Magnesium in PDB 3mbc: Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp

All present enzymatic activity of Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp:
1.1.1.42;

The structure of Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp, PDB code: 3mbc was solved by N.S.Sidhu, S.Aich, G.M.Sheldrick, L.T.J.Delbaere, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.74 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.840, 52.730, 236.370, 90.00, 103.41, 90.00
R / Rfree (%)	18.9 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp (pdb code 3mbc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp, PDB code: 3mbc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg739 b:11.8 occ:1.00 O A:HOH1110 1.8 25.1 1.0 OD2 A:ASP346 2.1 22.4 1.0 O A:HOH1109 2.1 20.1 1.0 OD2 A:ASP544 2.1 17.9 1.0 OD1 A:ASP548 2.2 25.2 1.0 O A:ASP544 2.4 16.0 1.0 CG A:ASP544 3.1 21.9 1.0 CG A:ASP548 3.2 22.7 1.0 CG A:ASP346 3.2 22.1 1.0 C A:ASP544 3.3 12.6 1.0 CA A:ASP544 3.6 12.9 1.0 OD2 A:ASP548 3.6 22.2 1.0 O A:HOH1029 3.9 34.6 1.0 CB A:ASP346 3.9 15.8 1.0 CB A:ASP544 3.9 13.3 1.0 OD1 A:ASP544 4.0 20.2 1.0 O A:HOH1324 4.1 30.2 1.0 OD1 A:ASP346 4.1 22.5 1.0 CB A:ASP548 4.3 13.2 1.0 N A:TYR545 4.4 12.4 1.0 O A:HOH1239 4.5 38.6 1.0 OG1 A:THR547 4.5 13.3 1.0 NZ A:LYS253 4.6 22.9 1.0 N A:ASP548 4.8 14.3 1.0 CA A:TYR545 4.8 12.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Monomeric Isocitrate Dehydrogenase From Corynebacterium Glutamicum in Complex with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg739 b:30.4 occ:1.00 O B:HOH832 1.8 42.9 1.0 O B:HOH833 1.8 36.0 1.0 OD2 B:ASP544 2.0 39.4 1.0 OD1 B:ASP548 2.1 40.3 1.0 OD1 B:ASP346 2.1 45.1 1.0 O B:ASP544 2.2 40.2 1.0 CG B:ASP544 3.1 42.9 1.0 C B:ASP544 3.1 38.9 1.0 CG B:ASP548 3.2 43.6 1.0 CG B:ASP346 3.3 44.9 1.0 CA B:ASP544 3.6 40.1 1.0 OD2 B:ASP548 3.8 45.0 1.0 CB B:ASP544 3.9 43.9 1.0 CB B:ASP346 3.9 42.8 1.0 OD1 B:ASP544 4.0 40.5 1.0 N B:TYR545 4.2 38.1 1.0 OD2 B:ASP346 4.3 44.6 1.0 CB B:ASP548 4.3 42.9 1.0 OG1 B:THR547 4.5 37.9 1.0 NZ B:LYS253 4.5 44.0 1.0 CA B:TYR545 4.6 35.6 1.0 N B:ASP548 4.8 36.4 1.0

N.S.Sidhu, L.T.Delbaere, G.M.Sheldrick. Structure of A Highly Nadp+-Specific Isocitrate Dehydrogenase. Acta Crystallogr.,Sect.D V. 67 856 2011.
ISSN: ISSN 0907-4449
PubMed: 21931217
DOI: 10.1107/S0907444911028575