Magnesium in PDB 8w49: Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium

All present enzymatic activity of Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium:
1.1.1.42;

The structure of Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium, PDB code: 8w49 was solved by B.S.Kang, H.Y.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.90 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.627, 93.448, 111.275, 90, 113.9, 90
R / Rfree (%)	17 / 20.5

The binding sites of Magnesium atom in the Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium (pdb code 8w49). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium, PDB code: 8w49:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:10.6 occ:1.00 OD2 A:ASP252 2.2 23.6 1.0 O7 B:ICT502 2.2 28.3 1.0 OD1 B:ASP275 2.2 21.3 1.0 O B:HOH768 2.2 20.0 1.0 O B:HOH703 2.3 27.8 1.0 O2 B:ICT502 2.3 23.4 1.0 C2 B:ICT502 2.8 41.4 1.0 C1 B:ICT502 2.9 38.9 1.0 CG A:ASP252 3.3 24.1 1.0 CG B:ASP275 3.4 28.4 1.0 CB A:ASP252 3.8 19.4 1.0 OD2 B:ASP275 3.9 28.4 1.0 NZ A:LYS212 4.0 24.9 1.0 O1 B:ICT502 4.0 37.8 1.0 O B:ASP275 4.1 12.5 1.0 O B:ALA308 4.1 24.4 1.0 O A:HOH649 4.2 32.0 1.0 C3 B:ICT502 4.2 35.8 1.0 OD1 B:ASP279 4.3 28.2 1.0 C5N B:NAP501 4.3 19.7 1.0 O B:HOH732 4.3 17.9 1.0 OD1 A:ASP252 4.4 23.0 1.0 NH1 B:ARG109 4.4 17.2 1.0 C6 B:ICT502 4.5 48.3 1.0 CB B:ASP275 4.5 11.5 1.0 OD2 B:ASP279 4.6 22.5 1.0 C4N B:NAP501 4.6 23.6 1.0 CG B:ASP279 4.6 24.1 1.0 O5 B:ICT502 4.6 37.6 1.0 C B:ASP275 4.6 11.8 1.0 CA B:ASP275 4.7 9.5 1.0 C4 B:ICT502 4.8 35.5 1.0 NH1 B:ARG132 4.8 15.7 1.0 O A:HOH756 4.9 17.4 1.0 O6 B:ICT502 5.0 38.7 1.0

Magnesium binding site 2 out of 4 in the Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:10.2 occ:1.00 O7 A:ICT504 2.0 27.6 1.0 O A:HOH656 2.0 24.0 1.0 OD2 B:ASP252 2.1 20.0 1.0 OD1 A:ASP275 2.2 21.0 1.0 O A:HOH692 2.2 21.4 1.0 O2 A:ICT504 2.2 30.0 1.0 C2 A:ICT504 2.7 47.2 1.0 C1 A:ICT504 2.8 48.3 1.0 CG B:ASP252 3.3 24.8 1.0 CG A:ASP275 3.3 23.6 1.0 OD2 A:ASP275 3.8 29.8 1.0 CB B:ASP252 3.8 19.1 1.0 NZ B:LYS212 4.0 23.5 1.0 O1 A:ICT504 4.1 45.7 1.0 C3 A:ICT504 4.1 40.3 1.0 O A:ALA308 4.1 20.9 1.0 O B:HOH670 4.2 29.9 1.0 O A:ASP275 4.2 11.6 1.0 C5N A:NAP501 4.3 15.6 1.0 OD1 B:ASP252 4.3 20.6 1.0 O A:HOH721 4.3 15.2 1.0 NH1 A:ARG109 4.4 17.2 1.0 C6 A:ICT504 4.4 47.2 1.0 OD2 A:ASP279 4.4 23.2 1.0 OD1 A:ASP279 4.4 25.8 1.0 C4N A:NAP501 4.5 23.7 1.0 CB A:ASP275 4.6 11.7 1.0 CG A:ASP279 4.6 19.4 1.0 O6 A:ICT504 4.7 45.3 1.0 C A:ASP275 4.7 12.4 1.0 CA A:ASP275 4.7 7.6 1.0 C4 A:ICT504 4.8 35.5 1.0 O5 A:ICT504 4.8 39.8 1.0 O B:HOH741 4.9 14.4 1.0 NH1 A:ARG132 4.9 17.8 1.0

