Magnesium in PDB 6t23: Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged)

The binding sites of Magnesium atom in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged) (pdb code 6t23). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged), PDB code: 6t23:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged)


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 Jasplakinolide-Stabilized F-Actin (Aged) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg378 b:15.9 occ:1.00 O3 A:PO4377 2.1 15.8 1.0 OE1 A:GLN137 2.3 17.8 1.0 O2B A:ADP376 2.3 18.1 1.0 CD A:GLN137 3.5 16.8 1.0 P A:PO4377 3.6 14.4 1.0 PB A:ADP376 3.6 13.4 1.0 OD2 A:ASP154 3.8 14.9 1.0 O3B A:ADP376 3.9 13.7 1.0 OD2 A:ASP11 4.0 18.7 1.0 OD1 A:ASP154 4.1 13.8 1.0 O4 A:PO4377 4.1 13.2 1.0 O2 A:PO4377 4.2 15.1 1.0 NE2 A:GLN137 4.2 18.1 1.0 OD1 A:ASP11 4.3 21.3 1.0 CG A:ASP154 4.4 13.9 1.0 O1 A:PO4377 4.5 14.2 1.0 O1B A:ADP376 4.5 14.5 1.0 O2A A:ADP376 4.5 13.0 1.0 CG A:ASP11 4.6 20.0 1.0 O3A A:ADP376 4.6 12.0 1.0 CG A:GLN137 4.7 16.4 1.0 CA A:GLY156 4.8 10.7 1.0 NZ A:LYS18 4.9 15.1 1.0 PA A:ADP376 5.0 10.7 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged)


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 Jasplakinolide-Stabilized F-Actin (Aged) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg378 b:15.9 occ:1.00 O3 B:PO4377 2.1 15.8 1.0 OE1 B:GLN137 2.3 17.8 1.0 O2B B:ADP376 2.3 18.1 1.0 CD B:GLN137 3.5 16.8 1.0 P B:PO4377 3.6 14.4 1.0 PB B:ADP376 3.6 13.4 1.0 OD2 B:ASP154 3.8 14.9 1.0 O3B B:ADP376 3.9 13.7 1.0 OD2 B:ASP11 4.0 18.7 1.0 OD1 B:ASP154 4.1 13.8 1.0 O4 B:PO4377 4.1 13.2 1.0 O2 B:PO4377 4.2 15.1 1.0 NE2 B:GLN137 4.2 18.1 1.0 OD1 B:ASP11 4.3 21.3 1.0 CG B:ASP154 4.4 13.9 1.0 O1 B:PO4377 4.5 14.2 1.0 O1B B:ADP376 4.5 14.5 1.0 O2A B:ADP376 4.5 13.0 1.0 CG B:ASP11 4.6 20.0 1.0 O3A B:ADP376 4.6 12.0 1.0 CG B:GLN137 4.7 16.4 1.0 CA B:GLY156 4.8 10.7 1.0 NZ B:LYS18 4.9 15.1 1.0 PA B:ADP376 5.0 10.7 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged)


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 Jasplakinolide-Stabilized F-Actin (Aged) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg378 b:15.9 occ:1.00 O3 C:PO4377 2.1 15.8 1.0 OE1 C:GLN137 2.3 17.8 1.0 O2B C:ADP376 2.3 18.1 1.0 CD C:GLN137 3.5 16.8 1.0 P C:PO4377 3.6 14.4 1.0 PB C:ADP376 3.6 13.4 1.0 OD2 C:ASP154 3.8 14.9 1.0 O3B C:ADP376 3.9 13.7 1.0 OD2 C:ASP11 4.0 18.7 1.0 OD1 C:ASP154 4.1 13.8 1.0 O4 C:PO4377 4.1 13.2 1.0 O2 C:PO4377 4.2 15.1 1.0 NE2 C:GLN137 4.2 18.1 1.0 OD1 C:ASP11 4.3 21.3 1.0 CG C:ASP154 4.4 13.9 1.0 O1 C:PO4377 4.5 14.2 1.0 O1B C:ADP376 4.5 14.5 1.0 O2A C:ADP376 4.5 13.0 1.0 CG C:ASP11 4.6 20.0 1.0 O3A C:ADP376 4.6 12.0 1.0 CG C:GLN137 4.7 16.4 1.0 CA C:GLY156 4.8 10.7 1.0 NZ C:LYS18 4.9 15.1 1.0 PA C:ADP376 5.0 10.7 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged)


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 Jasplakinolide-Stabilized F-Actin (Aged) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg378 b:15.9 occ:1.00 O3 D:PO4377 2.1 15.8 1.0 OE1 D:GLN137 2.3 17.8 1.0 O2B D:ADP376 2.3 18.1 1.0 CD D:GLN137 3.5 16.8 1.0 P D:PO4377 3.6 14.4 1.0 PB D:ADP376 3.6 13.4 1.0 OD2 D:ASP154 3.8 14.9 1.0 O3B D:ADP376 3.9 13.7 1.0 OD2 D:ASP11 4.0 18.7 1.0 OD1 D:ASP154 4.1 13.8 1.0 O4 D:PO4377 4.1 13.2 1.0 O2 D:PO4377 4.2 15.1 1.0 NE2 D:GLN137 4.2 18.1 1.0 OD1 D:ASP11 4.3 21.3 1.0 CG D:ASP154 4.4 13.9 1.0 O1 D:PO4377 4.5 14.2 1.0 O1B D:ADP376 4.5 14.5 1.0 O2A D:ADP376 4.5 13.0 1.0 CG D:ASP11 4.6 20.0 1.0 O3A D:ADP376 4.6 12.0 1.0 CG D:GLN137 4.7 16.4 1.0 CA D:GLY156 4.8 10.7 1.0 NZ D:LYS18 4.9 15.1 1.0 PA D:ADP376 5.0 10.7 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin (Aged)


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 Jasplakinolide-Stabilized F-Actin (Aged) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg378 b:15.9 occ:1.00 O3 E:PO4377 2.1 15.8 1.0 OE1 E:GLN137 2.3 17.8 1.0 O2B E:ADP376 2.3 18.1 1.0 CD E:GLN137 3.5 16.8 1.0 P E:PO4377 3.6 14.4 1.0 PB E:ADP376 3.6 13.4 1.0 OD2 E:ASP154 3.8 14.9 1.0 O3B E:ADP376 3.9 13.7 1.0 OD2 E:ASP11 4.0 18.7 1.0 OD1 E:ASP154 4.1 13.8 1.0 O4 E:PO4377 4.1 13.2 1.0 O2 E:PO4377 4.2 15.1 1.0 NE2 E:GLN137 4.2 18.1 1.0 OD1 E:ASP11 4.3 21.3 1.0 CG E:ASP154 4.4 13.9 1.0 O1 E:PO4377 4.5 14.2 1.0 O1B E:ADP376 4.5 14.5 1.0 O2A E:ADP376 4.5 13.0 1.0 CG E:ASP11 4.6 20.0 1.0 O3A E:ADP376 4.6 12.0 1.0 CG E:GLN137 4.7 16.4 1.0 CA E:GLY156 4.8 10.7 1.0 NZ E:LYS18 4.9 15.1 1.0 PA E:ADP376 5.0 10.7 1.0

S.Pospich, F.Merino, S.Raunser. Structural Effects and Functional Implications of Phalloidin and Jasplakinolide Binding to Actin Filaments. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32084355
DOI: 10.1016/J.STR.2020.01.014