Magnesium in PDB 1xbx: Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound D-Ribulose 5-Phosphate

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound D-Ribulose 5-Phosphate, PDB code: 1xbx 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)	90.00 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.000, 41.831, 91.068, 90.00, 97.47, 90.00
R / Rfree (%)	14.1 / 17.8

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound D-Ribulose 5-Phosphate (pdb code 1xbx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound D-Ribulose 5-Phosphate, PDB code: 1xbx:
Jump to Magnesium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound D-Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:9.3 occ:1.00 OE2 A:GLU33 2.0 8.6 1.0 OD2 A:ASP62 2.1 7.8 1.0 O A:HOH676 2.1 8.9 1.0 O A:HOH677 2.1 10.7 1.0 O6 A:HMS501 2.2 9.6 1.0 C4 A:HMS501 2.8 12.8 1.0 C3 A:HMS501 3.0 11.4 1.0 CD A:GLU33 3.0 9.1 1.0 CG A:ASP62 3.2 10.9 1.0 OE1 A:GLU33 3.4 11.7 1.0 CB A:ASP62 3.8 9.2 1.0 C2 A:HMS501 3.8 11.4 1.0 C5 A:HMS501 4.1 10.4 1.0 O A:HOH678 4.1 12.9 1.0 OD1 A:ASP11 4.2 9.6 1.0 OD1 A:ASP62 4.2 10.0 1.0 OD2 A:ASP11 4.2 11.4 1.0 NZ A:LYS64 4.3 17.4 1.0 CG A:GLU33 4.3 8.6 1.0 CE A:LYS64 4.4 13.4 1.0 OG1 A:THR36 4.4 10.2 1.0 N A:THR36 4.4 9.0 1.0 O A:HOH684 4.4 15.0 1.0 CA A:GLY35 4.4 7.7 1.0 CE1 A:HIS136 4.6 18.3 1.0 CB A:ALA9 4.6 11.2 1.0 C1 A:HMS501 4.6 9.8 1.0 CG A:ASP11 4.7 12.0 1.0 O5 A:HMS501 5.0 12.1 1.0 C A:GLY35 5.0 7.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/R139V/T169A Mutant with Bound D-Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:10.3 occ:1.00 OD2 B:ASP62 2.0 8.1 1.0 OE2 B:GLU33 2.1 9.0 1.0 O4 B:5RP502 2.1 10.5 1.0 O B:HOH703 2.1 10.0 1.0 O B:HOH704 2.1 8.2 1.0 O13 B:5RP502 2.2 8.4 1.0 C3 B:5RP502 2.8 12.8 1.0 C5 B:5RP502 2.9 10.5 1.0 CD B:GLU33 3.1 10.2 1.0 CG B:ASP62 3.2 9.5 1.0 OE1 B:GLU33 3.5 9.6 1.0 C6 B:5RP502 3.8 11.1 1.0 CB B:ASP62 3.8 8.6 1.0 C2 B:5RP502 4.1 8.8 1.0 OD1 B:ASP62 4.1 9.1 1.0 O B:HOH775 4.1 13.1 1.0 OD2 B:ASP11 4.2 12.4 1.0 OD1 B:ASP11 4.2 9.6 1.0 NZ B:LYS64 4.3 16.0 1.0 CG B:GLU33 4.4 6.8 1.0 O B:HOH705 4.4 13.7 1.0 OG1 B:THR36 4.4 10.1 1.0 CE B:LYS64 4.4 16.6 1.0 CA B:GLY35 4.5 8.1 1.0 CE1 B:HIS136 4.5 16.5 1.0 N B:THR36 4.5 7.8 1.0 C7 B:5RP502 4.6 8.6 1.0 CB B:ALA9 4.6 9.3 1.0 CG B:ASP11 4.7 10.6 1.0 O14 B:5RP502 5.0 11.2 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