Magnesium in PDB 5yfm: Human Isocitrate Dehydrogenase 1 Bound with Nadp

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

The structure of Human Isocitrate Dehydrogenase 1 Bound with Nadp, PDB code: 5yfm 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)	100.50 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.020, 85.580, 86.070, 90.00, 98.08, 90.00
R / Rfree (%)	17.3 / 23.9

The binding sites of Magnesium atom in the Human Isocitrate Dehydrogenase 1 Bound with Nadp (pdb code 5yfm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Isocitrate Dehydrogenase 1 Bound with Nadp, PDB code: 5yfm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Isocitrate Dehydrogenase 1 Bound with Nadp


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 Nadp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:24.2 occ:1.00 OD1 A:ASP275 2.1 14.3 1.0 OD2 A:ASP279 2.3 15.7 1.0 O A:ASP275 2.4 17.1 1.0 OD2 B:ASP252 2.4 15.6 1.0 CG A:ASP279 3.2 16.2 1.0 CG A:ASP275 3.2 15.0 1.0 C A:ASP275 3.3 15.5 1.0 CG B:ASP252 3.4 16.4 1.0 OD1 A:ASP279 3.4 16.1 1.0 CA A:ASP275 3.7 15.0 1.0 CB B:ASP252 3.9 15.1 1.0 CB A:ASP275 4.0 14.7 1.0 OD2 A:ASP275 4.0 13.8 1.0 OD1 B:ASP252 4.4 16.2 1.0 CB A:ASP279 4.5 16.1 1.0 N A:VAL276 4.5 15.1 1.0 NH1 A:ARG132 4.9 14.8 1.0 OG A:SER278 4.9 16.8 1.0 CA A:VAL276 5.0 15.8 1.0

Magnesium binding site 2 out of 3 in the Human Isocitrate Dehydrogenase 1 Bound with Nadp


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 Nadp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.2 occ:1.00 OD1 B:ASP275 2.3 12.8 1.0 OD2 A:ASP252 2.3 16.7 1.0 OD2 B:ASP279 2.3 14.4 1.0 O B:ASP275 2.9 17.4 1.0 CG A:ASP252 3.2 14.7 1.0 CG B:ASP279 3.3 14.7 1.0 CG B:ASP275 3.4 13.8 1.0 OD1 B:ASP279 3.5 14.2 1.0 CB A:ASP252 3.6 14.3 1.0 C B:ASP275 4.0 16.1 1.0 OD2 B:ASP275 4.1 12.3 1.0 OD1 A:ASP252 4.2 14.7 1.0 CA B:ASP275 4.5 14.3 1.0 CB B:ASP275 4.5 13.8 1.0 CB B:ASP279 4.6 14.7 1.0 NZ A:LYS212 4.8 11.8 1.0 CA A:ASP252 4.9 14.1 1.0

Magnesium binding site 3 out of 3 in the Human Isocitrate Dehydrogenase 1 Bound with Nadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Isocitrate Dehydrogenase 1 Bound with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.8 occ:1.00 OD1 C:ASP275 2.2 27.9 1.0 OD2 C:ASP279 2.2 25.1 1.0 O C:ASP275 3.0 25.9 1.0 CG C:ASP279 3.1 24.3 1.0 O C:HOH669 3.2 32.2 1.0 OD1 C:ASP279 3.3 25.9 1.0 CG C:ASP275 3.4 24.0 1.0 C C:ASP275 3.7 21.5 1.0 CA C:ASP275 4.0 21.2 1.0 OD2 C:ASP275 4.1 25.0 1.0 CB C:ASP275 4.3 22.4 1.0 CB C:ASP279 4.4 23.8 1.0 O C:HOH683 4.8 22.7 1.0 N C:VAL276 4.8 20.0 1.0

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