Magnesium in PDB 8d17: Straight Adp-F-Actin 1

The binding sites of Magnesium atom in the Straight Adp-F-Actin 1 (pdb code 8d17). 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 1, PDB code: 8d17:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.2 occ:1.00 O2B A:ADP401 2.4 36.4 1.0 O3B A:ADP401 3.3 36.4 1.0 PB A:ADP401 3.4 36.4 1.0 HA3 A:GLY156 3.5 32.8 1.0 HA2 A:GLY156 3.8 32.8 1.0 OE1 A:GLN137 3.9 40.9 1.0 HG21 A:VAL339 3.9 41.4 1.0 HA2 A:GLY13 4.0 41.0 1.0 HE22 A:GLN137 4.0 40.9 1.0 CA A:GLY156 4.1 32.8 1.0 HA3 A:GLY13 4.2 41.0 1.0 O3A A:ADP401 4.2 36.4 1.0 CD A:GLN137 4.3 40.9 1.0 NE2 A:GLN137 4.3 40.9 1.0 O2A A:ADP401 4.3 36.4 1.0 OD2 A:ASP11 4.5 46.2 1.0 HA2 A:GLY301 4.5 34.6 1.0 O1B A:ADP401 4.5 36.4 1.0 OD2 A:ASP154 4.6 34.1 1.0 CA A:GLY13 4.6 41.0 1.0 OD1 A:ASP154 4.7 34.1 1.0 H A:ASP157 4.8 34.8 1.0 PA A:ADP401 4.8 36.4 1.0 N A:GLY156 4.8 32.8 1.0 H A:GLY156 4.8 32.8 1.0 H A:SER14 4.8 37.8 1.0 HE21 A:GLN137 4.9 40.9 1.0 CG2 A:VAL339 4.9 41.4 1.0 O1A A:ADP401 4.9 36.4 1.0 HB A:VAL339 5.0 41.4 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.1 occ:1.00 O3B B:ADP401 1.8 34.0 1.0 HE22 B:GLN137 2.5 36.8 1.0 NE2 B:GLN137 3.0 36.8 1.0 PB B:ADP401 3.1 34.0 1.0 HE21 B:GLN137 3.3 36.8 1.0 O2B B:ADP401 3.4 34.0 1.0 HZ1 B:LYS18 3.8 37.4 1.0 HA2 B:GLY13 3.8 35.4 1.0 CD B:GLN137 3.9 36.8 1.0 O1B B:ADP401 4.0 34.0 1.0 HA3 B:GLY13 4.0 35.4 1.0 HA3 B:GLY156 4.1 29.9 1.0 OE1 B:GLN137 4.2 36.8 1.0 OD1 B:ASP11 4.2 39.2 1.0 O3A B:ADP401 4.2 34.0 1.0 OD2 B:ASP11 4.3 39.2 1.0 CA B:GLY13 4.4 35.4 1.0 HA2 B:GLY156 4.4 29.9 1.0 HG21 B:VAL339 4.5 36.5 1.0 OD2 B:ASP154 4.5 31.5 1.0 HZ3 B:LYS18 4.5 37.4 1.0 NZ B:LYS18 4.5 37.4 1.0 H B:SER14 4.7 34.2 1.0 CG B:ASP11 4.7 39.2 1.0 O2A B:ADP401 4.7 34.0 1.0 CA B:GLY156 4.8 29.9 1.0 HG11 B:VAL339 4.9 36.5 1.0 HZ2 B:LYS18 4.9 37.4 1.0

