Magnesium in PDB 8jol: Cryo-Em Structure of the Ced-4/Ced-3 Holoenzyme

All present enzymatic activity of Cryo-Em Structure of the Ced-4/Ced-3 Holoenzyme:
3.4.22.60;

The binding sites of Magnesium atom in the Cryo-Em Structure of the Ced-4/Ced-3 Holoenzyme (pdb code 8jol). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of the Ced-4/Ced-3 Holoenzyme, PDB code: 8jol:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the Ced-4/Ced-3 Holoenzyme


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 Ced-4/Ced-3 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:313.4 occ:1.00 O2G A:ATP602 2.8 143.5 1.0 OG A:SER166 2.9 108.8 1.0 NZ A:LYS191 3.0 155.1 1.0 O2A A:ATP602 3.1 117.0 1.0 CB A:SER166 3.3 128.2 1.0 O1B A:ATP602 3.4 120.0 1.0 OD2 A:ASP250 3.6 136.1 1.0 OD1 A:ASP250 4.2 119.4 1.0 PG A:ATP602 4.2 149.2 1.0 CE A:LYS191 4.3 145.6 1.0 CG A:ASP250 4.3 123.2 1.0 PA A:ATP602 4.6 116.1 1.0 PB A:ATP602 4.7 109.9 1.0 O3B A:ATP602 4.7 313.5 1.0 CA A:SER166 4.8 109.8 1.0 CE1 A:TYR369 4.9 114.1 1.0 O3G A:ATP602 5.0 92.3 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the Ced-4/Ced-3 Holoenzyme


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 Ced-4/Ced-3 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:80.8 occ:1.00 OG B:SER166 2.3 110.8 1.0 O1B B:ATP602 2.7 110.3 1.0 CB B:SER166 3.0 126.0 1.0 O1G B:ATP602 3.1 107.6 1.0 O2A B:ATP602 3.4 112.6 1.0 OD2 B:ASP250 3.4 123.9 1.0 NZ B:LYS191 3.5 152.2 1.0 OD1 B:ASP250 3.5 116.4 1.0 CG B:ASP250 3.9 118.5 1.0 PG B:ATP602 3.9 128.4 1.0 O2G B:ATP602 4.0 105.6 1.0 PB B:ATP602 4.1 111.0 1.0 O3B B:ATP602 4.2 278.9 1.0 CE B:LYS191 4.4 144.5 1.0 CA B:SER166 4.5 107.8 1.0 PA B:ATP602 4.7 117.3 1.0 N B:SER166 4.8 112.6 1.0 O3A B:ATP602 4.9 110.5 1.0 CB B:ASP251 5.0 124.0 1.0

Y.Li, L.Tian, Y.Zhang, Y.Shi. Structure of A Ternary Complex of Ced-4 with Ced-3 Card and Ced-3 Catalytic Domain To Be Published.