Magnesium in PDB 4di8: Crystal Structure of the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5

The structure of Crystal Structure of the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5, PDB code: 4di8 was solved by V.N.Malashkevich, R.Toro, M.E.Hobbs, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.348, 52.131, 76.539, 90.00, 93.73, 90.00
R / Rfree (%)	15.7 / 18.7

The binding sites of Magnesium atom in the Crystal Structure of the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5 (pdb code 4di8). 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 the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5, PDB code: 4di8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5


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 the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:37.8 occ:1.00 O B:HOH741 2.1 19.4 1.0 O B:HOH591 2.1 15.8 1.0 O B:HOH701 2.1 21.9 1.0 O B:HOH688 2.1 20.7 1.0 O B:HOH759 2.2 24.2 1.0 O B:HOH783 2.7 34.2 1.0 OD1 B:ASP6 4.1 25.9 1.0 O B:ASP6 4.2 19.6 1.0 O B:HOH784 4.2 22.4 1.0 O B:HOH706 4.3 20.8 1.0 OD2 B:ASP6 4.4 26.2 1.0 CG B:ASP6 4.6 33.2 1.0 O B:HOH692 4.6 16.2 1.0 O B:HOH845 4.7 23.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5


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 the D248A Mutant of 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase From Sphingomonas Paucimobilis Complexed with Substrate at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:30.8 occ:1.00 O B:HOH719 2.0 17.9 1.0 O B:HOH781 2.0 14.4 1.0 O B:HOH630 2.1 19.3 1.0 O B:HOH674 2.1 24.4 1.0 O B:HOH737 2.2 20.6 1.0 O B:HOH789 4.0 26.0 1.0 CE B:LYS18 4.0 41.0 1.0 O B:PRO19 4.2 11.5 1.0 O B:TYR21 4.2 13.0 1.0 OG1 B:THR22 4.3 17.9 1.0 O B:LEU66 4.3 12.5 1.0 O B:HIS65 4.6 14.2 1.0 CA B:THR22 4.6 14.1 1.0 CG B:LYS18 4.6 40.3 1.0 CD B:PRO19 4.7 11.3 1.0 CG2 B:THR22 4.7 18.2 1.0 C B:LEU66 4.7 12.3 1.0 CB B:THR22 4.8 15.1 1.0 CA B:GLY67 4.9 13.6 1.0 O B:HOH560 4.9 16.2 1.0 CD B:LYS18 4.9 21.5 1.0 CD B:PRO23 5.0 14.5 1.0 NZ B:LYS18 5.0 24.0 1.0

M.E.Hobbs, V.Malashkevich, H.J.Williams, C.Xu, J.M.Sauder, S.K.Burley, S.C.Almo, F.M.Raushel. Structure and Catalytic Mechanism of Ligi: Insight Into the Amidohydrolase Enzymes of COG3618 and Lignin Degradation. Biochemistry V. 51 3497 2012.
ISSN: ISSN 0006-2960
PubMed: 22475079
DOI: 10.1021/BI300307B