Manganese 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:

Magnesium

(Mg)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Monoclinic Form of Idi-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1180 b:17.4 occ:1.00 OE2 A:GLU116 1.9 19.9 1.0 OE2 A:GLU114 2.0 23.2 1.0 NE2 A:HIS69 2.0 16.3 1.0 NE2 A:HIS32 2.2 24.6 1.0 NE2 A:HIS25 2.2 24.0 1.0 OE1 A:GLU114 2.3 21.7 1.0 CD A:GLU114 2.5 20.3 1.0 CE1 A:HIS32 2.9 20.7 1.0 CE1 A:HIS69 3.0 19.5 1.0 CD A:GLU116 3.0 22.5 1.0 CD2 A:HIS69 3.1 15.5 1.0 CD2 A:HIS25 3.1 22.5 1.0 CE1 A:HIS25 3.2 18.7 1.0 CD2 A:HIS32 3.4 20.8 1.0 CG A:GLU116 3.5 16.9 1.0 CG A:GLU114 4.0 19.6 1.0 ND1 A:HIS32 4.1 22.3 1.0 OE1 A:GLU116 4.1 15.1 1.0 ND1 A:HIS69 4.1 17.5 1.0 CG A:HIS69 4.2 17.4 1.0 CG A:HIS25 4.3 23.9 1.0 ND1 A:HIS25 4.3 23.9 1.0 CG A:HIS32 4.4 22.5 1.0 C11 A:DED1182 4.7 16.1 1.0 N12 A:DED1182 4.8 17.3 1.0 CB A:GLU114 4.8 21.6 1.0 CB A:ALA34 4.9 17.2 1.0 C14 A:DED1182 4.9 20.3 1.0 CG1 A:VAL6 4.9 25.4 1.0 CB A:GLU116 5.0 18.3 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Monoclinic Form of Idi-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1184 b:15.6 occ:1.00 OE2 B:GLU116 1.9 21.1 1.0 NE2 B:HIS69 2.0 15.1 1.0 OE2 B:GLU114 2.1 17.9 1.0 NE2 B:HIS32 2.1 26.9 1.0 NE2 B:HIS25 2.3 21.7 1.0 OE1 B:GLU114 2.4 22.3 1.0 CD B:GLU114 2.5 19.7 1.0 CD B:GLU116 2.9 20.1 1.0 CE1 B:HIS69 3.0 14.0 1.0 CD2 B:HIS69 3.0 13.3 1.0 CD2 B:HIS32 3.1 23.2 1.0 CE1 B:HIS32 3.1 22.3 1.0 CD2 B:HIS25 3.2 20.8 1.0 CE1 B:HIS25 3.4 22.5 1.0 CG B:GLU116 3.6 22.0 1.0 OE1 B:GLU116 3.9 18.5 1.0 ND1 B:HIS69 4.1 15.6 1.0 CG B:GLU114 4.1 18.5 1.0 C10 B:DED1186 4.1 27.4 1.0 CG B:HIS69 4.1 17.9 1.0 ND1 B:HIS32 4.2 23.7 1.0 CG B:HIS32 4.3 21.3 1.0 CG B:HIS25 4.4 22.1 1.0 ND1 B:HIS25 4.5 24.8 1.0 C11 B:DED1186 4.8 20.8 1.0 CB B:GLU114 4.8 21.5 1.0 CG1 B:VAL6 5.0 20.6 1.0 CB B:ALA34 5.0 19.0 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