Magnesium in PDB 7cp1: Crystal Structure of Isocitrate Lyase in Complex with Succinate and Itaconate

All present enzymatic activity of Crystal Structure of Isocitrate Lyase in Complex with Succinate and Itaconate:
4.1.3.1;

The structure of Crystal Structure of Isocitrate Lyase in Complex with Succinate and Itaconate, PDB code: 7cp1 was solved by S.Kwon, H.H.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.03 / 2.58
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.32, 131.32, 284.882, 90, 90, 120
R / Rfree (%)	15.4 / 19.4

The binding sites of Magnesium atom in the Crystal Structure of Isocitrate Lyase in Complex with Succinate and Itaconate (pdb code 7cp1). 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 Isocitrate Lyase in Complex with Succinate and Itaconate, PDB code: 7cp1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Isocitrate Lyase in Complex with Succinate and Itaconate


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 Isocitrate Lyase in Complex with Succinate and Itaconate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.0 occ:1.00 O A:HOH697 2.4 28.5 1.0 OD2 A:ASP153 2.7 26.2 1.0 OE1 A:GLU155 2.8 34.8 1.0 OD1 A:ASP108 2.8 37.6 1.0 OE2 A:GLU155 3.0 29.7 1.0 O A:HOH698 3.1 32.2 1.0 CD A:GLU155 3.2 29.4 1.0 O1 A:SIN501 3.4 37.9 1.0 CG A:ASP108 3.6 36.9 1.0 OD2 A:ASP108 3.6 34.0 1.0 C1 A:SIN501 3.6 34.5 1.0 CG A:ASP153 3.7 23.6 1.0 O2 A:SIN501 3.7 37.0 1.0 N A:TRP93 3.7 25.4 1.0 OD1 A:ASP153 3.9 22.5 1.0 C A:GLY92 4.1 23.3 1.0 O A:HOH710 4.1 30.3 1.0 O A:HOH610 4.3 30.2 1.0 O A:HOH627 4.3 37.8 1.0 CA A:TRP93 4.3 25.4 1.0 CA A:GLY92 4.4 20.8 1.0 C2 A:SIN501 4.5 43.5 1.0 CB A:TRP93 4.5 25.1 1.0 CG A:GLU155 4.6 26.8 1.0 N A:GLY92 4.7 25.7 1.0 O A:GLY92 4.8 22.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Isocitrate Lyase in Complex with Succinate and Itaconate


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 Isocitrate Lyase in Complex with Succinate and Itaconate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:22.6 occ:1.00 OD1 B:ASP108 2.7 34.8 1.0 OD2 B:ASP153 2.7 34.5 1.0 OE1 B:GLU155 2.8 39.1 1.0 O B:HOH655 2.9 27.8 1.0 OE2 B:GLU155 3.2 33.9 1.0 CD B:GLU155 3.3 35.9 1.0 OD2 B:ASP108 3.4 35.2 1.0 CG B:ASP108 3.4 34.5 1.0 N B:TRP93 3.5 28.9 1.0 O1 B:ITN501 3.5 37.0 1.0 O B:HOH753 3.7 34.8 1.0 CG B:ASP153 3.7 29.2 1.0 C1 B:ITN501 3.8 29.4 1.0 O2 B:ITN501 3.9 31.9 1.0 O B:HOH615 3.9 32.8 1.0 C B:GLY92 3.9 28.6 1.0 OD1 B:ASP153 4.0 27.7 1.0 CA B:GLY92 4.1 25.2 1.0 CA B:TRP93 4.2 25.6 1.0 O B:HOH622 4.2 28.8 1.0 CB B:TRP93 4.3 28.8 1.0 O B:HOH625 4.4 36.1 1.0 N B:GLY92 4.4 25.0 1.0 CG B:GLU155 4.6 28.3 1.0 C2 B:ITN501 4.7 34.1 1.0 O B:GLY92 4.7 26.6 1.0 CB B:ASP108 4.8 26.4 1.0

S.Kwon, H.L.Chun, H.J.Ha, S.Y.Lee, H.H.Park. Heterogeneous Multimeric Structure of Isocitrate Lyase in Complex with Succinate and Itaconate Provides Novel Insights Into Its Inhibitory Mechanism. Plos One V. 16 51067 2021.
ISSN: ESSN 1932-6203
PubMed: 33951112
DOI: 10.1371/JOURNAL.PONE.0251067