Magnesium in PDB 5ood: Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin in Complex with Adp-Pi

The binding sites of Magnesium atom in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin in Complex with Adp-Pi (pdb code 5ood). 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 in Complex with Adp-Pi, PDB code: 5ood:
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 in Complex with Adp-Pi


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 in Complex with Adp-Pi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:46.4 occ:1.00 O3 A:PO4402 2.0 43.4 1.0 O3B A:ADP401 2.0 37.8 1.0 PB A:ADP401 3.2 33.5 1.0 P A:PO4402 3.4 49.7 1.0 O2B A:ADP401 3.5 40.0 1.0 O4 A:PO4402 3.6 44.3 1.0 O1B A:ADP401 3.7 37.1 1.0 OD1 A:ASP154 3.8 42.5 1.0 O1 A:PO4402 4.1 40.5 1.0 OE1 A:GLN137 4.2 44.6 1.0 OD2 A:ASP154 4.2 48.8 1.0 O2A A:ADP401 4.3 39.1 1.0 O2 A:PO4402 4.3 44.2 1.0 O3A A:ADP401 4.4 33.4 1.0 CG A:ASP154 4.5 42.8 1.0 CA A:GLY156 4.5 37.5 1.0 O1A A:ADP401 4.6 39.2 1.0 CD A:GLN137 4.6 50.3 1.0 PA A:ADP401 4.6 35.6 1.0 N A:GLY156 4.8 34.1 1.0 NE2 A:GLN137 4.8 51.4 1.0 OD2 A:ASP11 4.8 50.7 1.0 CG2 A:VAL339 4.9 45.9 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin in Complex with Adp-Pi


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 in Complex with Adp-Pi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:49.0 occ:1.00 O3 B:PO4402 2.0 47.2 1.0 O3B B:ADP401 2.0 40.6 1.0 PB B:ADP401 3.2 32.9 1.0 P B:PO4402 3.4 60.0 1.0 O2B B:ADP401 3.5 41.7 1.0 O4 B:PO4402 3.6 46.5 1.0 O1B B:ADP401 3.7 38.9 1.0 OD1 B:ASP154 3.8 45.2 1.0 O1 B:PO4402 4.1 43.6 1.0 OE1 B:GLN137 4.2 46.9 1.0 OD2 B:ASP154 4.2 47.0 1.0 O2A B:ADP401 4.3 42.0 1.0 O2 B:PO4402 4.3 50.2 1.0 O3A B:ADP401 4.4 32.7 1.0 CG B:ASP154 4.4 46.6 1.0 CA B:GLY156 4.5 38.2 1.0 O1A B:ADP401 4.6 39.0 1.0 CD B:GLN137 4.6 50.9 1.0 PA B:ADP401 4.6 32.8 1.0 N B:GLY156 4.8 36.6 1.0 NE2 B:GLN137 4.8 50.8 1.0 OD2 B:ASP11 4.8 52.6 1.0 CG2 B:VAL339 4.9 47.7 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin in Complex with Adp-Pi


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 in Complex with Adp-Pi within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:50.1 occ:1.00 O3 C:PO4402 2.0 42.7 1.0 O3B C:ADP401 2.0 38.6 1.0 PB C:ADP401 3.2 37.2 1.0 P C:PO4402 3.4 51.3 1.0 O2B C:ADP401 3.5 38.0 1.0 O4 C:PO4402 3.6 42.4 1.0 O1B C:ADP401 3.7 41.1 1.0 OD1 C:ASP154 3.8 43.9 1.0 O1 C:PO4402 4.1 42.8 1.0 OE1 C:GLN137 4.2 39.5 1.0 OD2 C:ASP154 4.2 41.1 1.0 O2A C:ADP401 4.3 39.4 1.0 O2 C:PO4402 4.3 46.2 1.0 O3A C:ADP401 4.4 36.9 1.0 CG C:ASP154 4.4 41.9 1.0 CA C:GLY156 4.5 38.0 1.0 O1A C:ADP401 4.6 37.1 1.0 CD C:GLN137 4.6 40.2 1.0 PA C:ADP401 4.6 36.0 1.0 N C:GLY156 4.8 35.6 1.0 NE2 C:GLN137 4.8 43.8 1.0 OD2 C:ASP11 4.8 41.6 1.0 CG2 C:VAL339 4.9 38.3 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin in Complex with Adp-Pi


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 in Complex with Adp-Pi within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:48.3 occ:1.00 O3 D:PO4402 2.0 44.6 1.0 O3B D:ADP401 2.0 38.6 1.0 PB D:ADP401 3.2 31.4 1.0 P D:PO4402 3.4 63.6 1.0 O2B D:ADP401 3.5 39.8 1.0 O4 D:PO4402 3.6 44.6 1.0 O1B D:ADP401 3.7 37.8 1.0 OD1 D:ASP154 3.8 45.6 1.0 O1 D:PO4402 4.1 44.2 1.0 OE1 D:GLN137 4.2 45.1 1.0 OD2 D:ASP154 4.2 49.1 1.0 O2A D:ADP401 4.3 35.3 1.0 O2 D:PO4402 4.3 44.7 1.0 O3A D:ADP401 4.4 36.0 1.0 CG D:ASP154 4.4 46.7 1.0 CA D:GLY156 4.5 38.2 1.0 O1A D:ADP401 4.6 42.0 1.0 CD D:GLN137 4.6 53.8 1.0 PA D:ADP401 4.6 34.8 1.0 N D:GLY156 4.8 36.2 1.0 NE2 D:GLN137 4.8 57.8 1.0 OD2 D:ASP11 4.8 45.5 1.0 CG2 D:VAL339 4.9 46.6 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Jasplakinolide-Stabilized F-Actin in Complex with Adp-Pi


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 in Complex with Adp-Pi within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg403 b:57.0 occ:1.00 O3 E:PO4402 2.0 51.6 1.0 O3B E:ADP401 2.0 47.5 1.0 PB E:ADP401 3.2 45.9 1.0 P E:PO4402 3.4 60.3 1.0 O2B E:ADP401 3.5 52.5 1.0 O4 E:PO4402 3.6 53.2 1.0 O1B E:ADP401 3.7 48.5 1.0 OD1 E:ASP154 3.8 50.4 1.0 O1 E:PO4402 4.1 48.5 1.0 OE1 E:GLN137 4.2 49.9 1.0 OD2 E:ASP154 4.2 48.3 1.0 O2A E:ADP401 4.3 51.1 1.0 O2 E:PO4402 4.3 58.1 1.0 O3A E:ADP401 4.4 47.3 1.0 CG E:ASP154 4.5 51.2 1.0 CA E:GLY156 4.5 44.8 1.0 O1A E:ADP401 4.6 45.9 1.0 CD E:GLN137 4.6 51.6 1.0 PA E:ADP401 4.6 46.3 1.0 N E:GLY156 4.8 41.0 1.0 NE2 E:GLN137 4.8 55.7 1.0 OD2 E:ASP11 4.8 58.5 1.0 CG2 E:VAL339 4.9 47.7 1.0

F.Merino, S.Pospich, J.Funk, T.Wagner, F.Kullmer, H.D.Arndt, P.Bieling, S.Raunser. Structural Transitions of F-Actin Upon Atp Hydrolysis at Near-Atomic Resolution Revealed By Cryo-Em. Nat. Struct. Mol. Biol. V. 25 528 2018.
ISSN: ESSN 1545-9985
PubMed: 29867215
DOI: 10.1038/S41594-018-0074-0