Magnesium in PDB 6djm: Cryo-Em Structure of Amppnp-Actin Filaments

The binding sites of Magnesium atom in the Cryo-Em Structure of Amppnp-Actin Filaments (pdb code 6djm). 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 Amppnp-Actin Filaments, PDB code: 6djm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Amppnp-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 Amppnp-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:44.6 occ:1.00 O3G A:ANP802 2.1 47.7 1.0 O2G A:ANP802 2.1 47.7 1.0 O2B A:ANP802 2.2 47.7 1.0 PG A:ANP802 2.6 47.7 1.0 PB A:ANP802 3.3 47.7 1.0 N3B A:ANP802 3.6 47.7 1.0 OE1 A:GLN137 3.8 53.0 1.0 O1G A:ANP802 3.8 47.7 1.0 O1B A:ANP802 3.9 47.7 1.0 CD A:GLN137 4.1 53.0 1.0 NZ A:LYS18 4.2 48.6 1.0 NE2 A:GLN137 4.2 53.0 1.0 O1A A:ANP802 4.2 47.7 1.0 OD2 A:ASP11 4.3 53.9 1.0 CG2 A:VAL339 4.3 48.4 1.0 OD1 A:ASP11 4.4 53.9 1.0 O3A A:ANP802 4.6 47.7 1.0 O A:HOH901 4.6 45.2 1.0 CB A:VAL339 4.7 48.4 1.0 OD1 A:ASP154 4.7 46.6 1.0 CG A:ASP11 4.8 53.9 1.0 OD2 A:ASP154 4.8 46.6 1.0 PA A:ANP802 4.9 47.7 1.0 CG1 A:VAL339 4.9 48.4 1.0 CA A:GLY13 4.9 50.8 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Amppnp-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 Amppnp-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:43.4 occ:1.00 O2G B:ANP802 2.1 47.3 1.0 O2B B:ANP802 2.1 47.3 1.0 PG B:ANP802 3.4 47.3 1.0 PB B:ANP802 3.5 47.3 1.0 O1G B:ANP802 3.7 47.3 1.0 OE1 B:GLN137 3.9 53.9 1.0 O1A B:ANP802 3.9 47.3 1.0 O1B B:ANP802 4.0 47.3 1.0 N3B B:ANP802 4.1 47.3 1.0 CG2 B:VAL339 4.2 47.3 1.0 NZ B:LYS18 4.3 47.5 1.0 CD B:GLN137 4.3 53.9 1.0 OD1 B:ASP154 4.4 48.2 1.0 OD2 B:ASP11 4.5 52.6 1.0 NE2 B:GLN137 4.5 53.9 1.0 O B:HOH901 4.5 50.3 1.0 OD2 B:ASP154 4.6 48.2 1.0 O3G B:ANP802 4.6 47.3 1.0 O3A B:ANP802 4.6 47.3 1.0 OD1 B:ASP11 4.7 52.6 1.0 CB B:VAL339 4.7 47.3 1.0 PA B:ANP802 4.7 47.3 1.0 CA B:GLY156 4.9 47.3 1.0 CG B:ASP154 4.9 48.2 1.0 CG1 B:VAL339 4.9 47.3 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Amppnp-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 Amppnp-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:41.9 occ:1.00 O2G C:ANP802 2.1 47.2 1.0 O2B C:ANP802 2.1 47.2 1.0 PG C:ANP802 3.4 47.2 1.0 PB C:ANP802 3.6 47.2 1.0 O1G C:ANP802 3.6 47.2 1.0 OE1 C:GLN137 3.8 52.1 1.0 CG2 C:VAL339 4.1 45.7 1.0 N3B C:ANP802 4.1 47.2 1.0 OD1 C:ASP154 4.2 47.9 1.0 CD C:GLN137 4.3 52.1 1.0 O2A C:ANP802 4.3 47.2 1.0 O1B C:ANP802 4.4 47.2 1.0 OD2 C:ASP154 4.4 47.9 1.0 O C:HOH901 4.4 48.8 1.0 NZ C:LYS18 4.4 46.5 1.0 O3A C:ANP802 4.4 47.2 1.0 NE2 C:GLN137 4.5 52.1 1.0 OD2 C:ASP11 4.5 52.1 1.0 O3G C:ANP802 4.6 47.2 1.0 CB C:VAL339 4.6 45.7 1.0 O1A C:ANP802 4.7 47.2 1.0 PA C:ANP802 4.7 47.2 1.0 CG C:ASP154 4.7 47.9 1.0 OD1 C:ASP11 4.8 52.1 1.0 CG1 C:VAL339 4.9 45.7 1.0 CA C:GLY156 4.9 47.4 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Amppnp-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 Amppnp-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:42.7 occ:1.00 O2G D:ANP802 2.1 46.4 1.0 O2B D:ANP802 2.1 46.4 1.0 PG D:ANP802 3.4 46.4 1.0 PB D:ANP802 3.5 46.4 1.0 O1G D:ANP802 3.7 46.4 1.0 OE1 D:GLN137 3.9 51.3 1.0 O1A D:ANP802 4.0 46.4 1.0 N3B D:ANP802 4.1 46.4 1.0 O1B D:ANP802 4.1 46.4 1.0 CG2 D:VAL339 4.2 45.6 1.0 OD1 D:ASP154 4.2 46.7 1.0 O D:HOH901 4.3 46.8 1.0 CD D:GLN137 4.4 51.3 1.0 NZ D:LYS18 4.4 46.5 1.0 OD2 D:ASP154 4.4 46.7 1.0 NE2 D:GLN137 4.6 51.3 1.0 O3A D:ANP802 4.6 46.4 1.0 O3G D:ANP802 4.6 46.4 1.0 OD2 D:ASP11 4.6 51.3 1.0 CB D:VAL339 4.7 45.6 1.0 PA D:ANP802 4.7 46.4 1.0 CG D:ASP154 4.8 46.7 1.0 CA D:GLY156 4.8 46.1 1.0 OD1 D:ASP11 4.9 51.3 1.0 CA D:GLY301 5.0 46.2 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