Magnesium in PDB 5j32: Isopropylmalate Dehydrogenase in Complex with Isopropylmalate

All present enzymatic activity of Isopropylmalate Dehydrogenase in Complex with Isopropylmalate:
1.1.1.85;

The structure of Isopropylmalate Dehydrogenase in Complex with Isopropylmalate, PDB code: 5j32 was solved by J.M.Jez, S.G.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.48 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	96.059, 49.622, 158.969, 90.00, 105.44, 90.00
R / Rfree (%)	15.9 / 19.8

The binding sites of Magnesium atom in the Isopropylmalate Dehydrogenase in Complex with Isopropylmalate (pdb code 5j32). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Isopropylmalate Dehydrogenase in Complex with Isopropylmalate, PDB code: 5j32:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Isopropylmalate Dehydrogenase in Complex with Isopropylmalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Isopropylmalate Dehydrogenase in Complex with Isopropylmalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:19.4 occ:1.00 OD2 B:ASP264 2.1 23.8 1.0 O A:HOH657 2.1 25.7 1.0 OD1 A:ASP288 2.2 15.0 1.0 O1 A:IPM502 2.3 22.3 1.0 O3 A:IPM502 2.3 33.9 1.0 OD2 A:ASP292 2.4 28.4 1.0 O A:HOH623 2.5 22.5 1.0 C1 A:IPM502 3.1 32.7 1.0 CG B:ASP264 3.2 16.5 1.0 C2 A:IPM502 3.2 27.5 1.0 CG A:ASP292 3.4 24.1 1.0 CG A:ASP288 3.4 14.0 1.0 CB B:ASP264 3.7 7.2 1.0 OD1 A:ASP292 3.8 25.7 1.0 OD2 A:ASP288 4.0 18.8 1.0 O A:HOH785 4.0 43.5 1.0 O A:ASP288 4.1 8.5 1.0 OD1 B:ASP264 4.2 18.0 1.0 O B:HOH722 4.3 24.9 1.0 O2 A:IPM502 4.3 36.3 1.0 O A:HOH666 4.3 28.7 1.0 O4 A:IPM502 4.4 14.1 1.0 C4 A:IPM502 4.4 17.0 1.0 C3 A:IPM502 4.4 16.4 1.0 NZ B:LYS232 4.5 11.5 1.0 CB A:ASP288 4.5 9.0 1.0 CB A:ASP292 4.6 14.9 1.0 NH1 A:ARG146 4.6 11.6 0.5 NH1 A:ARG146 4.6 10.1 0.5 C A:ASP288 4.7 13.9 1.0 CA A:ASP288 4.8 7.9 1.0 O5 A:IPM502 4.9 17.1 1.0

Magnesium binding site 2 out of 4 in the Isopropylmalate Dehydrogenase in Complex with Isopropylmalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Isopropylmalate Dehydrogenase in Complex with Isopropylmalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:29.7 occ:1.00 OD2 A:ASP264 2.0 21.2 1.0 OD1 B:ASP288 2.2 21.4 1.0 O1 A:IPM504 2.2 22.2 1.0 O B:HOH655 2.3 34.8 1.0 OD2 B:ASP292 2.5 25.1 1.0 O2 A:IPM504 2.6 29.8 1.0 O B:HOH654 2.7 37.3 1.0 CG A:ASP264 3.1 21.8 1.0 C2 A:IPM504 3.3 23.6 1.0 C1 A:IPM504 3.3 23.5 1.0 CG B:ASP288 3.4 25.0 1.0 O B:HOH763 3.4 36.8 1.0 CG B:ASP292 3.5 22.0 1.0 CB A:ASP264 3.6 13.1 1.0 O A:HOH793 3.7 37.9 1.0 OD1 B:ASP292 3.9 22.8 1.0 OD2 B:ASP288 4.0 25.8 1.0 O B:ASP288 4.1 12.5 1.0 O5 A:IPM504 4.2 13.1 1.0 OD1 A:ASP264 4.2 24.7 1.0 NZ A:LYS232 4.2 13.9 1.0 O A:HOH871 4.3 47.5 1.0 C4 A:IPM504 4.3 17.3 1.0 O A:HOH726 4.4 18.6 1.0 C3 A:IPM504 4.4 20.4 1.0 O3 A:IPM504 4.5 23.3 1.0 CB B:ASP288 4.5 13.3 1.0 NH1 B:ARG146 4.6 17.3 1.0 C B:ASP288 4.7 11.1 1.0 CB B:ASP292 4.7 11.4 1.0 CA B:ASP288 4.8 9.6 1.0 O4 A:IPM504 5.0 15.9 1.0

