Magnesium in PDB 2vnp: Monoclinic Form of Idi-1

All present enzymatic activity of Monoclinic Form of Idi-1:
5.3.3.2;

The structure of Monoclinic Form of Idi-1, PDB code: 2vnp was solved by J.De Ruyck, Y.Oudjama, J.Wouters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.20 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.200, 69.100, 62.400, 90.00, 100.30, 90.00
R / Rfree (%)	19.4 / 25.5

The structure of Monoclinic Form of Idi-1 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Monoclinic Form of Idi-1 (pdb code 2vnp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Monoclinic Form of Idi-1, PDB code: 2vnp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Monoclinic Form of Idi-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Monoclinic Form of Idi-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1181 b:9.1 occ:1.00 OE2 A:GLU87 2.1 20.8 1.0 O A:CYS67 2.1 18.6 1.0 O6 A:DED1182 2.2 28.3 1.0 O A:HOH2008 2.3 18.6 1.0 O2 A:DED1182 2.3 26.8 1.0 O A:HOH2017 2.4 24.1 1.0 CD A:GLU87 3.1 22.9 1.0 C A:CYS67 3.3 18.9 1.0 OE1 A:GLU87 3.4 22.2 1.0 P4 A:DED1182 3.5 27.1 1.0 P8 A:DED1182 3.6 23.7 1.0 O5 A:DED1182 3.7 27.2 1.0 N A:CYS67 4.1 19.1 1.0 N A:GLY68 4.2 17.7 1.0 CA A:CYS67 4.2 20.8 1.0 NH2 A:ARG83 4.3 19.3 1.0 CA A:GLY68 4.3 15.5 1.0 O A:HOH2004 4.3 13.7 1.0 NE A:ARG83 4.4 24.5 1.0 OE1 A:GLU135 4.4 27.3 1.0 O3 A:DED1182 4.5 27.4 1.0 CG A:GLU87 4.5 20.3 1.0 O9 A:DED1182 4.5 27.2 1.0 NH1 A:ARG51 4.5 19.7 1.0 O A:HOH2016 4.6 17.4 1.0 O1 A:DED1182 4.6 25.6 1.0 CB A:CYS67 4.6 21.3 1.0 NZ A:LYS55 4.7 20.2 1.0 O7 A:DED1182 4.7 23.4 1.0 C10 A:DED1182 4.7 22.2 1.0 CZ A:ARG83 4.8 23.0 1.0

Magnesium binding site 2 out of 2 in the Monoclinic Form of Idi-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Monoclinic Form of Idi-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1185 b:9.4 occ:1.00 OE2 B:GLU87 2.0 24.1 1.0 O B:CYS67 2.1 17.6 1.0 O1 B:DED1186 2.2 20.5 1.0 O B:HOH2025 2.2 18.2 1.0 O6 B:DED1186 2.3 25.5 1.0 O B:HOH2015 2.5 13.6 1.0 CD B:GLU87 2.8 23.6 1.0 OE1 B:GLU87 2.9 23.3 1.0 C B:CYS67 3.4 18.1 1.0 P4 B:DED1186 3.5 23.8 1.0 P8 B:DED1186 3.5 23.6 1.0 O5 B:DED1186 3.7 25.9 1.0 N B:CYS67 4.1 19.1 1.0 OE1 B:GLU135 4.2 29.2 1.0 O9 B:DED1186 4.2 29.1 1.0 CA B:CYS67 4.2 20.4 1.0 O2 B:DED1186 4.3 21.6 1.0 N B:GLY68 4.3 16.0 1.0 CG B:GLU87 4.3 21.5 1.0 NH2 B:ARG83 4.3 24.3 1.0 CA B:GLY68 4.4 15.9 1.0 O B:HOH2004 4.4 19.0 1.0 NE B:ARG83 4.4 22.2 1.0 CB B:CYS67 4.4 21.6 1.0 NH1 B:ARG51 4.5 17.1 1.0 O3 B:DED1186 4.6 24.6 1.0 NZ B:LYS55 4.7 17.7 1.0 O7 B:DED1186 4.8 31.1 1.0 CZ B:ARG83 4.9 27.2 1.0

J.De Ruyck, Y.Oudjama, J.Wouters. Monoclinic Form of Isopentenyl Diphosphate Isomerase: A Case of Polymorphism in Biomolecular Crystals. Acta Crystallogr.,Sect.F V. 64 239 2008.
ISSN: ISSN 1744-3091
PubMed: 18391416
DOI: 10.1107/S174430910800568X