Magnesium in PDB 3vmj: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1:
1.1.1.85;

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1, PDB code: 3vmj was solved by T.Nagae, N.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.37 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.683, 57.495, 76.330, 90.00, 119.03, 90.00
R / Rfree (%)	17.7 / 21.5

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 (pdb code 3vmj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1, PDB code: 3vmj:

Magnesium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:13.8 occ:1.00 OD1 A:ASP249 2.0 13.2 1.0 O A:HOH834 2.1 14.7 1.0 O A:HOH832 2.1 14.9 1.0 O1 A:IPM401 2.2 14.8 1.0 O3 A:IPM401 2.2 17.7 1.0 C1 A:IPM401 3.0 16.7 1.0 C2 A:IPM401 3.0 16.2 1.0 CG A:ASP249 3.1 11.8 1.0 OD2 A:ASP249 3.7 12.0 1.0 O A:ASP249 4.0 11.8 1.0 C4 A:IPM401 4.1 12.6 1.0 O A:HOH597 4.1 27.4 1.0 OD2 A:ASP253 4.2 16.2 1.0 C3 A:IPM401 4.2 11.6 1.0 O2 A:IPM401 4.2 18.5 1.0 O A:HOH560 4.2 21.4 1.0 O5 A:IPM401 4.2 15.2 1.0 CB A:ASP249 4.3 9.8 1.0 OD1 A:ASP253 4.3 16.4 1.0 CG A:ASP253 4.3 11.7 1.0 O A:HOH838 4.4 26.4 1.0 O4 A:IPM401 4.5 15.1 1.0 CA A:ASP249 4.5 11.3 1.0 C A:ASP249 4.6 11.8 1.0 NH1 A:ARG107 4.6 28.6 1.0 NH1 A:ARG136 4.8 14.1 1.0 O A:HOH859 4.9 30.7 1.0

T.Nagae, C.Kato, N.Watanabe. Structural Analysis of 3-Isopropylmalate Dehydrogenase From the Obligate Piezophile Shewanella Benthica DB21MT-2 and the Nonpiezophile Shewanella Oneidensis Mr-1 Acta Crystallogr.,Sect.F V. 68 265 2012.
ISSN: ESSN 1744-3091
PubMed: 22442218
DOI: 10.1107/S1744309112001443