Magnesium in PDB 8jns: Cryo-Em Structure of A Ced-4 Hexamer

The binding sites of Magnesium atom in the Cryo-Em Structure of A Ced-4 Hexamer (pdb code 8jns). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of A Ced-4 Hexamer, PDB code: 8jns:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of A Ced-4 Hexamer


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 A Ced-4 Hexamer 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 O3B A:ATP602 4.7 313.5 1.0 PB A:ATP602 4.7 109.9 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 6 in the Cryo-Em Structure of A Ced-4 Hexamer


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

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of A Ced-4 Hexamer


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

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of A Ced-4 Hexamer


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

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of A Ced-4 Hexamer


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

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of A Ced-4 Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of A Ced-4 Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:313.4 occ:1.00 O2G F:ATP602 2.8 143.5 1.0 OG F:SER166 2.9 108.8 1.0 NZ F:LYS191 3.0 155.1 1.0 O2A F:ATP602 3.1 117.0 1.0 CB F:SER166 3.3 128.2 1.0 O1B F:ATP602 3.4 120.0 1.0 OD2 F:ASP250 3.6 136.1 1.0 OD1 F:ASP250 4.2 119.4 1.0 PG F:ATP602 4.2 149.2 1.0 CE F:LYS191 4.3 145.6 1.0 CG F:ASP250 4.3 123.2 1.0 PA F:ATP602 4.6 116.1 1.0 O3B F:ATP602 4.7 313.5 1.0 PB F:ATP602 4.7 109.9 1.0 CA F:SER166 4.8 109.8 1.0 CE1 F:TYR369 4.9 114.1 1.0 O3G F:ATP602 5.0 92.3 1.0

Y.Li, L.Tian, Y.Zhang, Y.Shi. Structural Insights Into Ced-3 Activation To Be Published.