Magnesium in PDB 1q6l: Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Threonohydroxamate 4-Phosphate

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Threonohydroxamate 4-Phosphate, PDB code: 1q6l 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 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.963, 41.931, 91.457, 90.00, 96.91, 90.00
R / Rfree (%)	17.2 / 21.8

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Threonohydroxamate 4-Phosphate (pdb code 1q6l). 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- Threonohydroxamate 4-Phosphate, PDB code: 1q6l:
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- Threonohydroxamate 4-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- Threonohydroxamate 4-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5300 b:17.8 occ:1.00 OE2 A:GLU33 2.0 16.8 1.0 OD2 A:ASP62 2.1 16.0 1.0 O2 A:TX45301 2.1 15.3 1.0 O A:HOH5372 2.1 16.9 1.0 O1 A:TX45301 2.1 17.6 1.0 O A:HOH5373 2.2 18.1 1.0 C1 A:TX45301 2.9 22.0 1.0 C2 A:TX45301 3.0 18.3 1.0 CD A:GLU33 3.1 16.2 1.0 CG A:ASP62 3.2 20.5 1.0 OE1 A:GLU33 3.5 17.2 1.0 O3 A:TX45301 3.7 19.4 1.0 CB A:ASP62 3.9 17.8 1.0 C3 A:TX45301 3.9 17.1 1.0 O A:HOH5374 4.0 16.8 1.0 NZ A:LYS64 4.1 30.3 1.0 N A:TX45301 4.1 19.5 1.0 OD1 A:ASP11 4.1 16.9 1.0 OD2 A:ASP11 4.1 18.7 1.0 OD1 A:ASP62 4.2 17.4 1.0 O A:HOH5376 4.2 21.1 1.0 CG A:GLU33 4.3 14.8 1.0 OG1 A:THR36 4.4 18.2 1.0 CA A:GLY35 4.4 14.6 1.0 N A:THR36 4.5 17.2 1.0 ON A:TX45301 4.5 21.5 1.0 CB A:ALA9 4.6 14.9 1.0 CG A:ASP11 4.6 19.6 1.0 C4 A:TX45301 4.7 15.5 1.0 CE A:LYS64 4.8 28.7 1.0

Magnesium binding site 2 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Threonohydroxamate 4-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- Threonohydroxamate 4-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg9300 b:17.5 occ:1.00 OE2 B:GLU33 2.0 12.8 1.0 OD2 B:ASP62 2.1 15.2 1.0 O1 B:TX49301 2.1 18.0 1.0 O B:HOH9407 2.1 17.0 1.0 O2 B:TX49301 2.2 13.5 1.0 O B:HOH9408 2.2 17.6 1.0 C1 B:TX49301 2.8 23.2 1.0 C2 B:TX49301 3.0 15.9 1.0 CD B:GLU33 3.1 17.0 1.0 CG B:ASP62 3.2 19.9 1.0 OE1 B:GLU33 3.4 15.9 1.0 O3 B:TX49301 3.7 17.1 1.0 C3 B:TX49301 3.8 14.0 1.0 CB B:ASP62 3.9 17.1 1.0 N B:TX49301 4.0 21.5 1.0 O B:HOH9412 4.1 22.4 1.0 OD2 B:ASP11 4.1 16.1 1.0 OD1 B:ASP11 4.2 14.6 1.0 O B:HOH9411 4.2 21.5 1.0 OD1 B:ASP62 4.2 16.3 1.0 CE B:LYS64 4.3 24.4 1.0 OG1 B:THR36 4.3 16.9 1.0 CG B:GLU33 4.4 13.9 1.0 NZ B:LYS64 4.4 32.1 1.0 N B:THR36 4.4 14.4 1.0 CA B:GLY35 4.5 13.3 1.0 ON B:TX49301 4.6 23.4 1.0 CB B:ALA9 4.6 16.6 1.0 CG B:ASP11 4.6 18.5 1.0 C4 B:TX49301 4.7 14.4 1.0 CE1 B:HIS136 5.0 17.3 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