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Magnesium in PDB 5j33: Isopropylmalate Dehydrogenase in Complex with Nad+

Enzymatic activity of Isopropylmalate Dehydrogenase in Complex with Nad+

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

Protein crystallography data

The structure of Isopropylmalate Dehydrogenase in Complex with Nad+, PDB code: 5j33 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) 46.73 / 3.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.200, 132.868, 349.426, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Isopropylmalate Dehydrogenase in Complex with Nad+ (pdb code 5j33). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Isopropylmalate Dehydrogenase in Complex with Nad+, PDB code: 5j33:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5j33

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Magnesium binding site 1 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


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 Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:37.8
occ:1.00
 OD1 A:ASP288 2.2 59.1 1.0
OD2 B:ASP264 2.7 41.1 1.0
CG A:ASP288 3.3 54.4 1.0
OD2 A:ASP292 3.5 49.2 1.0
OD1 A:ASP292 3.5 46.1 1.0
O1 A:SO4502 3.5 63.4 1.0
CG B:ASP264 3.6 38.7 1.0
CG A:ASP292 3.6 46.8 1.0
CB B:ASP264 3.6 37.8 1.0
O4 A:SO4502 3.7 0.8 1.0
NH1 A:ARG146 3.8 60.2 1.0
OD2 A:ASP288 3.8 57.9 1.0
S A:SO4502 3.9 72.8 1.0
O2 A:SO4502 4.0 59.0 1.0
O A:ILE320 4.0 40.5 1.0
O A:ASP288 4.1 38.8 1.0
C4N A:NAD501 4.3 0.7 1.0
C5N A:NAD501 4.3 0.5 1.0
CB A:ASP288 4.6 42.5 1.0
CA A:ASP288 4.6 37.4 1.0
NH2 A:ARG146 4.6 61.9 1.0
CB A:ASP292 4.7 44.3 1.0
CZ A:ARG146 4.7 56.6 1.0
C A:ASP288 4.7 37.1 1.0
OD1 B:ASP264 4.7 38.6 1.0

Magnesium binding site 2 out of 7 in 5j33

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Magnesium binding site 2 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


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 Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:32.4
occ:1.00
 OD1 B:ASP288 2.5 49.7 1.0
OD2 A:ASP264 2.7 56.5 1.0
O2 A:SO4505 2.8 50.8 1.0
OD1 B:ASP292 3.5 48.0 1.0
O4 A:SO4505 3.5 43.6 1.0
CG A:ASP264 3.6 54.1 1.0
CG B:ASP288 3.6 50.6 1.0
S A:SO4505 3.7 47.6 1.0
CB A:ASP264 3.8 51.0 1.0
O B:ILE320 3.8 60.6 1.0
C4N A:NAD504 3.8 81.1 1.0
CG B:ASP292 4.0 47.5 1.0
OD2 B:ASP288 4.1 57.1 1.0
O1 A:SO4505 4.1 74.7 1.0
C5N A:NAD504 4.1 72.7 1.0
NH1 B:ARG146 4.2 39.4 1.0
CB B:ASP292 4.6 42.5 1.0
O B:ASP288 4.6 51.3 1.0
N7N A:NAD504 4.6 96.0 1.0
OD2 B:ASP292 4.7 50.8 1.0
OD1 A:ASP264 4.7 53.9 1.0
CB B:ASP288 4.9 44.9 1.0
C B:ILE320 4.9 53.6 1.0
O3 A:SO4505 5.0 40.3 1.0

Magnesium binding site 3 out of 7 in 5j33

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Magnesium binding site 3 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


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 Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:63.9
occ:1.00
 OD1 H:ASP288 2.0 0.0 1.0
OD2 C:ASP264 2.8 55.6 1.0
OD2 H:ASP292 2.9 63.8 1.0
CG H:ASP288 3.0 0.0 1.0
O4 H:SO4503 3.1 93.7 1.0
O3 H:SO4503 3.3 0.8 1.0
OD2 H:ASP288 3.3 1.0 1.0
CG C:ASP264 3.4 55.7 1.0
O1 H:SO4503 3.4 1.0 1.0
S H:SO4503 3.4 0.2 1.0
CB C:ASP264 3.5 48.9 1.0
CG H:ASP292 3.8 64.7 1.0
C5N H:NAD501 3.9 0.7 1.0
C4N H:NAD501 4.1 0.5 1.0
O H:ILE320 4.1 54.0 1.0
CB H:ASP292 4.1 59.3 1.0
O H:ASP288 4.1 44.0 1.0
CB H:ASP288 4.4 81.7 1.0
NH2 H:ARG146 4.5 57.9 1.0
OD1 C:ASP264 4.5 61.8 1.0
CA H:ASP288 4.6 53.7 1.0
C H:ASP288 4.7 45.4 1.0
OD1 H:ASP292 4.8 69.4 1.0
NH1 H:ARG146 4.8 54.7 1.0
CA C:ASP264 4.9 44.6 1.0
O2 H:SO4503 4.9 0.1 1.0

Magnesium binding site 4 out of 7 in 5j33

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Magnesium binding site 4 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


