Magnesium in PDB 1q6q: Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate, PDB code: 1q6q was solved by E.L.Wise, W.S.Yew, 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 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.182, 41.727, 92.125, 90.00, 95.87, 90.00
R / Rfree (%)	17.2 / 20.7

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate (pdb code 1q6q). 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 with Bound Xylitol 5-Phosphate, PDB code: 1q6q:
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 with Bound Xylitol 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 with Bound Xylitol 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7300 b:14.9 occ:1.00 OD2 A:ASP62 2.0 12.5 1.0 OE2 A:GLU33 2.0 14.9 1.0 O A:HOH7376 2.1 14.9 1.0 O A:HOH7513 2.1 16.4 1.0 O3 A:LXP7301 2.2 13.7 1.0 O2 A:LXP7301 2.2 18.1 1.0 CG A:ASP62 3.1 15.0 1.0 CD A:GLU33 3.1 16.1 1.0 C2 A:LXP7301 3.1 14.8 1.0 C3 A:LXP7301 3.2 17.1 1.0 OE1 A:GLU33 3.5 15.1 1.0 CB A:ASP62 3.7 14.7 1.0 O4 A:LXP7301 3.8 15.6 1.0 C1 A:LXP7301 3.9 21.5 1.0 C4 A:LXP7301 4.0 14.6 1.0 O A:HOH7377 4.1 18.0 1.0 OD1 A:ASP11 4.1 21.0 1.0 OD1 A:ASP62 4.1 12.5 1.0 NZ A:LYS64 4.1 20.1 1.0 OD2 A:ASP11 4.2 17.2 1.0 CG A:GLU33 4.4 14.9 1.0 OG1 A:THR36 4.4 16.3 1.0 O1 A:LXP7301 4.4 25.2 1.0 NE2 A:HIS136 4.4 23.8 1.0 CA A:GLY35 4.5 15.3 1.0 N A:THR36 4.6 15.0 1.0 CG A:ASP11 4.6 20.0 1.0 CB A:ALA9 4.7 17.1 1.0 C5 A:LXP7301 4.7 17.4 1.0 O A:HOH7387 4.9 22.1 1.0 O A:HOH7385 5.0 28.3 1.0

Magnesium binding site 2 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 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 with Bound Xylitol 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg9300 b:14.0 occ:1.00 OE2 B:GLU33 2.0 13.9 1.0 O3 B:LXP9301 2.1 14.3 1.0 O B:HOH9499 2.1 14.8 1.0 OD2 B:ASP62 2.1 13.0 1.0 O B:HOH9390 2.1 13.8 1.0 O2 B:LXP9301 2.2 14.9 1.0 CD B:GLU33 3.0 11.9 1.0 C3 B:LXP9301 3.1 13.5 1.0 C2 B:LXP9301 3.1 18.0 1.0 CG B:ASP62 3.2 14.3 1.0 OE1 B:GLU33 3.4 13.8 1.0 O4 B:LXP9301 3.7 14.4 1.0 CB B:ASP62 3.8 12.2 1.0 C1 B:LXP9301 3.8 16.1 1.0 C4 B:LXP9301 3.9 14.1 1.0 NZ B:LYS64 4.1 19.2 1.0 OD2 B:ASP11 4.2 15.0 1.0 O B:HOH9392 4.2 17.6 1.0 OD1 B:ASP11 4.2 17.4 1.0 OD1 B:ASP62 4.2 14.2 1.0 OG1 B:THR36 4.3 15.7 1.0 NE2 B:HIS136 4.4 23.4 1.0 O1 B:LXP9301 4.4 20.4 1.0 CG B:GLU33 4.4 14.4 1.0 CB B:ALA9 4.6 14.2 1.0 C5 B:LXP9301 4.6 15.3 1.0 CA B:GLY35 4.6 12.8 1.0 CG B:ASP11 4.6 14.7 1.0 N B:THR36 4.7 12.6 1.0

E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment. Structural Evidence For A 1,2-Enediolate Intermediate in the Reaction Catalyzed By 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, A Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Biochemistry V. 42 12133 2003.
ISSN: ISSN 0006-2960
PubMed: 14567674
DOI: 10.1021/BI0348819