Magnesium binding site 3 out of 4 in the Isopropylmalate Dehydrogenase in Complex with Isopropylmalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Isopropylmalate Dehydrogenase in Complex with Isopropylmalate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:16.3 occ:1.00 OD2 D:ASP264 2.1 23.1 1.0 O2 C:IPM502 2.3 35.8 1.0 O1 C:IPM502 2.3 20.9 1.0 O C:HOH622 2.4 36.8 1.0 OD1 C:ASP288 2.4 23.7 1.0 OD2 C:ASP292 2.5 23.5 1.0 O C:HOH803 2.6 34.3 1.0 C1 C:IPM502 3.1 30.0 1.0 CG D:ASP264 3.2 19.1 1.0 C2 C:IPM502 3.2 26.5 1.0 CG C:ASP292 3.3 18.1 1.0 CG C:ASP288 3.6 19.8 1.0 CB D:ASP264 3.6 16.8 1.0 OD1 C:ASP292 3.6 20.6 1.0 O C:HOH773 3.8 52.5 1.0 OD2 C:ASP288 4.1 19.1 1.0 O C:ASP288 4.2 10.6 1.0 OD1 D:ASP264 4.2 20.1 1.0 O3 C:IPM502 4.3 25.1 1.0 O D:HOH720 4.3 26.8 1.0 O5 C:IPM502 4.3 13.7 1.0 O C:HOH756 4.3 41.5 1.0 C4 C:IPM502 4.3 20.8 1.0 C3 C:IPM502 4.4 20.6 1.0 NZ D:LYS232 4.5 14.8 1.0 CB C:ASP292 4.6 8.6 1.0 NH1 C:ARG146 4.7 19.8 0.5 CB C:ASP288 4.7 12.4 1.0 NH1 C:ARG146 4.8 17.1 0.6 C C:ASP288 4.8 15.1 1.0 O4 C:IPM502 4.9 17.4 1.0 CA C:ASP288 4.9 9.2 1.0

Magnesium binding site 4 out of 4 in the Isopropylmalate Dehydrogenase in Complex with Isopropylmalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Isopropylmalate Dehydrogenase in Complex with Isopropylmalate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:28.7 occ:1.00 OD2 C:ASP264 2.1 22.1 1.0 O C:HOH625 2.1 26.4 1.0 OD1 D:ASP288 2.2 21.8 1.0 O3 C:IPM504 2.4 36.9 1.0 O D:HOH799 2.4 41.5 1.0 O1 C:IPM504 2.4 26.0 1.0 OD2 D:ASP292 2.6 26.7 1.0 C1 C:IPM504 3.2 31.8 1.0 CG C:ASP264 3.2 19.9 1.0 C2 C:IPM504 3.3 29.8 1.0 CG D:ASP288 3.4 15.5 1.0 CG D:ASP292 3.5 24.6 1.0 CB C:ASP264 3.6 12.1 1.0 OD1 D:ASP292 3.8 24.9 1.0 OD2 D:ASP288 3.9 17.9 1.0 O D:ASP288 4.1 9.8 1.0 OD1 C:ASP264 4.3 21.9 1.0 O2 C:IPM504 4.3 27.3 1.0 O4 C:IPM504 4.3 20.9 1.0 NZ C:LYS232 4.4 17.8 1.0 C4 C:IPM504 4.4 22.5 1.0 O C:HOH848 4.5 61.5 1.0 C3 C:IPM504 4.5 21.7 1.0 O C:HOH749 4.5 23.8 1.0 CB D:ASP288 4.6 13.7 1.0 CB D:ASP292 4.7 14.9 1.0 NH1 D:ARG146 4.7 20.6 0.5 C D:ASP288 4.7 12.7 1.0 CA D:ASP288 4.8 14.8 1.0 NH1 D:ARG146 4.8 19.7 0.5 O D:HOH817 4.8 52.0 1.0

S.G.Lee, R.Nwumeh, J.M.Jez. Structure and Mechanism of Isopropylmalate Dehydrogenase From Arabidopsis Thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis. J.Biol.Chem. V. 291 13421 2016.
ISSN: ESSN 1083-351X
PubMed: 27137927
DOI: 10.1074/JBC.M116.730358