Magnesium in PDB 7ebc: Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae

All present enzymatic activity of Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae:
4.1.3.1;

The structure of Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae, PDB code: 7ebc was solved by K.Hiragi, K.Nishio, S.Moriyama, T.Hamaguchi, A.Mizoguchi, K.Yonekura, K.Tani, T.Mizushima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.522, 129.377, 210.787, 90, 90, 90
R / Rfree (%)	18.9 / 22

The binding sites of Magnesium atom in the Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae (pdb code 7ebc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae, PDB code: 7ebc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae


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-1 From Saccaromyces Cervisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:39.9 occ:1.00 O A:HOH703 2.4 27.3 1.0 O A:HOH724 2.4 28.2 1.0 OD2 A:ASP179 2.4 29.6 1.0 O A:HOH847 2.8 27.3 1.0 O A:HOH835 2.9 20.7 1.0 OD2 A:ASP123 3.4 31.4 1.0 CG A:ASP179 3.5 25.4 1.0 N A:TRP108 3.9 22.2 1.0 OD1 A:ASP181 4.0 21.7 1.0 OD1 A:ASP179 4.1 26.6 1.0 OD1 A:ASP123 4.1 30.6 1.0 CG A:ASP123 4.2 25.9 1.0 CA A:GLY107 4.2 25.5 1.0 N A:GLY107 4.2 25.3 1.0 C A:GLY107 4.3 24.5 1.0 NH1 A:ARG254 4.4 29.7 1.0 CB A:ASP179 4.7 26.3 1.0 OE2 A:GLU208 4.7 27.1 1.0 CA A:TRP108 4.7 26.9 1.0 CB A:TRP108 4.8 26.4 1.0 OH A:TYR104 5.0 25.5 1.0 CE1 A:HIS206 5.0 24.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae


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-1 From Saccaromyces Cervisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:38.4 occ:1.00 O B:HOH702 2.0 26.4 1.0 O B:HOH704 2.3 27.5 1.0 OD2 B:ASP179 2.5 32.9 1.0 O B:HOH807 2.8 26.6 1.0 O B:HOH817 2.9 30.6 1.0 OD2 B:ASP123 3.3 34.1 1.0 CG B:ASP179 3.6 26.6 1.0 N B:TRP108 4.0 27.3 1.0 OD1 B:ASP181 4.1 25.5 1.0 OD1 B:ASP123 4.1 30.0 1.0 CG B:ASP123 4.1 30.2 1.0 OD1 B:ASP179 4.2 30.3 1.0 CA B:GLY107 4.3 25.7 1.0 N B:GLY107 4.3 26.3 1.0 NH1 B:ARG254 4.4 33.4 1.0 C B:GLY107 4.4 25.5 1.0 OE2 B:GLU208 4.7 32.8 1.0 CB B:TRP108 4.8 25.7 1.0 CA B:TRP108 4.8 25.6 1.0 CB B:ASP179 4.8 26.8 1.0 NH2 B:ARG254 4.9 32.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:46.7 occ:1.00 O C:HOH712 2.2 30.8 1.0 O C:HOH704 2.3 26.7 1.0 O C:HOH824 2.7 35.0 1.0 OD2 C:ASP179 2.9 32.8 1.0 OD2 C:ASP123 3.1 34.1 1.0 O C:HOH791 3.1 24.0 1.0 CG C:ASP179 4.0 28.7 1.0 CG C:ASP123 4.0 31.1 1.0 NH1 C:ARG254 4.1 39.0 1.0 OD1 C:ASP123 4.1 30.2 1.0 N C:TRP108 4.2 26.9 1.0 OD1 C:ASP181 4.3 23.3 1.0 OD1 C:ASP179 4.4 27.2 1.0 OE2 C:GLU208 4.5 38.6 1.0 NH2 C:ARG254 4.6 38.2 1.0 CA C:GLY107 4.7 25.9 1.0 N C:GLY107 4.7 28.5 1.0 C C:GLY107 4.8 25.1 1.0 CZ C:ARG254 4.8 36.4 1.0 CB C:TRP108 4.8 27.0 1.0 CA C:TRP108 4.9 26.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Isocitrate Lyase-1 From Saccaromyces Cervisiae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:45.5 occ:1.00 O D:HOH706 2.2 23.4 1.0 O D:HOH738 2.3 24.9 1.0 OD2 D:ASP179 2.5 29.1 1.0 O D:HOH837 2.6 33.6 1.0 O D:HOH832 3.1 22.2 1.0 OD2 D:ASP123 3.3 39.0 1.0 CG D:ASP179 3.6 23.4 1.0 N D:TRP108 4.1 29.8 1.0 OD1 D:ASP179 4.1 25.0 1.0 CG D:ASP123 4.2 33.3 1.0 OD1 D:ASP181 4.2 30.8 1.0 OD1 D:ASP123 4.2 42.5 1.0 NH1 D:ARG254 4.3 39.7 1.0 N D:GLY107 4.4 30.5 1.0 CA D:GLY107 4.4 27.8 1.0 C D:GLY107 4.6 27.9 1.0 OE2 D:GLU208 4.7 35.4 1.0 CB D:TRP108 4.8 33.0 1.0 CB D:ASP179 4.8 24.2 1.0 CA D:TRP108 4.9 31.8 1.0 NH2 D:ARG254 4.9 33.2 1.0 CE1 D:HIS206 5.0 24.7 1.0 OH D:TYR104 5.0 31.9 1.0

K.Hiragi, K.Nishio, S.Moriyama, T.Hamaguchi, A.Mizoguchi, K.Yonekura, K.Tani, T.Mizushima. Structural Insights Into the Targeting Specificity of Ubiquitin Ligase For S. Cerevisiae Isocitrate Lyase But Not C. Albicans Isocitrate Lyase. J.Struct.Biol. V. 213 07748 2021.
ISSN: ESSN 1095-8657
PubMed: 34033899
DOI: 10.1016/J.JSB.2021.107748