Magnesium binding site 3 out of 7 in the Straight Adp-F-Actin 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:35.6 occ:1.00 O2B C:ADP401 2.4 33.5 1.0 O3B C:ADP401 3.3 33.5 1.0 PB C:ADP401 3.4 33.5 1.0 HA3 C:GLY156 3.4 32.4 1.0 HZ1 C:LYS18 3.5 39.3 1.0 HE22 C:GLN137 3.5 37.4 1.0 HA2 C:GLY156 3.8 32.4 1.0 NE2 C:GLN137 3.9 37.4 1.0 HG21 C:VAL339 4.0 39.5 1.0 OD1 C:ASP154 4.0 34.2 1.0 O2A C:ADP401 4.0 33.5 1.0 CA C:GLY156 4.1 32.4 1.0 HA2 C:GLY13 4.2 36.5 1.0 HE21 C:GLN137 4.2 37.4 1.0 O3A C:ADP401 4.2 33.5 1.0 HA2 C:GLY301 4.2 35.2 1.0 NZ C:LYS18 4.3 39.3 1.0 CD C:GLN137 4.3 37.4 1.0 OE1 C:GLN137 4.4 37.4 1.0 HZ2 C:LYS18 4.5 39.3 1.0 O1B C:ADP401 4.5 33.5 1.0 OD2 C:ASP11 4.6 41.1 1.0 PA C:ADP401 4.6 33.5 1.0 HA3 C:GLY13 4.7 36.5 1.0 HZ3 C:LYS18 4.7 39.3 1.0 H C:ASP157 4.7 31.9 1.0 H C:GLY156 4.7 32.4 1.0 N C:GLY156 4.8 32.4 1.0 O1A C:ADP401 4.8 33.5 1.0 CG2 C:VAL339 4.8 39.5 1.0 HG23 C:VAL339 4.8 39.5 1.0 HB C:VAL339 4.8 39.5 1.0 H C:GLY302 4.9 34.2 1.0 CA C:GLY13 4.9 36.5 1.0 H C:SER14 5.0 33.8 1.0 HA3 C:GLY301 5.0 35.2 1.0 OD1 C:ASP11 5.0 41.1 1.0

Magnesium binding site 4 out of 7 in the Straight Adp-F-Actin 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:42.4 occ:1.00 O3B D:ADP401 2.5 37.7 1.0 O2B D:ADP401 2.6 37.7 1.0 HZ1 D:LYS18 2.6 42.0 1.0 PB D:ADP401 3.1 37.7 1.0 NZ D:LYS18 3.5 42.0 1.0 O2A D:ADP401 3.6 37.7 1.0 HZ3 D:LYS18 3.8 42.0 1.0 HZ2 D:LYS18 3.9 42.0 1.0 O3A D:ADP401 3.9 37.7 1.0 HA3 D:GLY156 4.0 35.3 1.0 OD2 D:ASP11 4.0 43.7 1.0 HA3 D:GLY13 4.1 39.2 1.0 HA2 D:GLY301 4.1 37.5 1.0 PA D:ADP401 4.2 37.7 1.0 HA2 D:GLY13 4.2 39.2 1.0 HE22 D:GLN137 4.2 40.9 1.0 OE1 D:GLN137 4.2 40.9 1.0 HA2 D:GLY156 4.2 35.3 1.0 HG21 D:VAL339 4.2 42.9 1.0 O1B D:ADP401 4.2 37.7 1.0 O1A D:ADP401 4.3 37.7 1.0 HE3 D:LYS18 4.3 42.0 1.0 CE D:LYS18 4.3 42.0 1.0 HE2 D:LYS18 4.4 42.0 1.0 CA D:GLY156 4.6 35.3 1.0 NE2 D:GLN137 4.6 40.9 1.0 CA D:GLY13 4.6 39.2 1.0 OD1 D:ASP11 4.6 43.7 1.0 OD1 D:ASP154 4.6 38.6 1.0 CD D:GLN137 4.7 40.9 1.0 H D:GLY302 4.7 37.1 1.0 HB D:VAL339 4.7 42.9 1.0 H D:ASP157 4.8 36.1 1.0 CG D:ASP11 4.8 43.7 1.0 H D:SER14 4.9 37.2 1.0

Magnesium binding site 5 out of 7 in the Straight Adp-F-Actin 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:34.9 occ:1.00 OE1 E:GLN137 2.8 35.0 1.0 O2B E:ADP401 3.3 34.8 1.0 HG21 E:VAL339 3.6 36.0 1.0 OD1 E:ASP154 3.6 30.8 1.0 HA3 E:GLY156 3.8 31.0 1.0 HZ1 E:LYS18 3.8 38.5 1.0 O3B E:ADP401 3.8 34.8 1.0 CD E:GLN137 4.0 35.0 1.0 PB E:ADP401 4.0 34.8 1.0 OD2 E:ASP154 4.0 30.8 1.0 HA2 E:GLY156 4.1 31.0 1.0 CG E:ASP154 4.3 30.8 1.0 HA2 E:GLY301 4.3 32.3 1.0 HE22 E:GLN137 4.4 35.0 1.0 CA E:GLY156 4.4 31.0 1.0 O3A E:ADP401 4.5 34.8 1.0 CG2 E:VAL339 4.5 36.0 1.0 OD2 E:ASP11 4.5 39.5 1.0 O2A E:ADP401 4.5 34.8 1.0 HB E:VAL339 4.5 36.0 1.0 HG23 E:VAL339 4.6 36.0 1.0 NE2 E:GLN137 4.6 35.0 1.0 NZ E:LYS18 4.7 38.5 1.0 HA3 E:GLY301 4.8 32.3 1.0 HG11 E:VAL339 4.8 36.0 1.0 HA3 E:GLY13 5.0 36.9 1.0 HB3 E:GLN137 5.0 35.0 1.0 HA2 E:GLY13 5.0 36.9 1.0 CA E:GLY301 5.0 32.3 1.0 CB E:VAL339 5.0 36.0 1.0

