Magnesium in PDB 5yfn: Human Isocitrate Dehydrogenase 1 Bound with Isocitrate

All present enzymatic activity of Human Isocitrate Dehydrogenase 1 Bound with Isocitrate:
1.1.1.42;

The structure of Human Isocitrate Dehydrogenase 1 Bound with Isocitrate, PDB code: 5yfn was solved by P.Nordlund, D.Chen, A.Jansson, A.Larsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.80 / 2.50
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.560, 92.000, 138.835, 90.00, 109.94, 90.00
R / Rfree (%)	17.3 / 22.6

The structure of Human Isocitrate Dehydrogenase 1 Bound with Isocitrate also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Human Isocitrate Dehydrogenase 1 Bound with Isocitrate (pdb code 5yfn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Isocitrate Dehydrogenase 1 Bound with Isocitrate, PDB code: 5yfn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Isocitrate Dehydrogenase 1 Bound with Isocitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Isocitrate Dehydrogenase 1 Bound with Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:34.3 occ:1.00 O7 A:ICT502 2.0 20.0 1.0 OD1 A:ASP275 2.2 21.6 1.0 HO7 A:ICT502 2.4 20.0 1.0 OD2 B:ASP252 2.6 29.2 1.0 O2 A:ICT502 2.7 20.0 1.0 C2 A:ICT502 3.1 20.0 1.0 C1 A:ICT502 3.3 20.0 1.0 CG A:ASP275 3.3 23.2 1.0 H2 A:ICT502 3.5 20.0 1.0 CG B:ASP252 3.6 23.8 1.0 OD1 A:ASP279 3.6 22.3 1.0 O A:ASP275 3.6 23.0 1.0 NH2 A:ARG109 3.8 23.1 1.0 OD2 A:ASP279 3.8 23.7 1.0 CB B:ASP252 3.9 22.9 1.0 CG A:ASP279 3.9 22.0 1.0 OD2 A:ASP275 4.0 20.9 1.0 CA A:ASP275 4.2 24.1 1.0 C A:ASP275 4.3 23.8 1.0 CB A:ASP275 4.3 23.6 1.0 C3 A:ICT502 4.3 20.0 1.0 O1 A:ICT502 4.5 20.0 1.0 NH1 A:ARG132 4.6 26.5 1.0 OD1 B:ASP252 4.6 23.6 1.0 C6 A:ICT502 4.7 20.0 1.0 OG A:SER278 4.7 18.6 1.0 NE2 A:HIS309 4.7 51.4 1.0 H3 A:ICT502 4.7 20.0 1.0 CZ A:ARG109 4.9 23.4 1.0 O5 A:ICT502 4.9 20.0 1.0 CB A:ASP279 5.0 21.2 1.0

Magnesium binding site 2 out of 2 in the Human Isocitrate Dehydrogenase 1 Bound with Isocitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Isocitrate Dehydrogenase 1 Bound with Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:36.7 occ:1.00 O7 A:ICT505 2.2 20.0 1.0 O1 A:ICT505 2.2 20.0 1.0 OD1 B:ASP275 2.2 27.1 1.0 OD2 A:ASP252 2.2 29.3 1.0 HO7 A:ICT505 2.6 20.0 1.0 C1 A:ICT505 2.9 20.0 1.0 C2 A:ICT505 3.0 20.0 1.0 CG B:ASP275 3.3 23.9 1.0 CG A:ASP252 3.3 24.0 1.0 H2 A:ICT505 3.5 20.0 1.0 O B:ASP275 3.7 24.4 1.0 CB A:ASP252 3.8 24.8 1.0 OD2 B:ASP275 3.9 26.8 1.0 NH2 B:ARG109 3.9 31.5 1.0 OD1 B:ASP279 4.0 25.5 1.0 OD2 B:ASP279 4.0 25.9 1.0 O2 A:ICT505 4.1 20.0 1.0 CG B:ASP279 4.2 26.7 1.0 C3 A:ICT505 4.2 20.0 1.0 CA B:ASP275 4.2 21.9 1.0 C B:ASP275 4.3 22.3 1.0 CB B:ASP275 4.3 21.6 1.0 C6 A:ICT505 4.3 20.0 1.0 OD1 A:ASP252 4.3 26.3 1.0 O6 A:ICT505 4.4 20.0 1.0 NZ A:LYS212 4.6 21.4 1.0 NH1 B:ARG132 4.6 20.6 1.0 H3 A:ICT505 4.8 20.0 1.0 O5 A:ICT505 4.8 20.0 1.0 NE2 B:HIS309 4.9 36.9 1.0 CZ B:ARG109 5.0 27.6 1.0 OG B:SER278 5.0 23.6 1.0

P.Nordlund, D.Chen, A.Jansson, A.Larsson. Human Isocitrate Dehydrogenase 1 Bound with Isocitrate To Be Published.