Magnesium in PDB 6xxy: Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate.

All present enzymatic activity of Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate.:
1.1.1.85;

The structure of Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate., PDB code: 6xxy was solved by R.Miggiano, F.Rossi, S.Martignon, M.Rizzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.49 / 2.09
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	116.936, 116.936, 92.370, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate. (pdb code 6xxy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate., PDB code: 6xxy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate.


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 Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.7 occ:1.00 O11 A:O45404 2.2 14.7 1.0 O A:ASP250 2.6 17.6 1.0 C09 A:O45404 2.7 22.6 1.0 OD1 A:ASP250 2.7 15.2 1.0 O10 A:O45404 2.8 18.5 1.0 OD1 A:ASP254 2.9 16.2 1.0 NH1 A:ARG108 3.0 13.4 1.0 OG A:SER253 3.2 16.1 1.0 OD2 B:ASP226 3.3 13.6 1.0 C A:ASP250 3.5 15.1 1.0 CG A:ASP254 3.6 18.4 1.0 CA A:ASP250 3.8 14.5 1.0 CB B:ASP226 3.8 13.5 1.0 CG A:ASP250 3.9 16.0 1.0 CG B:ASP226 4.0 16.2 1.0 N A:ASP254 4.1 18.0 1.0 C07 A:O45404 4.1 26.1 1.0 CZ A:ARG108 4.2 16.4 1.0 O A:ALA282 4.2 15.0 1.0 OD2 A:ASP254 4.3 16.3 1.0 CB A:ASP254 4.3 16.6 1.0 CB A:ASP250 4.5 13.8 1.0 CB A:SER253 4.6 17.2 1.0 CA A:ASP254 4.6 19.5 1.0 NH2 A:ARG108 4.6 13.8 1.0 O08 A:O45404 4.7 20.9 1.0 C A:SER253 4.7 18.3 1.0 N A:ILE251 4.7 14.4 1.0 H061 A:O45404 4.8 22.9 1.0 O A:HOH570 4.8 10.2 1.0 O A:GLY249 4.8 14.5 1.0 N06 A:O45404 4.9 19.4 1.0 OD2 A:ASP250 4.9 16.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate.


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 Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase in Complex with O-Isobutenyl Oxalylhydroxamate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:28.8 occ:1.00 O11 B:O45402 1.6 34.9 1.0 OD1 B:ASP250 2.0 24.5 1.0 O B:HOH511 2.0 26.5 1.0 C09 B:O45402 2.1 35.8 1.0 OD2 A:ASP226 2.1 25.4 1.0 O10 B:O45402 2.2 36.6 1.0 O B:HOH509 2.3 34.0 1.0 CG A:ASP226 3.1 28.3 1.0 CG B:ASP250 3.2 26.9 1.0 OD1 B:ASP254 3.4 28.9 1.0 C07 B:O45402 3.4 37.1 1.0 CB A:ASP226 3.5 23.3 1.0 H061 B:O45402 3.6 43.6 1.0 O B:ASP250 3.6 22.5 1.0 OD2 B:ASP250 3.8 30.3 1.0 CG B:ASP254 3.8 30.2 1.0 OD2 B:ASP254 3.8 30.5 1.0 O B:HOH512 3.9 34.3 1.0 N06 B:O45402 3.9 36.7 1.0 NH1 B:ARG108 4.1 26.4 1.0 NZ A:LYS194 4.2 30.6 1.0 C B:ASP250 4.2 23.3 1.0 OD1 A:ASP226 4.2 26.0 1.0 O08 B:O45402 4.3 36.7 1.0 CA B:ASP250 4.3 21.7 1.0 CB B:ASP250 4.3 25.3 1.0 O A:HOH593 4.4 28.8 1.0 O B:ALA282 4.7 37.8 1.0 C5N B:NAD401 4.7 38.8 1.0 O A:HOH553 4.7 32.2 1.0 CB B:ASP254 4.9 25.0 1.0 OG B:SER253 4.9 24.4 1.0

R.Miggiano, S.Martignon, A.Minassi, F.Rossi, M.Rizzi. Crystal Structure of Haemophilus Influenzae 3-Isopropylmalate Dehydrogenase (Leub) in Complex with the Inhibitor O-Isobutenyl Oxalylhydroxamate. Biochem.Biophys.Res.Commun. 2020.
ISSN: ESSN 1090-2104
PubMed: 32059844
DOI: 10.1016/J.BBRC.2020.02.022