Magnesium in PDB 8d18: Straight Adp-F-Actin 2

The binding sites of Magnesium atom in the Straight Adp-F-Actin 2 (pdb code 8d18). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Straight Adp-F-Actin 2, PDB code: 8d18:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Straight Adp-F-Actin 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:36.8 occ:1.00 HE22 A:GLN137 2.6 32.9 1.0 O2B A:ADP401 3.1 29.5 1.0 OE1 A:GLN137 3.2 32.9 1.0 NE2 A:GLN137 3.3 32.9 1.0 HA2 A:GLY13 3.5 32.0 1.0 CD A:GLN137 3.6 32.9 1.0 HA3 A:GLY13 3.8 32.0 1.0 HA3 A:GLY156 3.9 24.0 1.0 H A:SER14 3.9 29.3 1.0 HG11 A:VAL159 3.9 24.9 1.0 HE21 A:GLN137 3.9 32.9 1.0 CA A:GLY13 4.1 32.0 1.0 HG A:SER14 4.2 29.3 1.0 HG13 A:VAL159 4.2 24.9 1.0 HB1 A:ALA108 4.4 29.5 1.0 CG1 A:VAL159 4.5 24.9 1.0 PB A:ADP401 4.5 29.5 1.0 HE1 A:HIS161 4.6 25.2 1.0 N A:SER14 4.6 29.3 1.0 H A:GLY158 4.7 25.6 1.0 HG12 A:VAL159 4.7 24.9 1.0 H A:VAL159 4.7 24.9 1.0 H A:ASP157 4.7 26.8 1.0 OD2 A:ASP154 4.8 26.4 1.0 O3B A:ADP401 4.8 29.5 1.0 CA A:GLY156 4.8 24.0 1.0 C A:GLY13 4.9 32.0 1.0 CG A:GLN137 5.0 32.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:31.8 occ:1.00 O2B B:ADP401 2.1 24.4 1.0 HA3 B:GLY156 3.0 22.4 1.0 HE22 B:GLN137 3.3 27.1 1.0 OE1 B:GLN137 3.3 27.1 1.0 HA2 B:GLY156 3.4 22.4 1.0 PB B:ADP401 3.5 24.4 1.0 OD1 B:ASP154 3.6 23.0 1.0 CA B:GLY156 3.7 22.4 1.0 O3B B:ADP401 3.7 24.4 1.0 NE2 B:GLN137 3.8 27.1 1.0 CD B:GLN137 3.8 27.1 1.0 H B:ASP157 4.2 24.5 1.0 O1B B:ADP401 4.3 24.4 1.0 O3A B:ADP401 4.4 24.4 1.0 HA2 B:GLY301 4.4 22.0 1.0 HG22 B:VAL339 4.4 26.9 1.0 HE21 B:GLN137 4.5 27.1 1.0 N B:GLY156 4.5 22.4 1.0 H B:GLY156 4.5 22.4 1.0 CG B:ASP154 4.6 23.0 1.0 OD2 B:ASP154 4.7 23.0 1.0 HA2 B:GLY13 4.8 28.2 1.0 H B:SER14 4.8 25.6 1.0 N B:ASP157 4.8 24.5 1.0 C B:GLY156 4.8 22.4 1.0 HZ1 B:LYS18 4.8 28.9 1.0 HA3 B:GLY13 4.9 28.2 1.0 O2A B:ADP401 4.9 24.4 1.0 HA3 B:GLY301 4.9 22.0 1.0

Magnesium binding site 3 out of 7 in the Straight Adp-F-Actin 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:22.4 occ:1.00 O2B C:ADP401 2.0 26.2 1.0 PB C:ADP401 3.2 26.2 1.0 O3B C:ADP401 3.3 26.2 1.0 HA3 C:GLY156 3.8 23.3 1.0 HE22 C:GLN137 3.8 29.0 1.0 HZ1 C:LYS18 3.8 29.7 1.0 HA2 C:GLY13 3.9 27.3 1.0 O1B C:ADP401 4.1 26.2 1.0 OE1 C:GLN137 4.1 29.0 1.0 NE2 C:GLN137 4.2 29.0 1.0 HG21 C:VAL339 4.2 29.9 1.0 O3A C:ADP401 4.2 26.2 1.0 HA3 C:GLY13 4.2 27.3 1.0 O2A C:ADP401 4.3 26.2 1.0 OD1 C:ASP154 4.3 24.4 1.0 CD C:GLN137 4.3 29.0 1.0 OD2 C:ASP11 4.6 29.6 1.0 CA C:GLY13 4.6 27.3 1.0 H C:SER14 4.6 24.7 1.0 HA2 C:GLY156 4.6 23.3 1.0 CA C:GLY156 4.6 23.3 1.0 HE21 C:GLN137 4.7 29.0 1.0 NZ C:LYS18 4.7 29.7 1.0 H C:ASP157 4.7 24.7 1.0 HA2 C:GLY301 4.8 25.6 1.0 PA C:ADP401 4.8 26.2 1.0 OD1 C:ASP11 4.9 29.6 1.0 HZ2 C:LYS18 4.9 29.7 1.0

