Magnesium in PDB 5j34: Isopropylmalate Dehydrogenase K232M Mutant

All present enzymatic activity of Isopropylmalate Dehydrogenase K232M Mutant:
1.1.1.85;

The structure of Isopropylmalate Dehydrogenase K232M Mutant, PDB code: 5j34 was solved by S.G.Lee, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.41 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.803, 76.820, 209.497, 90.00, 90.22, 90.00
R / Rfree (%)	16.5 / 18.6

The binding sites of Magnesium atom in the Isopropylmalate Dehydrogenase K232M Mutant (pdb code 5j34). 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 K232M Mutant, PDB code: 5j34:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Isopropylmalate Dehydrogenase K232M Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Isopropylmalate Dehydrogenase K232M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:43.0 occ:1.00 O A:HOH714 2.0 32.0 1.0 O A:HOH778 2.1 32.9 1.0 O A:HOH691 2.1 37.1 1.0 OD2 C:ASP264 2.2 33.0 1.0 OD1 A:ASP288 2.2 29.9 1.0 OD2 A:ASP292 2.3 32.4 1.0 CG C:ASP264 3.2 37.3 1.0 CG A:ASP288 3.2 26.4 1.0 CG A:ASP292 3.3 34.6 1.0 O A:HOH692 3.6 33.4 1.0 OD2 A:ASP288 3.6 27.7 1.0 OD1 A:ASP292 3.7 33.2 1.0 CB C:ASP264 3.7 27.0 1.0 O A:HOH667 4.0 44.2 1.0 O1 A:SO4504 4.2 49.3 1.0 OD1 C:ASP264 4.2 40.8 1.0 O A:ASP288 4.3 25.1 1.0 O2 A:SO4504 4.3 45.6 1.0 CB A:ASP292 4.5 22.2 1.0 CB A:ASP288 4.6 21.5 1.0 C A:ASP288 4.7 29.0 1.0 CA A:ASP288 4.8 22.6 1.0 S A:SO4504 4.9 41.4 1.0

Magnesium binding site 2 out of 4 in the Isopropylmalate Dehydrogenase K232M Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Isopropylmalate Dehydrogenase K232M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:39.5 occ:1.00 O B:HOH753 1.9 34.4 1.0 OD2 D:ASP264 2.1 26.5 1.0 O B:HOH662 2.2 32.5 1.0 O B:HOH665 2.2 33.9 1.0 OD1 B:ASP288 2.2 31.4 1.0 OD2 B:ASP292 2.3 29.7 1.0 CG D:ASP264 3.1 37.1 1.0 CG B:ASP292 3.3 29.9 1.0 CG B:ASP288 3.3 30.2 1.0 O D:HOH624 3.4 43.1 1.0 O B:HOH667 3.5 32.5 1.0 CB D:ASP264 3.6 28.0 1.0 OD1 B:ASP292 3.6 30.6 1.0 OD2 B:ASP288 3.7 29.6 1.0 O D:HOH647 3.8 60.9 1.0 O B:HOH672 4.0 38.9 1.0 OD1 D:ASP264 4.1 37.6 1.0 O4 B:SO4502 4.2 48.1 1.0 O B:ASP288 4.3 23.8 1.0 O3 B:SO4502 4.3 52.0 1.0 CB B:ASP292 4.5 20.8 1.0 CB B:ASP288 4.6 24.2 1.0 C B:ASP288 4.7 28.3 1.0 O D:HOH743 4.7 44.6 1.0 O D:HOH867 4.8 60.0 1.0 CA B:ASP288 4.8 22.2 1.0 S B:SO4502 4.9 43.2 1.0

Magnesium binding site 3 out of 4 in the Isopropylmalate Dehydrogenase K232M Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Isopropylmalate Dehydrogenase K232M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:43.4 occ:1.00 O C:HOH789 2.1 33.9 1.0 O C:HOH656 2.1 32.1 1.0 OD2 A:ASP264 2.2 32.6 1.0 OD1 C:ASP288 2.2 30.7 1.0 O C:HOH644 2.2 36.6 1.0 OD2 C:ASP292 2.3 30.2 1.0 CG A:ASP264 3.2 37.2 1.0 CG C:ASP292 3.2 31.6 1.0 CG C:ASP288 3.2 30.5 1.0 O A:HOH634 3.5 44.4 1.0 O C:HOH651 3.5 33.9 1.0 OD1 C:ASP292 3.6 28.9 1.0 OD2 C:ASP288 3.6 28.2 1.0 CB A:ASP264 3.7 27.3 1.0 O C:HOH653 4.0 38.9 1.0 O3 C:SO4502 4.2 50.7 1.0 O4 C:SO4502 4.2 51.6 1.0 O C:ASP288 4.2 23.4 1.0 OD1 A:ASP264 4.3 37.5 1.0 CB C:ASP292 4.5 22.4 1.0 CB C:ASP288 4.6 24.9 1.0 C C:ASP288 4.7 25.5 1.0 O A:HOH796 4.8 46.5 1.0 CA C:ASP288 4.8 21.3 1.0 S C:SO4502 4.9 43.0 1.0

Magnesium binding site 4 out of 4 in the Isopropylmalate Dehydrogenase K232M Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Isopropylmalate Dehydrogenase K232M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:40.1 occ:1.00 O D:HOH745 2.0 30.6 1.0 OD2 B:ASP264 2.1 20.0 0.7 O D:HOH674 2.1 34.3 1.0 OD1 D:ASP288 2.2 31.2 1.0 OD2 D:ASP292 2.2 29.5 1.0 O D:HOH663 2.2 36.4 1.0 OD2 B:ASP264 3.1 53.4 0.3 CG B:ASP264 3.1 26.9 0.7 CG D:ASP292 3.2 34.8 1.0 O B:HOH625 3.3 45.4 1.0 CG D:ASP288 3.3 28.0 1.0 O D:HOH705 3.5 35.2 1.0 CG B:ASP264 3.5 40.0 0.3 CB B:ASP264 3.6 28.7 0.3 CB B:ASP264 3.6 27.3 0.7 OD1 D:ASP292 3.6 31.3 1.0 OD2 D:ASP288 3.7 28.4 1.0 OD1 B:ASP264 4.1 31.6 0.7 O D:HOH678 4.2 42.1 1.0 O D:ASP288 4.3 24.8 1.0 O2 D:SO4502 4.3 47.8 1.0 O1 D:SO4502 4.3 49.8 1.0 O D:HOH853 4.4 59.4 1.0 CB D:ASP292 4.5 21.1 1.0 OD1 B:ASP264 4.6 54.9 0.3 CB D:ASP288 4.6 24.1 1.0 C D:ASP288 4.7 28.2 1.0 O B:HOH804 4.8 44.1 1.0 CA D:ASP288 4.8 22.6 1.0 S D:SO4502 5.0 42.8 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