Magnesium in PDB 3vmk: 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2:
1.1.1.85;

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2, PDB code: 3vmk 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)	25.77 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.972, 59.208, 119.779, 90.00, 95.12, 90.00
R / Rfree (%)	19.3 / 23.2

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 (pdb code 3vmk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2, PDB code: 3vmk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2


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 Benthica DB21 Mt-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:7.6 occ:1.00 O A:HOH682 2.0 12.2 1.0 OD1 A:ASP249 2.0 10.7 1.0 O B:HOH741 2.1 12.9 1.0 OD1 B:ASP225 2.1 11.8 1.0 O3 A:IPM401 2.1 10.1 1.0 O1 A:IPM401 2.3 9.8 1.0 C1 A:IPM401 3.0 11.3 1.0 CG A:ASP249 3.1 9.2 1.0 C2 A:IPM401 3.1 9.2 1.0 CG B:ASP225 3.2 11.2 1.0 OD2 A:ASP249 3.8 9.9 1.0 CB B:ASP225 3.8 10.3 1.0 NZ B:LYS193 3.9 11.5 1.0 O A:ASP249 4.1 8.3 1.0 O2 A:IPM401 4.1 11.3 1.0 OD1 A:ASP253 4.1 13.3 1.0 C4 A:IPM401 4.2 9.2 1.0 O A:HOH519 4.2 15.6 1.0 OD2 B:ASP225 4.2 11.5 1.0 O5 A:IPM401 4.2 10.3 1.0 C3 A:IPM401 4.3 9.9 1.0 CB A:ASP249 4.3 8.7 1.0 O A:HOH634 4.3 19.7 1.0 CG A:ASP253 4.4 11.7 1.0 OD2 A:ASP253 4.4 17.0 1.0 CA A:ASP249 4.5 7.6 1.0 O A:HOH833 4.5 21.9 1.0 NH2 A:ARG107 4.5 15.6 1.0 NH1 A:ARG136 4.5 9.4 1.0 O4 A:IPM401 4.6 10.9 1.0 C A:ASP249 4.6 7.2 1.0 O B:HOH720 4.7 18.3 1.0

Magnesium binding site 2 out of 2 in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:12.2 occ:1.00 OD1 A:ASP225 2.0 12.0 1.0 OD1 B:ASP249 2.1 12.8 1.0 O A:HOH551 2.1 13.9 1.0 O B:HOH506 2.1 13.1 1.0 O1 B:IPM401 2.1 13.1 1.0 O3 B:IPM401 2.1 12.4 1.0 C1 B:IPM401 2.9 14.9 1.0 C2 B:IPM401 3.0 14.0 1.0 CG B:ASP249 3.2 13.7 1.0 CG A:ASP225 3.3 9.5 1.0 OD2 B:ASP249 3.7 11.4 1.0 NZ A:LYS193 3.8 10.8 1.0 CB A:ASP225 3.9 10.5 1.0 O2 B:IPM401 4.1 14.4 1.0 OD1 B:ASP253 4.1 13.3 1.0 O B:ASP249 4.1 10.0 1.0 O B:HOH556 4.2 16.7 1.0 O5 B:IPM401 4.2 13.9 1.0 C4 B:IPM401 4.2 12.2 1.0 C3 B:IPM401 4.2 12.3 1.0 OD2 A:ASP225 4.2 11.0 1.0 O B:HOH618 4.2 16.7 1.0 CB B:ASP249 4.3 9.1 1.0 O B:HOH517 4.4 29.7 1.0 NH1 B:ARG107 4.4 17.9 1.0 CG B:ASP253 4.4 10.6 1.0 O4 B:IPM401 4.5 14.0 1.0 NH1 B:ARG136 4.5 12.0 1.0 CA B:ASP249 4.6 8.4 1.0 OD2 B:ASP253 4.6 14.3 1.0 O B:HOH673 4.6 26.4 1.0 C B:ASP249 4.7 10.1 1.0 O A:HOH587 4.7 14.2 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