Magnesium in PDB 6djn: Cryo-Em Structure of Adp-Pi-Actin Filaments

The binding sites of Magnesium atom in the Cryo-Em Structure of Adp-Pi-Actin Filaments (pdb code 6djn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Adp-Pi-Actin Filaments, PDB code: 6djn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Adp-Pi-Actin Filaments


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:42.8 occ:1.00 O1B A:ADP802 2.1 44.6 1.0 O4 A:PO4803 2.1 50.5 1.0 PB A:ADP802 3.4 44.6 1.0 P A:PO4803 3.6 50.5 1.0 OE1 A:GLN137 3.7 52.9 1.0 O3B A:ADP802 3.8 44.6 1.0 CD A:GLN137 4.0 52.9 1.0 NE2 A:GLN137 4.0 52.9 1.0 O1 A:PO4803 4.1 50.5 1.0 OD2 A:ASP11 4.1 54.1 1.0 OD1 A:ASP11 4.2 54.1 1.0 O2B A:ADP802 4.2 44.6 1.0 NZ A:LYS18 4.3 47.6 1.0 O2 A:PO4803 4.3 50.5 1.0 CA A:GLY13 4.4 49.1 1.0 O1A A:ADP802 4.4 44.6 1.0 O3A A:ADP802 4.5 44.6 1.0 O3 A:PO4803 4.5 50.5 1.0 CG A:ASP11 4.5 54.1 1.0 CG2 A:VAL339 4.7 48.5 1.0 CG A:GLN137 4.9 52.9 1.0 CB A:VAL339 4.9 48.5 1.0 OD2 A:ASP154 5.0 47.0 1.0 CG1 A:VAL339 5.0 48.5 1.0 PA A:ADP802 5.0 44.6 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Adp-Pi-Actin Filaments


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:44.0 occ:1.00 O1B B:ADP802 2.1 45.7 1.0 O2 B:PO4803 2.2 52.8 1.0 PB B:ADP802 3.4 45.7 1.0 P B:PO4803 3.6 52.8 1.0 OE1 B:GLN137 3.8 54.0 1.0 O3B B:ADP802 3.8 45.7 1.0 O1A B:ADP802 4.0 45.7 1.0 CD B:GLN137 4.1 54.0 1.0 O1 B:PO4803 4.2 52.8 1.0 NE2 B:GLN137 4.2 54.0 1.0 OD2 B:ASP11 4.3 52.3 1.0 NZ B:LYS18 4.3 46.9 1.0 O4 B:PO4803 4.3 52.8 1.0 O3A B:ADP802 4.4 45.7 1.0 O2B B:ADP802 4.4 45.7 1.0 OD1 B:ASP11 4.4 52.3 1.0 O3 B:PO4803 4.6 52.8 1.0 CA B:GLY13 4.6 49.4 1.0 CG2 B:VAL339 4.6 47.7 1.0 PA B:ADP802 4.8 45.7 1.0 CA B:GLY156 4.8 48.2 1.0 CG B:ASP11 4.8 52.3 1.0 OD2 B:ASP154 4.9 50.2 1.0 OD1 B:ASP154 4.9 50.2 1.0 CB B:VAL339 4.9 47.7 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Adp-Pi-Actin Filaments


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:42.4 occ:1.00 O1B C:ADP802 2.1 45.8 1.0 O2 C:PO4803 2.2 49.6 1.0 PB C:ADP802 3.5 45.8 1.0 P C:PO4803 3.6 49.6 1.0 OE1 C:GLN137 3.7 50.6 1.0 NE2 C:GLN137 3.8 50.6 1.0 CD C:GLN137 3.8 50.6 1.0 O3B C:ADP802 4.0 45.8 1.0 OD1 C:ASP11 4.0 51.6 1.0 OD2 C:ASP11 4.0 51.6 1.0 CA C:GLY13 4.2 48.1 1.0 O1 C:PO4803 4.2 49.6 1.0 NZ C:LYS18 4.3 45.8 1.0 O2B C:ADP802 4.3 45.8 1.0 O3 C:PO4803 4.3 49.6 1.0 CG C:ASP11 4.4 51.6 1.0 O3A C:ADP802 4.5 45.8 1.0 O4 C:PO4803 4.5 49.6 1.0 O1A C:ADP802 4.6 45.8 1.0 CG2 C:VAL339 4.7 44.4 1.0 CG C:GLN137 4.7 50.6 1.0 N C:GLY13 4.9 48.1 1.0 CB C:VAL339 4.9 44.4 1.0 CG1 C:VAL339 4.9 44.4 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Adp-Pi-Actin Filaments


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:43.0 occ:1.00 O1B D:ADP802 2.1 46.2 1.0 O2 D:PO4803 2.1 49.7 1.0 PB D:ADP802 3.4 46.2 1.0 P D:PO4803 3.5 49.7 1.0 OE1 D:GLN137 3.7 51.0 1.0 O3B D:ADP802 3.9 46.2 1.0 O1 D:PO4803 3.9 49.7 1.0 CD D:GLN137 4.0 51.0 1.0 NE2 D:GLN137 4.1 51.0 1.0 OD2 D:ASP11 4.2 51.9 1.0 O3 D:PO4803 4.3 49.7 1.0 O1A D:ADP802 4.3 46.2 1.0 NZ D:LYS18 4.3 46.3 1.0 OD1 D:ASP11 4.4 51.9 1.0 O2B D:ADP802 4.4 46.2 1.0 O3A D:ADP802 4.4 46.2 1.0 CA D:GLY13 4.5 50.1 1.0 O4 D:PO4803 4.5 49.7 1.0 CG2 D:VAL339 4.6 45.6 1.0 CG D:ASP11 4.7 51.9 1.0 CA D:GLY156 4.8 46.6 1.0 OD2 D:ASP154 4.9 46.6 1.0 CG D:GLN137 4.9 51.0 1.0 CB D:VAL339 4.9 45.6 1.0 PA D:ADP802 4.9 46.2 1.0 OD1 D:ASP154 4.9 46.6 1.0

S.Z.Chou, T.D.Pollard. Mechanism of Actin Polymerization Revealed By Cryo-Em Structures of Actin Filaments with Three Different Bound Nucleotides. Proc.Natl.Acad.Sci.Usa V. 116 4265 2019.
ISSN: ESSN 1091-6490
PubMed: 30760599
DOI: 10.1073/PNAS.1807028115