Magnesium binding site 4 out of 7 in the Straight Adp-F-Actin 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:23.8 occ:1.00 O3B D:ADP401 2.1 26.2 1.0 HE22 D:GLN137 3.3 31.5 1.0 PB D:ADP401 3.5 26.2 1.0 OE1 D:GLN137 3.6 31.5 1.0 HG21 D:VAL339 3.7 31.4 1.0 NE2 D:GLN137 3.7 31.5 1.0 HA3 D:GLY156 3.7 24.5 1.0 CD D:GLN137 3.9 31.5 1.0 HZ1 D:LYS18 3.9 32.0 1.0 HA2 D:GLY156 3.9 24.5 1.0 OD1 D:ASP154 3.9 26.2 1.0 O1B D:ADP401 4.0 26.2 1.0 OD2 D:ASP11 4.0 32.2 1.0 O2B D:ADP401 4.1 26.2 1.0 HA2 D:GLY13 4.2 30.3 1.0 HA3 D:GLY13 4.2 30.3 1.0 OD1 D:ASP11 4.3 32.2 1.0 HE21 D:GLN137 4.3 31.5 1.0 CA D:GLY156 4.3 24.5 1.0 O3A D:ADP401 4.5 26.2 1.0 CG2 D:VAL339 4.5 31.4 1.0 CG D:ASP11 4.6 32.2 1.0 HG11 D:VAL339 4.6 31.4 1.0 O2A D:ADP401 4.6 26.2 1.0 CA D:GLY13 4.7 30.3 1.0 HG22 D:VAL339 4.7 31.4 1.0 NZ D:LYS18 4.7 32.0 1.0 HA2 D:GLY301 4.7 25.8 1.0 HZ3 D:LYS18 4.8 32.0 1.0 H D:ASP157 4.8 26.2 1.0 HB D:VAL339 4.8 31.4 1.0 CG D:ASP154 4.9 26.2 1.0 H D:SER14 4.9 27.3 1.0 HG2 D:GLN137 5.0 31.5 1.0 HB3 D:GLN137 5.0 31.5 1.0 H D:GLY156 5.0 24.5 1.0 OD2 D:ASP154 5.0 26.2 1.0

Magnesium binding site 5 out of 7 in the Straight Adp-F-Actin 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:26.3 occ:1.00 OE1 E:GLN137 2.3 28.4 1.0 O3B E:ADP401 2.4 26.8 1.0 HG21 E:VAL339 3.3 30.4 1.0 CD E:GLN137 3.5 28.4 1.0 OD1 E:ASP154 3.8 24.6 1.0 HA3 E:GLY156 3.9 24.1 1.0 PB E:ADP401 3.9 26.8 1.0 OD2 E:ASP154 3.9 24.6 1.0 HE22 E:GLN137 3.9 28.4 1.0 HA2 E:GLY301 4.0 25.8 1.0 NE2 E:GLN137 4.1 28.4 1.0 CG2 E:VAL339 4.2 30.4 1.0 HB3 E:GLN137 4.3 28.4 1.0 CG E:ASP154 4.3 24.6 1.0 O1B E:ADP401 4.4 26.8 1.0 HA2 E:GLY156 4.4 24.1 1.0 HG23 E:VAL339 4.4 30.4 1.0 O2B E:ADP401 4.5 26.8 1.0 HB E:VAL339 4.6 30.4 1.0 CA E:GLY156 4.6 24.1 1.0 CG E:GLN137 4.6 28.4 1.0 HG11 E:VAL339 4.6 30.4 1.0 HG2 E:GLN137 4.6 28.4 1.0 HA3 E:GLY301 4.8 25.8 1.0 CA E:GLY301 4.8 25.8 1.0 O3A E:ADP401 4.9 26.8 1.0 CB E:VAL339 4.9 30.4 1.0 HG22 E:VAL339 4.9 30.4 1.0 CB E:GLN137 4.9 28.4 1.0 OD2 E:ASP11 4.9 32.9 1.0 O2A E:ADP401 4.9 26.8 1.0 HE21 E:GLN137 5.0 28.4 1.0

