Magnesium in PDB 1kw1: Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L-Gulonate 6-Phosphate

The structure of Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L-Gulonate 6-Phosphate, PDB code: 1kw1 was solved by E.Wise, W.S.Yew, P.C.Babbitt, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.978, 42.071, 91.837, 90.00, 97.00, 90.00
R / Rfree (%)	18 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L-Gulonate 6-Phosphate (pdb code 1kw1). 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 with Bound L-Gulonate 6-Phosphate, PDB code: 1kw1:
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 with Bound L-Gulonate 6-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 with Bound L-Gulonate 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:23.1 occ:1.00 OD2 A:ASP62 2.2 24.1 1.0 O A:HOH681 2.4 18.6 1.0 OE2 A:GLU33 2.4 21.6 1.0 O A:HOH682 2.5 30.1 1.0 O3 A:LG6502 2.6 32.8 1.0 O4 A:LG6502 2.6 29.2 1.0 CG A:ASP62 3.2 21.5 1.0 CD A:GLU33 3.3 21.2 1.0 C3 A:LG6502 3.4 33.4 1.0 C4 A:LG6502 3.5 29.8 1.0 O2B A:LG6502 3.7 39.4 1.0 CB A:ASP62 3.7 19.9 1.0 OE1 A:GLU33 3.8 20.2 1.0 C1 A:LG6502 3.9 35.5 1.0 NZ A:LYS64 3.9 21.0 1.0 O5 A:LG6502 4.0 26.9 1.0 O A:HOH683 4.1 29.0 1.0 C2 A:LG6502 4.1 38.2 1.0 OD1 A:ASP11 4.2 23.0 1.0 OD1 A:ASP62 4.3 22.3 1.0 CA A:GLY35 4.3 14.7 1.0 OG1 A:THR36 4.3 16.1 1.0 C5 A:LG6502 4.4 28.4 1.0 N A:THR36 4.4 15.9 1.0 CG A:GLU33 4.5 16.9 1.0 OD2 A:ASP11 4.6 23.2 1.0 CG A:ASP11 4.9 23.5 1.0 C A:GLY35 4.9 16.1 1.0 CB A:ALA9 4.9 18.1 1.0 OE2 A:GLU112 5.0 33.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L-Gulonate 6-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 with Bound L-Gulonate 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:16.9 occ:1.00 OD2 B:ASP62 2.2 15.2 1.0 O B:HOH710 2.4 28.3 1.0 O B:HOH711 2.4 14.1 1.0 OE2 B:GLU33 2.4 12.4 1.0 O3 B:LG6501 2.5 32.9 1.0 O4 B:LG6501 2.5 26.5 1.0 CD B:GLU33 3.3 13.4 1.0 CG B:ASP62 3.4 18.6 1.0 C3 B:LG6501 3.4 30.7 1.0 C4 B:LG6501 3.5 28.1 1.0 OE1 B:GLU33 3.6 14.5 1.0 O2B B:LG6501 3.8 31.9 1.0 CB B:ASP62 3.9 17.5 1.0 O5 B:LG6501 3.9 25.6 1.0 C1 B:LG6501 4.0 33.9 1.0 NZ B:LYS64 4.1 23.7 1.0 OD1 B:ASP11 4.1 20.3 1.0 C2 B:LG6501 4.1 35.0 1.0 CA B:GLY35 4.3 14.9 1.0 C5 B:LG6501 4.3 26.4 1.0 OD2 B:ASP11 4.4 21.0 1.0 OD1 B:ASP62 4.4 18.3 1.0 N B:THR36 4.5 13.6 1.0 CG B:GLU33 4.6 12.7 1.0 OG1 B:THR36 4.6 15.0 1.0 CB B:ALA9 4.7 16.5 1.0 CG B:ASP11 4.7 19.9 1.0 C B:GLY35 5.0 14.3 1.0

E.Wise, W.S.Yew, P.C.Babbitt, J.A.Gerlt, I.Rayment. Homologous (Beta/Alpha)8-Barrel Enzymes That Catalyze Unrelated Reactions: Orotidine 5'-Monophosphate Decarboxylase and 3-Keto-L-Gulonate 6-Phosphate Decarboxylase. Biochemistry V. 41 3861 2002.
ISSN: ISSN 0006-2960
PubMed: 11900527
DOI: 10.1021/BI012174E