Magnesium in PDB 5e9f: Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae

All present enzymatic activity of Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae:
4.1.3.1; 4.1.3.30;

The structure of Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae, PDB code: 5e9f was solved by Y.Park, Y.Cho, Y.-H.Lee, Y.-W.Lee, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.40 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.583, 135.314, 158.880, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.6

The binding sites of Magnesium atom in the Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae (pdb code 5e9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae, PDB code: 5e9f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:41.8 occ:1.00 OD2 A:ASP177 2.4 31.7 1.0 OD1 A:ASP179 2.6 28.5 1.0 CG A:ASP177 3.3 30.0 1.0 OD1 A:ASP123 3.5 27.0 1.0 OD2 A:ASP123 3.6 25.8 1.0 CG A:ASP179 3.7 25.6 1.0 OD1 A:ASP177 3.7 26.9 1.0 OE2 A:GLU206 3.9 45.7 1.0 CA A:GLY107 3.9 27.4 1.0 CG A:ASP123 4.0 29.2 1.0 N A:TRP108 4.3 27.7 1.0 C A:GLY107 4.3 23.3 1.0 OD2 A:ASP179 4.3 25.9 1.0 O A:HOH717 4.3 19.5 1.0 N A:GLY107 4.4 24.2 1.0 CB A:ASP177 4.6 24.6 1.0 CB A:ASP179 4.8 22.0 1.0 CA A:ASP179 4.9 23.3 1.0

Magnesium binding site 2 out of 4 in the Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:30.6 occ:1.00 OD2 B:ASP177 2.3 28.1 1.0 OD1 B:ASP179 2.6 23.4 1.0 OD1 B:ASP123 3.2 32.1 1.0 CG B:ASP177 3.3 27.1 1.0 OD2 B:ASP123 3.6 34.7 1.0 OD1 B:ASP177 3.6 27.1 1.0 CA B:GLY107 3.7 24.6 1.0 CG B:ASP123 3.8 37.9 1.0 CG B:ASP179 3.8 29.7 1.0 C B:GLY107 4.0 26.5 1.0 N B:TRP108 4.0 29.4 1.0 OH B:TYR127 4.1 21.2 1.0 N B:GLY107 4.3 29.6 1.0 CB B:ASP177 4.5 26.0 1.0 O B:HOH712 4.5 20.2 1.0 OD2 B:ASP179 4.7 25.9 1.0 CB B:ASP179 4.7 31.3 1.0 O B:GLY107 4.7 29.0 1.0 CA B:ASP179 4.8 29.4 1.0 CA B:TRP108 5.0 34.2 1.0

Magnesium binding site 3 out of 4 in the Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:28.5 occ:1.00 OD2 C:ASP177 2.3 29.5 1.0 OD1 C:ASP179 2.4 30.7 1.0 CG C:ASP177 3.1 30.3 1.0 OD1 C:ASP177 3.2 31.8 1.0 OE1 C:GLU206 3.5 46.5 1.0 OD2 C:ASP123 3.6 31.8 1.0 CG C:ASP179 3.6 28.5 1.0 OD1 C:ASP123 3.9 32.6 1.0 CG C:ASP123 4.2 35.3 1.0 CA C:ASP179 4.3 29.2 1.0 CA C:GLY107 4.3 30.7 1.0 CB C:ASP179 4.3 27.1 1.0 CB C:ASP177 4.5 28.4 1.0 OD2 C:ASP179 4.6 26.3 1.0 CD C:GLU206 4.6 47.0 1.0 OH C:TYR127 4.7 29.7 1.0 N C:GLY107 4.8 28.6 1.0 O C:HOH713 4.8 22.7 1.0 N C:TRP108 4.8 27.1 1.0 N C:ASP179 4.8 28.5 1.0 C C:GLY107 4.8 28.4 1.0

Magnesium binding site 4 out of 4 in the Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insights of Isocitrate Lyases From Magnaporthe Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:36.9 occ:1.00 OD2 D:ASP177 2.5 34.3 1.0 OD1 D:ASP179 2.9 30.4 1.0 OD2 D:ASP123 3.1 38.3 1.0 OD1 D:ASP123 3.5 36.5 1.0 OE1 D:GLU206 3.5 53.1 1.0 CG D:ASP177 3.6 34.1 1.0 CG D:ASP123 3.7 37.8 1.0 OD1 D:ASP177 3.9 33.7 1.0 O D:HOH704 4.0 21.3 1.0 CG D:ASP179 4.1 34.6 1.0 CA D:GLY107 4.4 28.8 1.0 N D:TRP108 4.6 32.1 1.0 C D:GLY107 4.6 29.7 1.0 CD D:GLU206 4.7 45.7 1.0 CA D:ASP179 4.8 33.7 1.0 CB D:ASP179 4.8 32.0 1.0 CB D:ASP177 4.9 30.3 1.0 N D:GLY107 4.9 25.5 1.0 OH D:TYR127 5.0 24.8 1.0

Y.Park, Y.Cho, Y.-H.Lee, Y.-W.Lee, S.Rhee. Crystal Structure and Functional Analysis of Isocitrate Lyases From Magnaporthe Oryzae and Fusarium Graminearum J.Struct.Biol. V. 194 395 2016.
ISSN: ESSN 1095-8657
PubMed: 27016285
DOI: 10.1016/J.JSB.2016.03.019