Magnesium in PDB 1q6o: Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Gulonaet 6-Phosphate

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Gulonaet 6-Phosphate, PDB code: 1q6o 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 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.240, 41.775, 90.958, 90.00, 97.15, 90.00
R / Rfree (%)	14.1 / 16.1

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Gulonaet 6-Phosphate (pdb code 1q6o). 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 L- Gulonaet 6-Phosphate, PDB code: 1q6o:
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 L- Gulonaet 6-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 L- Gulonaet 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7300 b:9.5 occ:1.00 OE2 A:GLU33 2.0 9.8 1.0 OD2 A:ASP62 2.0 10.5 1.0 O A:HOH7382 2.1 10.7 1.0 O A:HOH7381 2.1 9.6 1.0 O3 A:LG67301 2.1 10.6 1.0 O4 A:LG67301 2.2 10.2 1.0 CD A:GLU33 3.0 10.3 1.0 C3 A:LG67301 3.1 11.2 1.0 C4 A:LG67301 3.1 10.1 1.0 CG A:ASP62 3.2 10.7 1.0 OE1 A:GLU33 3.5 10.6 1.0 O5 A:LG67301 3.7 10.6 1.0 CB A:ASP62 3.8 10.7 1.0 C1 A:LG67301 3.8 13.9 1.0 O2B A:LG67301 3.9 14.5 1.0 C5 A:LG67301 4.0 10.6 1.0 O A:HOH7516 4.0 16.1 1.0 NZ A:LYS64 4.0 16.7 1.0 O A:HOH7383 4.0 15.2 1.0 C2 A:LG67301 4.1 14.1 1.0 OD1 A:ASP11 4.2 11.9 1.0 OD1 A:ASP62 4.2 11.1 1.0 OD2 A:ASP11 4.2 12.0 1.0 CG A:GLU33 4.3 10.0 1.0 CA A:GLY35 4.4 9.7 1.0 N A:THR36 4.5 9.7 1.0 OG1 A:THR36 4.5 11.3 1.0 CB A:ALA9 4.6 10.0 1.0 CG A:ASP11 4.6 11.3 1.0 C6 A:LG67301 4.8 10.3 1.0 OE2 A:GLU112 4.9 21.3 1.0 O2A A:LG67301 5.0 16.3 1.0

Magnesium binding site 2 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Gulonaet 6-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 L- Gulonaet 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg9300 b:8.8 occ:1.00 OD2 B:ASP62 2.0 10.1 1.0 OE2 B:GLU33 2.0 9.2 1.0 O B:HOH9406 2.1 9.6 1.0 O B:HOH9407 2.1 9.6 1.0 O3 B:LG69301 2.1 10.1 1.0 O4 B:LG69301 2.2 9.7 1.0 CD B:GLU33 3.0 9.0 1.0 C3 B:LG69301 3.1 11.5 1.0 C4 B:LG69301 3.1 9.6 1.0 CG B:ASP62 3.2 10.4 1.0 OE1 B:GLU33 3.5 9.4 1.0 CB B:ASP62 3.7 9.9 1.0 O5 B:LG69301 3.7 10.3 1.0 C1 B:LG69301 3.8 15.7 1.0 O2B B:LG69301 4.0 17.3 1.0 NZ B:LYS64 4.0 20.5 1.0 C5 B:LG69301 4.0 10.2 1.0 O B:HOH9497 4.0 16.9 1.0 OD1 B:ASP11 4.1 11.1 1.0 O B:HOH9496 4.1 15.2 1.0 C2 B:LG69301 4.1 19.3 1.0 OD1 B:ASP62 4.2 11.5 1.0 OD2 B:ASP11 4.3 11.3 1.0 CG B:GLU33 4.3 9.0 1.0 CA B:GLY35 4.5 9.4 1.0 OG1 B:THR36 4.5 11.4 1.0 N B:THR36 4.6 9.2 1.0 CB B:ALA9 4.6 9.9 1.0 CG B:ASP11 4.6 10.2 1.0 C6 B:LG69301 4.8 10.1 1.0 O2A B:LG69301 4.9 21.8 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