Magnesium binding site 3 out of 4 in the Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:9.0 occ:1.00 O7 C:ICT504 1.9 31.7 1.0 O C:HOH644 2.1 23.8 1.0 OD1 C:ASP275 2.1 22.3 1.0 OD2 D:ASP252 2.1 23.1 1.0 O1 C:ICT504 2.2 39.0 1.0 O D:HOH677 2.2 23.1 1.0 C2 C:ICT504 2.6 45.0 1.0 C1 C:ICT504 2.7 35.0 1.0 CG D:ASP252 3.2 27.2 1.0 CG C:ASP275 3.3 25.4 1.0 OD2 C:ASP275 3.8 33.8 1.0 CB D:ASP252 3.8 17.6 1.0 NZ D:LYS212 3.9 19.0 1.0 O2 C:ICT504 4.0 46.5 1.0 C3 C:ICT504 4.0 33.8 1.0 O C:ASP275 4.1 13.4 1.0 O C:ALA308 4.1 19.1 1.0 O D:HOH740 4.1 31.2 1.0 C5N C:NAP501 4.2 18.1 1.0 C6 C:ICT504 4.2 52.5 1.0 OD1 D:ASP252 4.3 24.6 1.0 NH1 C:ARG109 4.3 17.4 1.0 O C:HOH734 4.4 14.9 1.0 OD1 C:ASP279 4.4 29.9 1.0 O5 C:ICT504 4.4 41.0 1.0 OD2 C:ASP279 4.4 28.6 1.0 C4N C:NAP501 4.5 15.4 1.0 CB C:ASP275 4.5 15.3 1.0 CG C:ASP279 4.6 25.8 1.0 C4 C:ICT504 4.6 36.8 1.0 C C:ASP275 4.6 12.7 1.0 CA C:ASP275 4.7 10.6 1.0 O6 C:ICT504 4.8 36.2 1.0 NH1 C:ARG132 4.9 14.0 1.0

Magnesium binding site 4 out of 4 in the Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:21.9 occ:1.00 O7 D:ICT501 1.9 40.8 1.0 OD1 D:ASP275 2.0 28.2 1.0 O1 D:ICT501 2.1 35.4 1.0 O D:HOH607 2.1 31.2 1.0 OD2 C:ASP252 2.4 45.3 1.0 C1 D:ICT501 2.7 36.8 1.0 C2 D:ICT501 2.7 51.2 1.0 CG D:ASP275 3.2 30.2 1.0 CG C:ASP252 3.4 33.5 1.0 OD2 D:ASP279 3.5 41.7 1.0 OD2 D:ASP275 3.8 40.9 1.0 CB C:ASP252 3.8 25.9 1.0 O2 D:ICT501 3.9 51.9 1.0 O D:ASP275 3.9 19.6 1.0 C3 D:ICT501 4.0 49.9 1.0 OD1 D:ASP279 4.0 38.2 1.0 CG D:ASP279 4.0 39.1 1.0 C6 D:ICT501 4.1 54.8 1.0 NZ C:LYS212 4.3 34.4 1.0 O5 D:ICT501 4.4 31.2 1.0 CB D:ASP275 4.4 16.0 1.0 C D:ASP275 4.4 16.8 1.0 CA D:ASP275 4.4 11.9 1.0 O6 D:ICT501 4.4 47.8 1.0 NH1 D:ARG109 4.4 28.8 1.0 OD1 C:ASP252 4.5 34.0 1.0 C4 D:ICT501 4.7 45.1 1.0 NH1 D:ARG132 4.7 19.4 1.0

B.S.Kang, H.Y.Cho. Mouse Isocitrate Dehydrogenase with Isocitrate and Magnesium To Be Published.