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

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:59.7 occ:1.00 O2B A:ADP401 2.1 50.9 1.0 PB A:ADP401 3.6 53.7 1.0 O2A A:ADP401 3.7 55.8 1.0 OD2 A:ASP11 3.9 62.6 1.0 OD2 A:ASP154 4.0 62.2 1.0 OD1 A:ASP11 4.1 64.9 1.0 O1A A:ADP401 4.1 55.5 1.0 PA A:ADP401 4.2 53.1 1.0 O1B A:ADP401 4.3 56.7 1.0 O3B A:ADP401 4.3 56.7 1.0 OE1 A:GLN137 4.3 62.8 1.0 O3A A:ADP401 4.4 52.3 1.0 OD1 A:ASP154 4.4 62.7 1.0 CG A:ASP11 4.4 66.0 1.0 CG2 A:VAL339 4.5 61.2 1.0 CD A:GLN137 4.6 64.6 1.0 CG A:ASP154 4.6 64.0 1.0 NE2 A:GLN137 4.8 68.7 1.0 CB A:VAL339 4.9 57.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:56.1 occ:1.00 O2B B:ADP401 2.1 49.7 1.0 PB B:ADP401 3.6 51.4 1.0 O2A B:ADP401 3.7 55.5 1.0 OD2 B:ASP11 3.9 60.7 1.0 OD2 B:ASP154 4.0 56.5 1.0 OD1 B:ASP11 4.1 60.9 1.0 O1A B:ADP401 4.1 49.6 1.0 PA B:ADP401 4.2 51.5 1.0 O1B B:ADP401 4.3 53.2 1.0 O3B B:ADP401 4.3 53.3 1.0 OE1 B:GLN137 4.3 59.4 1.0 O3A B:ADP401 4.4 49.2 1.0 OD1 B:ASP154 4.4 58.2 1.0 CG B:ASP11 4.4 64.3 1.0 CG2 B:VAL339 4.5 61.6 1.0 CD B:GLN137 4.6 61.4 1.0 CG B:ASP154 4.6 60.2 1.0 NE2 B:GLN137 4.8 64.6 1.0 CB B:VAL339 4.9 52.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:51.0 occ:1.00 O2B C:ADP401 2.0 49.2 1.0 PB C:ADP401 3.6 53.8 1.0 O2A C:ADP401 3.7 49.6 1.0 OD2 C:ASP11 3.9 58.4 1.0 OD2 C:ASP154 4.0 54.7 1.0 OD1 C:ASP11 4.1 54.7 1.0 O1A C:ADP401 4.1 48.6 1.0 PA C:ADP401 4.2 47.0 1.0 O1B C:ADP401 4.3 53.1 1.0 O3B C:ADP401 4.3 53.2 1.0 OE1 C:GLN137 4.3 52.3 1.0 O3A C:ADP401 4.4 47.5 1.0 OD1 C:ASP154 4.4 50.9 1.0 CG C:ASP11 4.4 59.1 1.0 CG2 C:VAL339 4.5 54.5 1.0 CD C:GLN137 4.6 55.0 1.0 CG C:ASP154 4.6 51.7 1.0 NE2 C:GLN137 4.8 58.5 1.0 CB C:VAL339 4.9 47.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:51.8 occ:1.00 O2B D:ADP401 2.1 48.0 1.0 PB D:ADP401 3.6 48.3 1.0 O2A D:ADP401 3.7 51.1 1.0 OD2 D:ASP11 3.9 52.5 1.0 OD2 D:ASP154 4.0 54.6 1.0 OD1 D:ASP11 4.1 53.2 1.0 O1A D:ADP401 4.1 47.8 1.0 PA D:ADP401 4.2 45.3 1.0 O1B D:ADP401 4.3 49.4 1.0 O3B D:ADP401 4.3 51.9 1.0 OE1 D:GLN137 4.3 54.5 1.0 O3A D:ADP401 4.4 46.2 1.0 OD1 D:ASP154 4.4 56.3 1.0 CG D:ASP11 4.4 54.4 1.0 CG2 D:VAL339 4.5 50.4 1.0 CD D:GLN137 4.6 58.1 1.0 CG D:ASP154 4.6 56.1 1.0 NE2 D:GLN137 4.8 60.9 1.0 CB D:VAL339 4.9 46.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:57.4 occ:1.00 O2B E:ADP401 2.0 51.3 1.0 PB E:ADP401 3.6 53.7 1.0 O2A E:ADP401 3.7 52.8 1.0 OD2 E:ASP11 3.9 59.5 1.0 OD2 E:ASP154 4.0 57.5 1.0 OD1 E:ASP11 4.1 54.0 1.0 O1A E:ADP401 4.1 51.3 1.0 PA E:ADP401 4.2 49.7 1.0 O1B E:ADP401 4.3 54.3 1.0 O3B E:ADP401 4.3 54.6 1.0 OE1 E:GLN137 4.3 52.9 1.0 O3A E:ADP401 4.4 49.6 1.0 OD1 E:ASP154 4.4 54.4 1.0 CG E:ASP11 4.4 57.1 1.0 CG2 E:VAL339 4.5 55.8 1.0 CD E:GLN137 4.6 54.4 1.0 CG E:ASP154 4.6 56.9 1.0 NE2 E:GLN137 4.8 57.7 1.0 CB E:VAL339 4.9 49.6 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