Magnesium in PDB 8d13: Helical Adp-F-Actin

The binding sites of Magnesium atom in the Helical Adp-F-Actin (pdb code 8d13). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Helical Adp-F-Actin, PDB code: 8d13:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Helical Adp-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Helical Adp-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg377 b:17.1 occ:1.00 O A:HOH411 2.1 17.7 1.0 O A:HOH393 2.1 16.3 1.0 O A:HOH388 2.1 16.3 1.0 O A:HOH387 2.1 14.7 1.0 O A:HOH397 2.1 16.2 1.0 O3B A:ADP376 2.3 15.8 1.0 PB A:ADP376 3.5 15.8 1.0 O2B A:ADP376 3.8 15.8 1.0 O3A A:ADP376 4.2 15.8 1.0 O2A A:ADP376 4.2 15.8 1.0 OD2 A:ASP154 4.2 15.5 1.0 OD2 A:ASP11 4.3 20.0 1.0 O A:HOH394 4.4 17.3 1.0 O A:HOH440 4.4 18.6 1.0 O A:HOH385 4.4 15.7 1.0 OE1 A:GLN137 4.4 19.4 1.0 CA A:GLY13 4.6 18.0 1.0 CD A:GLN137 4.6 19.4 1.0 OD1 A:ASP11 4.6 20.0 1.0 CA A:GLY156 4.6 14.9 1.0 NZ A:LYS18 4.6 18.1 1.0 PA A:ADP376 4.7 15.8 1.0 O1B A:ADP376 4.7 15.8 1.0 NE2 A:GLN137 4.7 19.4 1.0 O A:HOH470 4.8 21.0 1.0 CG A:ASP11 4.9 20.0 1.0 OD1 A:ASP154 4.9 15.5 1.0 O A:HOH421 4.9 17.9 1.0 O A:HOH448 5.0 19.1 1.0

Magnesium binding site 2 out of 3 in the Helical Adp-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Helical Adp-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg377 b:18.0 occ:1.00 O B:HOH388 2.1 17.7 1.0 O B:HOH387 2.1 15.2 1.0 O B:HOH393 2.1 17.4 1.0 O B:HOH397 2.1 17.2 1.0 O3B B:ADP376 2.3 17.2 1.0 O B:HOH411 2.3 17.7 1.0 PB B:ADP376 3.5 17.2 1.0 O2B B:ADP376 3.7 17.2 1.0 O3A B:ADP376 4.1 17.2 1.0 O2A B:ADP376 4.2 17.2 1.0 OD2 B:ASP154 4.2 15.8 1.0 O B:HOH440 4.3 18.8 1.0 OD2 B:ASP11 4.3 20.5 1.0 O B:HOH394 4.4 17.2 1.0 O B:HOH385 4.5 16.1 1.0 OE1 B:GLN137 4.5 19.5 1.0 O B:HOH421 4.6 17.5 1.0 O B:HOH470 4.6 20.5 1.0 CA B:GLY13 4.6 18.8 1.0 OD1 B:ASP11 4.6 20.5 1.0 CA B:GLY156 4.6 15.6 1.0 CD B:GLN137 4.6 19.5 1.0 NZ B:LYS18 4.6 19.0 1.0 PA B:ADP376 4.7 17.2 1.0 NE2 B:GLN137 4.7 19.5 1.0 O1B B:ADP376 4.7 17.2 1.0 CG B:ASP11 4.9 20.5 1.0 OD1 B:ASP154 4.9 15.8 1.0 O B:HOH448 5.0 20.4 1.0

Magnesium binding site 3 out of 3 in the Helical Adp-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Helical Adp-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg377 b:22.2 occ:1.00 O C:HOH411 2.1 21.5 1.0 O C:HOH393 2.1 21.7 1.0 O C:HOH387 2.1 19.6 1.0 O C:HOH388 2.1 20.2 1.0 O C:HOH397 2.1 22.2 1.0 O3B C:ADP376 2.2 19.5 1.0 PB C:ADP376 3.5 19.5 1.0 O2B C:ADP376 3.8 19.5 1.0 O3A C:ADP376 4.1 19.5 1.0 O2A C:ADP376 4.2 19.5 1.0 OD2 C:ASP154 4.2 21.2 1.0 O C:HOH394 4.3 23.2 1.0 OD2 C:ASP11 4.3 23.6 1.0 O C:HOH440 4.4 22.9 1.0 O C:HOH385 4.4 22.3 1.0 O C:HOH470 4.5 24.8 1.0 CA C:GLY13 4.6 21.4 1.0 OE1 C:GLN137 4.6 24.4 1.0 OD1 C:ASP11 4.6 23.6 1.0 CD C:GLN137 4.6 24.4 1.0 CA C:GLY156 4.6 18.9 1.0 PA C:ADP376 4.6 19.5 1.0 NZ C:LYS18 4.6 21.4 1.0 NE2 C:GLN137 4.6 24.4 1.0 O1B C:ADP376 4.7 19.5 1.0 CG C:ASP11 4.9 23.6 1.0 OD1 C:ASP154 4.9 21.2 1.0

M.J.Reynolds, C.Hachicho, A.G.Carl, R.Gong, G.M.Alushin. Bending Forces and Nucleotide State Jointly Regulate F-Actin Structure. Nature V. 611 380 2022.
ISSN: ESSN 1476-4687
PubMed: 36289330
DOI: 10.1038/S41586-022-05366-W