Magnesium in PDB 7k21: Cryo-Em Structure of Pyrene-Labeled Adp-Pi-Actin Filaments

The binding sites of Magnesium atom in the Cryo-Em Structure of Pyrene-Labeled Adp-Pi-Actin Filaments (pdb code 7k21). 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 Pyrene-Labeled Adp-Pi-Actin Filaments, PDB code: 7k21:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Pyrene-Labeled 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 Pyrene-Labeled Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:61.6 occ:1.00 O1B A:ADP802 2.1 68.8 1.0 PB A:ADP802 3.3 68.8 1.0 OE1 A:GLN137 3.6 74.0 1.0 O1 A:PO4803 3.6 73.5 1.0 O2B A:ADP802 3.7 68.8 1.0 O2 A:PO4803 3.7 73.5 1.0 O3A A:ADP802 3.8 68.8 1.0 CD A:GLN137 4.0 74.0 1.0 OD2 A:ASP11 4.0 76.2 1.0 P A:PO4803 4.1 73.5 1.0 NE2 A:GLN137 4.2 74.0 1.0 OD2 A:ASP154 4.4 67.3 1.0 O3 A:PO4803 4.4 73.5 1.0 CG2 A:VAL339 4.4 68.9 1.0 OD1 A:ASP11 4.5 76.2 1.0 O3B A:ADP802 4.6 68.8 1.0 CA A:GLY13 4.7 72.5 1.0 CG A:ASP11 4.7 76.2 1.0 OD1 A:ASP154 4.8 67.3 1.0 CB A:VAL339 4.8 68.9 1.0 NZ A:LYS18 4.9 69.8 1.0 CG1 A:VAL339 4.9 68.9 1.0 CA A:GLY156 4.9 67.2 1.0 CG A:GLN137 4.9 74.0 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Pyrene-Labeled 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 Pyrene-Labeled Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:60.8 occ:1.00 O1B B:ADP802 2.1 65.6 1.0 PB B:ADP802 3.3 65.6 1.0 OE1 B:GLN137 3.4 70.4 1.0 O2B B:ADP802 3.7 65.6 1.0 O2 B:PO4803 3.7 71.3 1.0 O3A B:ADP802 3.9 65.6 1.0 O1 B:PO4803 3.9 71.3 1.0 CD B:GLN137 3.9 70.4 1.0 OD2 B:ASP11 4.1 72.6 1.0 OD2 B:ASP154 4.1 64.9 1.0 NE2 B:GLN137 4.2 70.4 1.0 P B:PO4803 4.2 71.3 1.0 CG2 B:VAL339 4.3 64.7 1.0 O3 B:PO4803 4.4 71.3 1.0 OD1 B:ASP154 4.5 64.9 1.0 O3B B:ADP802 4.6 65.6 1.0 OD1 B:ASP11 4.6 72.6 1.0 CB B:VAL339 4.7 64.7 1.0 CG B:ASP154 4.8 64.9 1.0 CG B:ASP11 4.8 72.6 1.0 CG B:GLN137 4.8 70.4 1.0 CG1 B:VAL339 4.8 64.7 1.0 CA B:GLY156 4.9 64.4 1.0 CA B:GLY13 4.9 68.5 1.0 CB B:GLN137 5.0 70.4 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Pyrene-Labeled 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 Pyrene-Labeled Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:60.3 occ:1.00 O1B C:ADP802 2.1 65.3 1.0 O2 C:PO4803 3.3 70.8 1.0 PB C:ADP802 3.3 65.3 1.0 OE1 C:GLN137 3.4 69.9 1.0 O2B C:ADP802 3.7 65.3 1.0 OD2 C:ASP11 3.8 70.7 1.0 CD C:GLN137 3.8 69.9 1.0 O3A C:ADP802 3.9 65.3 1.0 O1 C:PO4803 4.0 70.8 1.0 NE2 C:GLN137 4.0 69.9 1.0 P C:PO4803 4.1 70.8 1.0 OD2 C:ASP154 4.3 65.2 1.0 O3 C:PO4803 4.4 70.8 1.0 OD1 C:ASP11 4.4 70.7 1.0 CG2 C:VAL339 4.5 62.7 1.0 CG C:ASP11 4.5 70.7 1.0 CA C:GLY13 4.5 67.0 1.0 O3B C:ADP802 4.6 65.3 1.0 CG C:GLN137 4.7 69.9 1.0 CB C:VAL339 4.8 62.7 1.0 OD1 C:ASP154 4.8 65.2 1.0 CG1 C:VAL339 4.9 62.7 1.0 NZ C:LYS18 4.9 64.6 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Pyrene-Labeled 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 Pyrene-Labeled Adp-Pi-Actin Filaments within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:61.2 occ:1.00 O1B D:ADP802 2.1 65.8 1.0 PB D:ADP802 3.3 65.8 1.0 OE1 D:GLN137 3.5 71.7 1.0 O2 D:PO4803 3.5 71.7 1.0 O3A D:ADP802 3.7 65.8 1.0 O1 D:PO4803 3.8 71.7 1.0 O2B D:ADP802 3.9 65.8 1.0 CD D:GLN137 4.0 71.7 1.0 P D:PO4803 4.1 71.7 1.0 OD2 D:ASP154 4.1 66.1 1.0 OD2 D:ASP11 4.2 70.8 1.0 O3 D:PO4803 4.3 71.7 1.0 NE2 D:GLN137 4.3 71.7 1.0 CG2 D:VAL339 4.4 64.6 1.0 OD1 D:ASP154 4.5 66.1 1.0 O3B D:ADP802 4.6 65.8 1.0 CA D:GLY156 4.7 66.2 1.0 OD1 D:ASP11 4.7 70.8 1.0 CG D:ASP154 4.8 66.1 1.0 CB D:VAL339 4.9 64.6 1.0 CA D:GLY13 4.9 67.7 1.0 CG D:ASP11 4.9 70.8 1.0 NZ D:LYS18 5.0 67.1 1.0

S.Z.Chou, T.D.Pollard. Cryo-Electron Microscopy Structures of Pyrene-Labeled Adp-P I - and Adp-Actin Filaments. Nat Commun V. 11 5897 2020.
ISSN: ESSN 2041-1723
PubMed: 33214556
DOI: 10.1038/S41467-020-19762-1