Magnesium in PDB 1xbz: Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate

The structure of Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate, PDB code: 1xbz was solved by E.L.Wise, W.S.Yew, J.Akana, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.29 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.776, 41.435, 91.011, 90.00, 96.72, 90.00
R / Rfree (%)	16.8 / 21

The binding sites of Magnesium atom in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate (pdb code 1xbz). 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 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate, PDB code: 1xbz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate


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 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:15.5 occ:1.00 MG A:MG602 0.0 15.5 1.0 O A:HOH755 2.0 15.6 1.0 OE2 A:GLU33 2.0 13.2 1.0 OD2 A:ASP62 2.0 12.9 1.0 O2 A:LX1501 2.1 17.4 1.0 O A:HOH746 2.2 17.9 1.0 O3 A:LX1501 2.2 15.2 1.0 C2 A:LX1501 3.0 19.7 1.0 CD A:GLU33 3.0 15.1 1.0 C3 A:LX1501 3.1 16.5 1.0 CG A:ASP62 3.1 19.4 1.0 OE1 A:GLU33 3.4 12.9 1.0 CB A:ASP62 3.8 13.0 1.0 O4 A:LX1501 3.9 20.3 1.0 OD1 A:ASP11 4.0 17.5 1.0 NZ A:LYS64 4.0 23.2 1.0 C4 A:LX1501 4.0 17.4 1.0 O A:HOH619 4.0 19.8 1.0 OD1 A:ASP62 4.2 15.8 1.0 C1 A:LX1501 4.3 16.5 1.0 OD2 A:ASP11 4.3 15.6 1.0 CG A:GLU33 4.3 13.8 1.0 O B:HOH533 4.3 23.8 1.0 CA A:GLY35 4.4 12.9 1.0 OG1 A:THR36 4.5 14.9 1.0 N A:THR36 4.5 16.1 1.0 CG A:ASP11 4.6 17.0 1.0 CB A:ALA9 4.7 16.4 1.0 C5 A:LX1501 4.8 17.9 1.0 CE A:LYS64 4.8 20.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate


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 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound L-Xylulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:15.5 occ:1.00 MG A:MG601 0.0 15.5 1.0 O A:HOH755 2.0 15.6 1.0 OE2 A:GLU33 2.0 13.2 1.0 OD2 A:ASP62 2.0 12.9 1.0 O2 A:LX1501 2.1 17.4 1.0 O A:HOH746 2.2 17.9 1.0 O3 A:LX1501 2.2 15.2 1.0 C2 A:LX1501 3.0 19.7 1.0 CD A:GLU33 3.0 15.1 1.0 C3 A:LX1501 3.1 16.5 1.0 CG A:ASP62 3.1 19.4 1.0 OE1 A:GLU33 3.4 12.9 1.0 CB A:ASP62 3.8 13.0 1.0 O4 A:LX1501 3.9 20.3 1.0 OD1 A:ASP11 4.0 17.5 1.0 NZ A:LYS64 4.0 23.2 1.0 C4 A:LX1501 4.0 17.4 1.0 O A:HOH619 4.0 19.8 1.0 OD1 A:ASP62 4.2 15.8 1.0 C1 A:LX1501 4.3 16.5 1.0 OD2 A:ASP11 4.3 15.6 1.0 CG A:GLU33 4.3 13.8 1.0 O B:HOH533 4.3 23.8 1.0 CA A:GLY35 4.4 12.9 1.0 OG1 A:THR36 4.5 14.9 1.0 N A:THR36 4.5 16.1 1.0 CG A:ASP11 4.6 17.0 1.0 CB A:ALA9 4.7 16.4 1.0 C5 A:LX1501 4.8 17.9 1.0 CE A:LYS64 4.8 20.6 1.0

E.L.Wise, W.S.Yew, J.Akana, J.A.Gerlt, I.Rayment. Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Structural Basis For Catalytic Promiscuity in Wild-Type and Designed Mutants of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase Biochemistry V. 44 1816 2005.
ISSN: ISSN 0006-2960
PubMed: 15697207
DOI: 10.1021/BI0478143