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

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/T169A Mutant with Bound D-Ribulose 5-Phosphate, PDB code: 1xby 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 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.785, 41.906, 91.225, 90.00, 97.46, 90.00
R / Rfree (%)	15.8 / 19.3

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/T169A Mutant with Bound D-Ribulose 5-Phosphate (pdb code 1xby). 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/T169A Mutant with Bound D-Ribulose 5-Phosphate, PDB code: 1xby:
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/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/T169A Mutant with Bound D-Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:13.9 occ:1.00 O4 A:5RP501 2.0 15.5 1.0 OE2 A:GLU33 2.0 14.4 1.0 OD2 A:ASP62 2.1 12.0 1.0 O13 A:5RP501 2.1 13.0 1.0 O A:HOH839 2.1 15.8 1.0 O A:HOH850 2.2 14.8 1.0 C3 A:5RP501 2.8 14.4 1.0 C5 A:5RP501 2.9 13.0 1.0 CD A:GLU33 3.1 12.1 1.0 CG A:ASP62 3.2 17.6 1.0 OE1 A:GLU33 3.5 13.4 1.0 CB A:ASP62 3.8 13.4 1.0 C6 A:5RP501 3.8 12.1 1.0 OD1 A:ASP11 4.1 15.8 1.0 C2 A:5RP501 4.1 10.3 1.0 O A:HOH616 4.1 16.2 1.0 OD1 A:ASP62 4.2 14.6 1.0 NZ A:LYS64 4.2 20.3 1.0 OD2 A:ASP11 4.2 15.4 1.0 CG A:GLU33 4.4 14.2 1.0 O A:HOH609 4.4 21.2 1.0 OG1 A:THR36 4.4 14.1 1.0 CE A:LYS64 4.4 17.1 1.0 CA A:GLY35 4.4 14.3 1.0 N A:THR36 4.5 12.2 1.0 CE1 A:HIS136 4.6 18.9 1.0 CB A:ALA9 4.6 13.8 1.0 CG A:ASP11 4.6 17.1 1.0 C7 A:5RP501 4.7 13.8 1.0 O14 A:5RP501 4.9 17.1 1.0

Magnesium binding site 2 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase E112D/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/T169A Mutant with Bound D-Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:12.8 occ:1.00 OE2 B:GLU33 2.0 13.2 1.0 OD2 B:ASP62 2.0 12.2 1.0 O4 B:5RP502 2.1 15.5 1.0 O B:HOH826 2.1 15.2 1.0 O13 B:5RP502 2.1 13.3 1.0 O B:HOH828 2.1 14.8 1.0 C3 B:5RP502 2.8 20.4 1.0 C5 B:5RP502 2.9 15.0 1.0 CD B:GLU33 3.0 11.3 1.0 CG B:ASP62 3.2 16.4 1.0 OE1 B:GLU33 3.4 12.9 1.0 CB B:ASP62 3.8 12.2 1.0 C6 B:5RP502 3.8 16.3 1.0 OD1 B:ASP62 4.1 15.1 1.0 O B:HOH609 4.1 15.4 1.0 OD2 B:ASP11 4.2 14.5 1.0 C2 B:5RP502 4.2 12.1 1.0 OD1 B:ASP11 4.3 14.9 1.0 NZ B:LYS64 4.3 19.5 1.0 CG B:GLU33 4.3 13.4 1.0 O B:HOH608 4.3 18.9 1.0 OG1 B:THR36 4.4 14.9 1.0 CE B:LYS64 4.4 18.1 1.0 CA B:GLY35 4.5 12.6 1.0 N B:THR36 4.5 12.1 1.0 NE2 B:HIS136 4.6 22.2 1.0 CB B:ALA9 4.6 12.3 1.0 CG B:ASP11 4.7 15.8 1.0 C7 B:5RP502 4.7 13.6 1.0 O14 B:5RP502 4.9 17.2 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