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 Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:32.6
occ:1.00
 O1 C:SO4502 2.1 52.3 1.0
OD1 C:ASP288 2.5 61.5 1.0
OD2 H:ASP264 2.9 53.3 1.0
OD1 C:ASP292 3.3 52.2 1.0
CG H:ASP264 3.4 54.9 1.0
S C:SO4502 3.4 48.5 1.0
CB H:ASP264 3.5 50.7 1.0
CG C:ASP288 3.6 59.6 1.0
C5N C:NAD501 3.7 51.6 1.0
O3 C:SO4502 3.9 47.5 1.0
CG C:ASP292 3.9 45.9 1.0
O C:ILE320 3.9 41.1 1.0
OD2 C:ASP292 4.0 46.8 1.0
C4N C:NAD501 4.0 57.8 1.0
OD2 C:ASP288 4.1 63.1 1.0
O4 C:SO4502 4.2 47.9 1.0
NH1 C:ARG146 4.2 48.7 1.0
OD1 H:ASP264 4.3 58.2 1.0
O2 C:SO4502 4.4 45.5 1.0
O C:ASP288 4.6 54.5 1.0
NH2 C:ARG146 4.7 45.4 1.0
C6N C:NAD501 4.9 47.9 1.0
CA H:ASP264 4.9 48.3 1.0
CB C:ASP288 4.9 53.5 1.0
NZ H:LYS232 4.9 42.3 1.0
CZ C:ARG146 4.9 45.7 1.0

Magnesium binding site 5 out of 7 in 5j33

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Magnesium binding site 5 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Isopropylmalate Dehydrogenase in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg505

b:80.0
occ:1.00
 OD1 F:ASP288 2.0 0.8 1.0
O2 D:SO4504 2.1 80.4 1.0
OD2 D:ASP264 2.3 58.6 1.0
CG F:ASP288 2.7 95.2 1.0
OD2 F:ASP288 2.7 96.9 1.0
O4 D:SO4504 3.1 74.7 1.0
S D:SO4504 3.1 78.9 1.0
CG D:ASP264 3.4 51.0 1.0
OD2 F:ASP292 3.7 43.8 1.0
C4N D:NAD503 3.7 79.2 1.0
O3 D:SO4504 3.8 92.7 1.0
CB D:ASP264 3.8 42.2 1.0
C5N D:NAD503 3.9 80.4 1.0
CB F:ASP288 4.2 82.7 1.0
O1 D:SO4504 4.3 76.7 1.0
NZ D:LYS232 4.3 42.0 1.0
OD1 D:ASP264 4.5 52.2 1.0
NH1 F:ARG146 4.5 62.5 1.0
O F:ILE320 4.6 51.6 1.0
N7N D:NAD503 4.6 95.5 1.0
CA F:ASP288 4.7 70.8 1.0
CG F:ASP292 4.8 48.1 1.0
O F:ASP288 4.8 64.3 1.0
C3N D:NAD503 5.0 74.6 1.0

Magnesium binding site 6 out of 7 in 5j33

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Magnesium binding site 6 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Isopropylmalate Dehydrogenase in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg506

b:47.2
occ:1.00
 OD1 D:ASP288 2.2 52.2 1.0
OD2 F:ASP264 2.4 43.5 1.0
O3 D:SO4502 2.8 89.4 1.0
CB F:ASP264 3.2 42.1 1.0
CG F:ASP264 3.2 42.8 1.0
CG D:ASP288 3.5 50.2 1.0
O D:ASP288 3.7 35.7 1.0
CG D:ASP292 3.8 49.3 1.0
S D:SO4502 3.8 85.0 1.0
NH1 D:ARG146 3.9 42.7 1.0
OD2 D:ASP292 3.9 42.3 1.0
OD1 D:ASP292 4.0 56.1 1.0
O2 D:SO4502 4.1 96.4 1.0
O1 D:SO4502 4.2 81.7 1.0
OD2 D:ASP288 4.2 52.9 1.0
CB D:ASP292 4.2 46.4 1.0
C D:ASP288 4.3 35.8 1.0
C5N D:NAD501 4.4 0.3 1.0
OD1 F:ASP264 4.4 42.8 1.0
CA D:ASP288 4.4 36.2 1.0
O D:ILE320 4.5 45.1 1.0
CB D:ASP288 4.5 41.8 1.0
C4N D:NAD501 4.7 97.1 1.0
CA F:ASP264 4.7 41.4 1.0
NH2 D:ARG146 4.8 44.1 1.0
CZ D:ARG146 4.9 43.3 1.0

Magnesium binding site 7 out of 7 in 5j33

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Magnesium binding site 7 out of 7 in the Isopropylmalate Dehydrogenase in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Isopropylmalate Dehydrogenase in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:71.4
occ:1.00
 O1 E:SO4502 2.2 59.9 1.0
OD1 E:ASP288 2.5 69.4 1.0
OD2 E:ASP292 2.7 60.6 1.0
S E:SO4502 3.2 69.2 1.0
O3 E:SO4502 3.3 96.2 1.0
OD2 G:ASP264 3.4 58.3 1.0
CG E:ASP288 3.5 69.1 1.0
O E:ILE320 3.6 38.5 1.0
NH1 E:ARG146 3.6 48.9 1.0
CG E:ASP292 3.8 54.6 1.0
OD2 E:ASP288 3.9 72.8 1.0
C5N E:NAD501 4.0 98.8 1.0
NH2 E:ARG146 4.1 50.4 1.0
C4N E:NAD501 4.1 99.0 1.0
O4 E:SO4502 4.2 68.2 1.0
O2 E:SO4502 4.2 58.5 1.0
CG G:ASP264 4.2 56.1 1.0
OD1 E:ASP292 4.3 50.8 1.0
CB G:ASP264 4.3 46.4 1.0
CZ E:ARG146 4.3 47.8 1.0
O E:ASP288 4.5 69.0 1.0
C E:ILE320 4.7 38.7 1.0
CB E:ASP288 4.7 64.3 1.0
CA E:ASP288 4.8 61.8 1.0

Reference:

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
Page generated: Tue Aug 12 12:04:44 2025

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