Magnesium in PDB 1xbv: Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound D-Ribulose 5-Phosphate

The structure of Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound D-Ribulose 5-Phosphate, PDB code: 1xbv 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 / 1.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.814, 41.471, 91.184, 90.00, 96.65, 90.00
R / Rfree (%)	16.2 / 19.4

The binding sites of Magnesium atom in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound D-Ribulose 5-Phosphate (pdb code 1xbv). 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 D-Ribulose 5-Phosphate, PDB code: 1xbv:
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 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 Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound D-Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:20.2 occ:1.00 O A:HOH804 1.9 22.7 1.0 OD2 A:ASP62 2.0 17.8 1.0 OE2 A:GLU33 2.0 18.9 1.0 O A:HOH801 2.1 25.2 1.0 O4 A:5RP501 2.1 27.4 1.0 O13 A:5RP501 2.3 25.3 1.0 C3 A:5RP501 2.9 29.0 1.0 CD A:GLU33 3.1 16.7 1.0 CG A:ASP62 3.1 21.8 1.0 C5 A:5RP501 3.2 21.5 1.0 OE1 A:GLU33 3.5 16.6 1.0 O A:HOH625 3.6 23.3 1.0 CB A:ASP62 3.8 15.4 1.0 NZ A:LYS64 3.9 24.5 1.0 C6 A:5RP501 4.0 29.7 1.0 OD1 A:ASP11 4.1 21.6 1.0 OD1 A:ASP62 4.1 20.8 1.0 O A:HOH607 4.2 23.9 1.0 CA A:GLY35 4.3 15.3 1.0 C2 A:5RP501 4.3 25.9 1.0 CG A:GLU33 4.4 14.5 1.0 N A:THR36 4.5 16.0 1.0 OD2 A:ASP11 4.5 21.4 1.0 OG1 A:THR36 4.5 17.7 1.0 O A:HOH658 4.7 40.4 1.0 CB A:ALA9 4.7 16.4 1.0 CG A:ASP11 4.8 21.3 1.0 OE2 A:GLU112 4.9 31.6 1.0 O14 A:5RP501 4.9 40.0 1.0 C A:GLY35 5.0 14.6 1.0 CE1 A:HIS136 5.0 41.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase 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 Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound D-Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:19.4 occ:1.00 O B:HOH809 1.8 24.5 1.0 O B:HOH804 2.0 24.8 1.0 OE2 B:GLU33 2.0 17.6 1.0 OD2 B:ASP62 2.0 17.3 1.0 O4 B:5RP502 2.1 27.4 1.0 O13 B:5RP502 2.5 31.4 1.0 C3 B:5RP502 2.9 34.0 1.0 CD B:GLU33 3.0 18.0 1.0 CG B:ASP62 3.2 21.6 1.0 C5 B:5RP502 3.2 29.6 1.0 OE1 B:GLU33 3.4 15.6 1.0 O B:HOH687 3.6 32.6 1.0 CB B:ASP62 3.8 16.0 1.0 NZ B:LYS64 3.9 24.9 1.0 C6 B:5RP502 3.9 33.6 1.0 OD1 B:ASP62 4.1 19.4 1.0 OD1 B:ASP11 4.1 21.1 1.0 O B:HOH633 4.2 23.9 1.0 CG B:GLU33 4.3 13.8 1.0 C2 B:5RP502 4.3 35.6 1.0 CA B:GLY35 4.4 11.2 1.0 N B:THR36 4.5 14.1 1.0 OD2 B:ASP11 4.6 20.6 1.0 O14 B:5RP502 4.6 42.7 1.0 OG1 B:THR36 4.6 16.9 1.0 CB B:ALA9 4.7 14.8 1.0 O B:HOH642 4.7 32.2 1.0 CG B:ASP11 4.8 17.1 1.0 OE2 B:GLU112 4.9 39.6 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