Magnesium in PDB 5oof: Cryo-Em Structure of F-Actin in Complex with Adp-Befx

The binding sites of Magnesium atom in the Cryo-Em Structure of F-Actin in Complex with Adp-Befx (pdb code 5oof). 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 F-Actin in Complex with Adp-Befx, PDB code: 5oof:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of F-Actin in Complex with Adp-Befx


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 F-Actin in Complex with Adp-Befx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:38.1 occ:1.00 O1B A:ADP401 2.0 33.1 1.0 PB A:ADP401 3.3 31.2 1.0 O3B A:ADP401 3.6 34.8 1.0 O1A A:ADP401 4.0 34.4 1.0 OE1 A:GLN137 4.0 45.9 1.0 O3A A:ADP401 4.2 29.9 1.0 OD2 A:ASP11 4.2 39.0 1.0 OD1 A:ASP154 4.3 43.8 1.0 NE2 A:GLN137 4.3 45.3 1.0 CD A:GLN137 4.3 44.8 1.0 O2B A:ADP401 4.4 34.3 1.0 OD1 A:ASP11 4.4 39.5 1.0 OD2 A:ASP154 4.4 42.4 1.0 NZ A:LYS18 4.5 37.4 1.0 PA A:ADP401 4.5 32.6 1.0 CG A:ASP11 4.8 38.9 1.0 CG A:ASP154 4.8 43.9 1.0 O2A A:ADP401 4.8 37.1 1.0 CG2 A:VAL339 4.9 41.3 1.0 CA A:GLY13 5.0 33.2 1.0

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


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 F-Actin in Complex with Adp-Befx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.1 occ:1.00 O1B B:ADP401 2.0 33.0 1.0 PB B:ADP401 3.3 26.9 1.0 O3B B:ADP401 3.6 31.3 1.0 O1A B:ADP401 4.0 30.7 1.0 OE1 B:GLN137 4.0 44.3 1.0 O3A B:ADP401 4.2 25.7 1.0 OD2 B:ASP11 4.2 38.0 1.0 OD1 B:ASP154 4.3 36.8 1.0 NE2 B:GLN137 4.3 40.8 1.0 CD B:GLN137 4.3 42.8 1.0 O2B B:ADP401 4.4 30.7 1.0 OD1 B:ASP11 4.4 37.8 1.0 OD2 B:ASP154 4.4 37.8 1.0 NZ B:LYS18 4.5 32.7 1.0 PA B:ADP401 4.5 26.4 1.0 CG B:ASP11 4.8 38.4 1.0 CG B:ASP154 4.8 36.6 1.0 O2A B:ADP401 4.8 33.1 1.0 CG2 B:VAL339 4.9 34.7 1.0 CA B:GLY13 5.0 32.9 1.0

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


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 F-Actin in Complex with Adp-Befx within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:37.1 occ:1.00 O1B C:ADP401 2.0 32.5 1.0 PB C:ADP401 3.3 27.9 1.0 O3B C:ADP401 3.6 28.8 1.0 O1A C:ADP401 4.0 28.1 1.0 OE1 C:GLN137 4.0 40.1 1.0 O3A C:ADP401 4.2 23.4 1.0 OD2 C:ASP11 4.2 33.1 1.0 OD1 C:ASP154 4.3 40.1 1.0 NE2 C:GLN137 4.3 40.7 1.0 CD C:GLN137 4.3 40.5 1.0 O2B C:ADP401 4.4 30.1 1.0 OD1 C:ASP11 4.4 32.3 1.0 OD2 C:ASP154 4.4 36.7 1.0 NZ C:LYS18 4.5 30.2 1.0 PA C:ADP401 4.5 22.6 1.0 CG C:ASP11 4.8 31.9 1.0 CG C:ASP154 4.8 40.5 1.0 O2A C:ADP401 4.8 30.0 1.0 CG2 C:VAL339 4.9 31.2 1.0 CA C:GLY13 5.0 26.9 1.0

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


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 F-Actin in Complex with Adp-Befx within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:35.1 occ:1.00 O1B D:ADP401 2.0 33.2 1.0 PB D:ADP401 3.3 31.6 1.0 O3B D:ADP401 3.6 32.2 1.0 O1A D:ADP401 4.0 29.6 1.0 OE1 D:GLN137 4.0 41.1 1.0 O3A D:ADP401 4.2 27.3 1.0 OD2 D:ASP11 4.2 35.8 1.0 OD1 D:ASP154 4.3 41.5 1.0 NE2 D:GLN137 4.3 41.7 1.0 CD D:GLN137 4.3 39.8 1.0 O2B D:ADP401 4.4 31.1 1.0 OD1 D:ASP11 4.4 34.6 1.0 OD2 D:ASP154 4.4 42.1 1.0 NZ D:LYS18 4.5 31.8 1.0 PA D:ADP401 4.5 23.8 1.0 CG D:ASP11 4.8 36.0 1.0 CG D:ASP154 4.8 41.4 1.0 O2A D:ADP401 4.8 30.9 1.0 CG2 D:VAL339 4.9 31.1 1.0 CA D:GLY13 5.0 32.5 1.0

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


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 F-Actin in Complex with Adp-Befx within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:38.3 occ:1.00 O1B E:ADP401 2.0 36.5 1.0 PB E:ADP401 3.3 34.7 1.0 O3B E:ADP401 3.6 36.1 1.0 O1A E:ADP401 4.0 31.4 1.0 OE1 E:GLN137 4.0 42.0 1.0 O3A E:ADP401 4.2 27.2 1.0 OD2 E:ASP11 4.2 42.9 1.0 OD1 E:ASP154 4.3 41.8 1.0 NE2 E:GLN137 4.3 45.0 1.0 CD E:GLN137 4.3 42.0 1.0 O2B E:ADP401 4.4 36.9 1.0 OD1 E:ASP11 4.4 41.1 1.0 OD2 E:ASP154 4.4 40.6 1.0 NZ E:LYS18 4.5 36.3 1.0 PA E:ADP401 4.5 25.5 1.0 CG E:ASP11 4.8 41.6 1.0 CG E:ASP154 4.8 42.5 1.0 O2A E:ADP401 4.8 35.3 1.0 CG2 E:VAL339 4.9 35.2 1.0 CA E:GLY13 5.0 36.4 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