Magnesium binding site 6 out of 7 in the Straight Adp-F-Actin 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:32.6 occ:1.00 O3B F:ADP401 2.5 36.1 1.0 HG21 F:VAL339 3.7 39.0 1.0 OE1 F:GLN137 3.7 37.5 1.0 OD2 F:ASP154 3.8 33.8 1.0 HE22 F:GLN137 3.8 37.5 1.0 HA3 F:GLY156 3.9 33.3 1.0 PB F:ADP401 3.9 36.1 1.0 OD1 F:ASP154 4.0 33.8 1.0 HA2 F:GLY156 4.0 33.3 1.0 CD F:GLN137 4.1 37.5 1.0 NE2 F:GLN137 4.1 37.5 1.0 HZ1 F:LYS18 4.2 39.5 1.0 CG F:ASP154 4.3 33.8 1.0 HA2 F:GLY301 4.4 37.0 1.0 CA F:GLY156 4.4 33.3 1.0 O1B F:ADP401 4.5 36.1 1.0 CG2 F:VAL339 4.5 39.0 1.0 HA3 F:GLY13 4.6 37.4 1.0 HE21 F:GLN137 4.6 37.5 1.0 HB F:VAL339 4.6 39.0 1.0 O2A F:ADP401 4.6 36.1 1.0 HG23 F:VAL339 4.7 39.0 1.0 O3A F:ADP401 4.7 36.1 1.0 O2B F:ADP401 4.7 36.1 1.0 HB3 F:GLN137 4.7 37.5 1.0 HG11 F:VAL339 4.9 39.0 1.0 HA2 F:GLY13 4.9 37.4 1.0 HA3 F:GLY301 4.9 37.0 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:37.0 occ:1.00 OE1 G:GLN137 2.6 49.2 1.0 O2B G:ADP401 2.7 43.5 1.0 HE22 G:GLN137 3.2 49.2 1.0 CD G:GLN137 3.4 49.2 1.0 O3B G:ADP401 3.4 43.5 1.0 NE2 G:GLN137 3.6 49.2 1.0 HA3 G:GLY156 3.7 40.8 1.0 PB G:ADP401 3.7 43.5 1.0 HG12 G:VAL339 4.0 49.9 1.0 HA2 G:GLY13 4.0 47.2 1.0 OD2 G:ASP154 4.1 42.8 1.0 O1B G:ADP401 4.3 43.5 1.0 H G:SER14 4.3 43.3 1.0 HE21 G:GLN137 4.4 49.2 1.0 HA2 G:GLY156 4.5 40.8 1.0 CA G:GLY156 4.5 40.8 1.0 HA3 G:GLY13 4.5 47.2 1.0 HZ3 G:LYS18 4.6 51.0 1.0 HB3 G:GLN137 4.7 49.2 1.0 HG22 G:VAL339 4.7 49.9 1.0 OD2 G:ASP11 4.7 51.6 1.0 CG G:GLN137 4.7 49.2 1.0 HG G:SER14 4.7 43.3 1.0 OD1 G:ASP154 4.7 42.8 1.0 CA G:GLY13 4.7 47.2 1.0 OD1 G:ASP11 4.7 51.6 1.0 CG G:ASP154 4.9 42.8 1.0 HG2 G:GLN137 4.9 49.2 1.0 H G:ASP157 4.9 41.0 1.0 CG1 G:VAL339 4.9 49.9 1.0 HB G:VAL339 4.9 49.9 1.0 HZ1 G:LYS18 5.0 51.0 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