Magnesium in PDB 8d16: Bent Adp-Pi-F-Actin

The binding sites of Magnesium atom in the Bent Adp-Pi-F-Actin (pdb code 8d16). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Bent Adp-Pi-F-Actin, PDB code: 8d16:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:34.6 occ:1.00 O2 A:PO4403 2.2 29.2 1.0 O2B A:ADP401 3.0 28.8 1.0 OD1 A:ASP154 3.1 28.8 1.0 NE2 A:GLN137 3.3 33.6 1.0 P A:PO4403 3.6 29.2 1.0 CD A:GLN137 3.7 33.6 1.0 OE1 A:GLN137 3.8 33.6 1.0 CG A:ASP154 3.9 28.8 1.0 CA A:GLY156 3.9 27.1 1.0 O1 A:PO4403 4.0 29.2 1.0 OD2 A:ASP154 4.0 28.8 1.0 N A:GLY156 4.1 27.1 1.0 PB A:ADP401 4.3 28.8 1.0 CG2 A:VAL339 4.3 34.0 1.0 O3 A:PO4403 4.4 29.2 1.0 O4 A:PO4403 4.6 29.2 1.0 O3B A:ADP401 4.7 28.8 1.0 O3A A:ADP401 4.7 28.8 1.0 CG A:GLN137 4.8 33.6 1.0 CB A:VAL339 4.9 34.0 1.0

Magnesium binding site 2 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:32.5 occ:1.00 O2 B:PO4403 1.7 32.4 1.0 O2B B:ADP401 2.3 29.4 1.0 P B:PO4403 3.2 32.4 1.0 NE2 B:GLN137 3.3 34.0 1.0 PB B:ADP401 3.7 29.4 1.0 O1 B:PO4403 3.8 32.4 1.0 O3 B:PO4403 4.1 32.4 1.0 O4 B:PO4403 4.1 32.4 1.0 OD2 B:ASP11 4.1 33.8 1.0 CD B:GLN137 4.2 34.0 1.0 O3B B:ADP401 4.3 29.4 1.0 O1B B:ADP401 4.3 29.4 1.0 OD2 B:ASP154 4.5 29.7 1.0 OE1 B:GLN137 4.7 34.0 1.0 O3A B:ADP401 4.7 29.4 1.0 CG2 B:VAL339 4.7 33.6 1.0 CA B:GLY13 4.7 31.2 1.0 CA B:GLY156 5.0 28.2 1.0 OD1 B:ASP11 5.0 33.8 1.0 CG B:ASP11 5.0 33.8 1.0

Magnesium binding site 3 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:42.4 occ:1.00 O4 C:PO4403 2.7 36.8 1.0 O2 C:PO4403 2.7 36.8 1.0 P C:PO4403 3.0 36.8 1.0 CA C:GLY156 3.2 35.0 1.0 O1 C:PO4403 3.3 36.8 1.0 N C:GLY156 3.4 35.0 1.0 OD1 C:ASP154 3.5 36.9 1.0 O2B C:ADP401 3.7 35.8 1.0 NE2 C:GLN137 3.9 40.5 1.0 OD2 C:ASP154 4.0 36.9 1.0 O3B C:ADP401 4.1 35.8 1.0 CG C:ASP154 4.1 36.9 1.0 OE1 C:GLN137 4.1 40.5 1.0 CD C:GLN137 4.3 40.5 1.0 PB C:ADP401 4.3 35.8 1.0 C C:SER155 4.4 35.6 1.0 C C:GLY156 4.5 35.0 1.0 O3 C:PO4403 4.5 36.8 1.0 O3A C:ADP401 4.5 35.8 1.0 N C:ASP157 4.7 34.7 1.0 O C:VAL159 4.7 35.0 1.0 O2A C:ADP401 4.9 35.8 1.0 CA C:GLY301 4.9 38.0 1.0 N C:SER155 5.0 35.6 1.0

Magnesium binding site 4 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:35.8 occ:1.00 O2 D:PO4403 2.4 35.7 1.0 O3B D:ADP401 2.9 31.5 1.0 NE2 D:GLN137 3.1 35.9 1.0 OD2 D:ASP154 3.5 30.3 1.0 CD D:GLN137 3.8 35.9 1.0 P D:PO4403 3.9 35.7 1.0 OD1 D:ASP154 4.0 30.3 1.0 OE1 D:GLN137 4.1 35.9 1.0 CG D:ASP154 4.2 30.3 1.0 O3 D:PO4403 4.3 35.7 1.0 CG1 D:VAL339 4.3 37.1 1.0 PB D:ADP401 4.4 31.5 1.0 OD1 D:ASP11 4.5 37.9 1.0 O4 D:PO4403 4.6 35.7 1.0 CB D:VAL339 4.6 37.1 1.0 OD2 D:ASP11 4.6 37.9 1.0 CG D:GLN137 4.7 35.9 1.0 CG2 D:VAL339 4.8 37.1 1.0 O1B D:ADP401 4.8 31.5 1.0 O1 D:PO4403 4.9 35.7 1.0 CA D:GLY156 4.9 30.0 1.0 CG D:ASP11 5.0 37.9 1.0

