 CG2 a:THR48 4.0 245.9 1.0 OD2 a:ASP67 4.0 234.5 1.0 O2A a:GTP1001 4.2 258.6 1.0 N a:THR31 4.2 267.1 1.0 O a:ILE46 4.2 221.7 1.0 CG2 a:THR31 4.3 267.1 1.0 CA a:THR31 4.3 267.1 1.0 O1G a:GTP1001 4.4 258.6 1.0 O3A a:GTP1001 4.4 258.6 1.0 O1B a:GTP1001 4.4 258.6 1.0 PA a:GTP1001 4.6 258.6 1.0 C a:PRO47 4.7 244.7 1.0 O1A a:GTP1001 4.7 258.6 1.0 CE a:LYS30 4.8 260.8 1.0 NZ a:LYS30 4.9 260.8 1.0 CG a:ASP67 4.9 234.5 1.0 OD1 a:ASP67 5.0 234.5 1.0

Magnesium binding site 4 out of 4 in the Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Ap-3 Dimer Bound to Myristoylated ARF1 (Q71L) and LAMP1 Cargo on A Lipid Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg1000 b:118.2 occ:1.00 OG1 c:THR31 1.8 113.6 1.0 O2G c:GTP1001 1.9 136.4 1.0 O2B c:GTP1001 2.2 136.4 1.0 CB c:THR31 2.9 113.6 1.0 PG c:GTP1001 3.1 136.4 1.0 OG1 c:THR48 3.2 100.1 1.0 CB c:THR48 3.2 100.1 1.0 PB c:GTP1001 3.4 136.4 1.0 O3B c:GTP1001 3.5 136.4 1.0 CG2 c:THR31 3.6 113.6 1.0 O3G c:GTP1001 3.6 136.4 1.0 OD2 c:ASP67 3.7 109.6 1.0 N c:THR48 4.0 100.1 1.0 CA c:THR31 4.1 113.6 1.0 O2A c:GTP1001 4.2 136.4 1.0 CG2 c:THR48 4.2 100.1 1.0 CA c:THR48 4.2 100.1 1.0 N c:THR31 4.2 113.6 1.0 OD1 c:ASP67 4.3 109.6 1.0 O1G c:GTP1001 4.4 136.4 1.0 O3A c:GTP1001 4.4 136.4 1.0 CG c:ASP67 4.4 109.6 1.0 O1B c:GTP1001 4.4 136.4 1.0 PA c:GTP1001 4.6 136.4 1.0 O1A c:GTP1001 4.7 136.4 1.0 O c:THR48 4.8 100.1 1.0 C c:THR48 5.0 100.1 1.0

M.Begley, R.W.Baker. A Structure-Based Mechanism For Initiation of Ap-3 Coated Vesicle Formation To Be Published.