Magnesium in PDB 8f8t: Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin

The binding sites of Magnesium atom in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin (pdb code 8f8t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin, PDB code: 8f8t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


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 the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:116.8 occ:1.00 O1B A:ADP401 2.1 131.5 1.0 O2B A:ADP401 2.8 131.7 1.0 PB A:ADP401 2.9 140.4 1.0 OD2 A:ASP11 2.9 141.7 1.0 OD1 A:ASP11 3.4 140.9 1.0 CG A:ASP11 3.6 140.6 1.0 NZ A:LYS18 3.6 135.8 1.0 O3A A:ADP401 3.8 129.6 1.0 CE A:LYS18 4.2 131.0 1.0 O3B A:ADP401 4.2 127.2 1.0 CG2 A:VAL339 4.5 108.4 1.0 CA A:GLY13 4.5 133.2 1.0 CD A:GLN137 4.6 131.0 1.0 CG A:GLN137 4.6 128.0 1.0 NE2 A:GLN137 4.7 133.7 1.0 O1A A:ADP401 4.7 130.9 1.0 CB A:VAL339 4.7 103.8 1.0 PA A:ADP401 4.7 126.1 1.0 CG1 A:VAL339 4.8 108.5 1.0 N A:GLY13 4.9 130.2 1.0 OE1 A:GLN137 5.0 131.9 1.0

Magnesium binding site 2 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


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 the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:75.0 occ:1.00 O1B B:ADP401 2.8 121.7 1.0 OE1 B:GLN137 3.0 114.5 1.0 CD B:GLN137 3.7 116.8 1.0 NE2 B:GLN137 4.0 122.0 1.0 OD1 B:ASP154 4.1 113.7 1.0 PB B:ADP401 4.1 129.4 1.0 O1A B:ADP401 4.2 123.4 1.0 OD2 B:ASP11 4.4 147.9 1.0 CA B:GLY13 4.4 137.5 1.0 O3B B:ADP401 4.4 117.8 1.0 OD1 B:ASP11 4.5 148.3 1.0 NZ B:LYS18 4.8 122.9 1.0 CG B:ASP11 4.8 147.0 1.0 CG B:ASP154 5.0 106.5 1.0 CG B:GLN137 5.0 116.8 1.0 CG2 B:VAL339 5.0 107.9 1.0

Magnesium binding site 3 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


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 the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:50.2 occ:1.00 O1B C:ADP401 2.1 109.8 1.0 O1A C:ADP401 3.3 111.2 1.0 PB C:ADP401 3.4 113.8 1.0 OE1 C:GLN137 3.6 115.0 1.0 O3B C:ADP401 3.6 99.8 1.0 O3A C:ADP401 4.2 113.3 1.0 OD1 C:ASP154 4.3 120.7 1.0 PA C:ADP401 4.3 119.8 1.0 NZ C:LYS18 4.3 97.5 1.0 OD2 C:ASP11 4.4 126.6 1.0 CD C:GLN137 4.5 112.4 1.0 O2B C:ADP401 4.5 107.4 1.0 CA C:GLY156 4.6 100.0 1.0 CA C:GLY13 4.6 106.6 1.0 NE2 C:GLN137 4.8 108.4 1.0 OD1 C:ASP11 4.9 124.5 1.0

Magnesium binding site 4 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


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 the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:84.5 occ:1.00 O1B D:ADP401 2.4 134.2 1.0 O1A D:ADP401 3.1 134.8 1.0 PB D:ADP401 3.6 135.2 1.0 OE1 D:GLN137 3.7 134.5 1.0 O3B D:ADP401 3.9 123.5 1.0 OD1 D:ASP154 4.0 129.7 1.0 PA D:ADP401 4.2 141.0 1.0 O3A D:ADP401 4.3 138.4 1.0 NZ D:LYS18 4.3 109.5 1.0 OD2 D:ASP11 4.4 143.3 1.0 CD D:GLN137 4.5 130.1 1.0 CA D:GLY156 4.7 113.1 1.0 CG2 D:VAL339 4.8 111.4 1.0 O2A D:ADP401 4.9 135.5 1.0 O2B D:ADP401 4.9 130.8 1.0 CG D:ASP154 4.9 128.0 1.0 NE2 D:GLN137 5.0 127.0 1.0 OD2 D:ASP154 5.0 130.9 1.0

Magnesium binding site 5 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:88.5 occ:1.00 O1B E:ADP401 2.1 134.0 1.0 PB E:ADP401 3.4 128.3 1.0 OE1 E:GLN137 3.4 120.0 1.0 O1A E:ADP401 3.5 127.3 1.0 O3B E:ADP401 3.7 122.0 1.0 OD1 E:ASP154 4.2 138.2 1.0 CD E:GLN137 4.3 122.0 1.0 NZ E:LYS18 4.3 106.8 1.0 O3A E:ADP401 4.3 128.5 1.0 OD2 E:ASP11 4.5 134.6 1.0 PA E:ADP401 4.5 134.1 1.0 O2B E:ADP401 4.5 128.8 1.0 CA E:GLY13 4.5 129.0 1.0 NE2 E:GLN137 4.5 120.7 1.0 CA E:GLY156 4.6 122.3 1.0 OD1 E:ASP11 4.9 140.0 1.0

Magnesium binding site 6 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:62.3 occ:1.00 O1B F:ADP401 2.1 133.1 1.0 PB F:ADP401 3.2 130.2 1.0 O1A F:ADP401 3.2 132.4 1.0 O3B F:ADP401 3.3 121.5 1.0 OE1 F:GLN137 3.7 124.5 1.0 CA F:GLY156 4.1 115.9 1.0 OD1 F:ASP154 4.2 144.8 1.0 O3A F:ADP401 4.2 126.8 1.0 PA F:ADP401 4.3 135.0 1.0 O2B F:ADP401 4.4 132.2 1.0 CD F:GLN137 4.6 123.3 1.0 NZ F:LYS18 4.6 107.6 1.0 CA F:GLY13 4.6 134.8 1.0 N F:GLY156 4.8 113.4 1.0 NE2 F:GLN137 4.8 122.0 1.0 OD2 F:ASP11 4.9 140.8 1.0

Magnesium binding site 7 out of 7 in the Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Tropomodulin-Capped Pointed End of F-Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:91.0 occ:1.00 O1B G:ADP401 2.1 144.6 1.0 O1A G:ADP401 2.3 138.2 1.0 PB G:ADP401 3.1 147.2 1.0 O3B G:ADP401 3.1 132.0 1.0 PA G:ADP401 3.5 142.7 1.0 O3A G:ADP401 3.7 139.7 1.0 CA G:GLY156 4.0 133.7 1.0 OD1 G:ASP154 4.2 159.3 1.0 NZ G:LYS18 4.3 120.5 1.0 OE1 G:GLN137 4.3 135.8 1.0 O2A G:ADP401 4.3 140.9 1.0 O2B G:ADP401 4.4 139.5 1.0 N G:GLY156 4.7 132.2 1.0 O5' G:ADP401 4.7 137.7 1.0 OD2 G:ASP11 4.9 151.8 1.0

P.J.Carman, K.R.Barrie, G.Rebowski, R.Dominguez. Structures of the Free and Capped Ends of the Actin Filament. Science G6812 2023.
ISSN: ESSN 1095-9203
PubMed: 37228182
DOI: 10.1126/SCIENCE.ADG6812