Magnesium binding site 6 out of 7 in the Straight Adp-F-Actin 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:29.2 occ:1.00 O2B F:ADP401 2.2 31.6 1.0 HA3 F:GLY156 3.5 27.6 1.0 OE1 F:GLN137 3.6 33.7 1.0 PB F:ADP401 3.6 31.6 1.0 HG21 F:VAL339 3.7 35.9 1.0 HE22 F:GLN137 3.8 33.7 1.0 HA2 F:GLY156 3.8 27.6 1.0 OD2 F:ASP154 3.9 29.4 1.0 CD F:GLN137 4.1 33.7 1.0 CA F:GLY156 4.1 27.6 1.0 NE2 F:GLN137 4.1 33.7 1.0 O3B F:ADP401 4.2 31.6 1.0 OD1 F:ASP154 4.2 29.4 1.0 O3A F:ADP401 4.4 31.6 1.0 HZ1 F:LYS18 4.4 37.7 1.0 HA2 F:GLY301 4.4 31.7 1.0 O1B F:ADP401 4.4 31.6 1.0 HG23 F:VAL339 4.5 35.9 1.0 CG F:ASP154 4.5 29.4 1.0 CG2 F:VAL339 4.5 35.9 1.0 O2A F:ADP401 4.5 31.6 1.0 HA2 F:GLY13 4.7 35.4 1.0 N F:GLY156 4.7 27.6 1.0 OD2 F:ASP11 4.7 38.7 1.0 HE21 F:GLN137 4.8 33.7 1.0 H F:ASP157 4.8 29.4 1.0 HG12 F:VAL339 4.8 35.9 1.0 HB3 F:GLN137 4.9 33.7 1.0 H F:GLY156 4.9 27.6 1.0 HA3 F:GLY301 5.0 31.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Straight Adp-F-Actin 2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:40.5 occ:1.00 O3B G:ADP401 2.7 38.6 1.0 OD2 G:ASP11 2.9 45.7 1.0 HG21 G:VAL339 3.0 45.1 1.0 HB G:VAL339 3.4 45.1 1.0 HZ3 G:LYS18 3.8 42.3 1.0 CG2 G:VAL339 3.9 45.1 1.0 CG G:ASP11 3.9 45.7 1.0 HG11 G:VAL339 3.9 45.1 1.0 O2B G:ADP401 4.0 38.6 1.0 CB G:VAL339 4.0 45.1 1.0 PB G:ADP401 4.0 38.6 1.0 OD1 G:ASP11 4.1 45.7 1.0 HD2 G:LYS18 4.2 42.3 1.0 HG13 G:VAL339 4.3 45.1 1.0 CG1 G:VAL339 4.3 45.1 1.0 HA3 G:GLY13 4.3 41.5 1.0 HG23 G:VAL339 4.4 45.1 1.0 HG22 G:VAL339 4.5 45.1 1.0 HA2 G:GLY13 4.5 41.5 1.0 HE2 G:LYS18 4.6 42.3 1.0 NZ G:LYS18 4.6 42.3 1.0 O1B G:ADP401 4.7 38.6 1.0 NE2 G:GLN137 4.8 45.4 1.0 CD G:GLN137 4.8 45.4 1.0 HE22 G:GLN137 4.8 45.4 1.0 HA2 G:GLY301 4.8 40.2 1.0 OE1 G:GLN137 4.8 45.4 1.0 HG2 G:GLN137 4.8 45.4 1.0 O1A G:ADP401 4.9 38.6 1.0 HA2 G:GLY156 4.9 37.3 1.0 CA G:GLY13 4.9 41.5 1.0 O2A G:ADP401 4.9 38.6 1.0 OD2 G:ASP154 4.9 40.4 1.0 CE G:LYS18 5.0 42.3 1.0 HZ2 G:LYS18 5.0 42.3 1.0 CD G:LYS18 5.0 42.3 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