Magnesium binding site 5 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:34.9 occ:1.00 O2 E:PO4403 2.5 33.6 1.0 O3B E:ADP401 2.7 34.8 1.0 NE2 E:GLN137 3.7 36.4 1.0 P E:PO4403 3.9 33.6 1.0 PB E:ADP401 4.1 34.8 1.0 OD2 E:ASP11 4.2 38.9 1.0 OD2 E:ASP154 4.2 32.1 1.0 CD E:GLN137 4.3 36.4 1.0 O2A E:ADP401 4.3 34.8 1.0 CG2 E:VAL339 4.4 37.8 1.0 O2B E:ADP401 4.5 34.8 1.0 NZ E:LYS18 4.5 38.4 1.0 OD1 E:ASP11 4.5 38.9 1.0 O4 E:PO4403 4.5 33.6 1.0 O3 E:PO4403 4.5 33.6 1.0 OD1 E:ASP154 4.6 32.1 1.0 OE1 E:GLN137 4.7 36.4 1.0 CB E:VAL339 4.8 37.8 1.0 CG E:ASP11 4.8 38.9 1.0 O3A E:ADP401 4.8 34.8 1.0 O1 E:PO4403 4.9 33.6 1.0 CG E:ASP154 4.9 32.1 1.0 CG E:GLN137 4.9 36.4 1.0 CG1 E:VAL339 5.0 37.8 1.0 CA E:GLY13 5.0 35.5 1.0

Magnesium binding site 6 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:31.0 occ:1.00 O3B F:ADP401 2.4 33.0 1.0 O2 F:PO4403 3.2 25.9 1.0 NE2 F:GLN137 3.4 27.2 1.0 OD2 F:ASP11 3.7 30.2 1.0 PB F:ADP401 3.8 33.0 1.0 CG2 F:VAL339 4.0 28.0 1.0 OD1 F:ASP11 4.0 30.2 1.0 O2B F:ADP401 4.1 33.0 1.0 CD F:GLN137 4.1 27.2 1.0 O1B F:ADP401 4.2 33.0 1.0 CG F:ASP11 4.3 30.2 1.0 CB F:VAL339 4.3 28.0 1.0 O3 F:PO4403 4.4 25.9 1.0 P F:PO4403 4.4 25.9 1.0 CG1 F:VAL339 4.6 28.0 1.0 NZ F:LYS18 4.7 30.7 1.0 OE1 F:GLN137 4.7 27.2 1.0 OD1 F:ASP154 4.7 24.9 1.0 CG F:GLN137 4.8 27.2 1.0 CA F:GLY13 4.9 28.9 1.0 O3A F:ADP401 5.0 33.0 1.0

Magnesium binding site 7 out of 7 in the Bent Adp-Pi-F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Bent Adp-Pi-F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:40.2 occ:1.00 O3B G:ADP401 2.9 34.8 1.0 O2 G:PO4403 3.2 37.0 1.0 OD2 G:ASP154 3.6 36.1 1.0 O2B G:ADP401 3.8 34.8 1.0 PB G:ADP401 3.9 34.8 1.0 CA G:GLY301 3.9 36.5 1.0 CG2 G:VAL339 4.1 42.9 1.0 OD1 G:ASP154 4.1 36.1 1.0 O2A G:ADP401 4.2 34.8 1.0 CG G:ASP154 4.2 36.1 1.0 O4 G:PO4403 4.4 37.0 1.0 CA G:GLY156 4.5 33.8 1.0 P G:PO4403 4.5 37.0 1.0 CB G:VAL339 4.6 42.9 1.0 NE2 G:GLN137 4.6 42.1 1.0 NZ G:LYS18 4.6 41.5 1.0 OD2 G:ASP11 4.6 43.4 1.0 O3A G:ADP401 4.6 34.8 1.0 N G:GLY301 4.6 36.5 1.0 PA G:ADP401 4.9 34.8 1.0 N G:GLY156 4.9 33.8 1.0 OG G:SER300 5.0 38.0 1.0 O1A G:ADP401 5.0 34.8 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