Magnesium in PDB 8ogh: Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound

All present enzymatic activity of Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound:
2.2.1.7;

The structure of Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound, PDB code: 8ogh was solved by O.V.Gawriljuk, R.Oerlemans, R.M.Groves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.462, 127.775, 79.583, 90, 106.88, 90
R / Rfree (%)	15.5 / 17.2

The binding sites of Magnesium atom in the Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound (pdb code 8ogh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound, PDB code: 8ogh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg710 b:15.7 occ:0.94 O A:HOH1019 2.1 17.0 1.0 O A:HOH946 2.1 15.7 1.0 OD1 A:ASN173 2.1 15.4 1.0 OD1 A:ASP144 2.1 16.0 1.0 O7 A:VMI701 2.1 14.7 1.0 O11 A:VMI701 2.1 16.2 1.0 CG A:ASN173 3.0 17.8 1.0 CG A:ASP144 3.1 15.1 1.0 P3 A:VMI701 3.2 17.6 1.0 P2 A:VMI701 3.3 15.6 1.0 ND2 A:ASN173 3.4 17.2 1.0 OD2 A:ASP144 3.5 19.8 1.0 O8 A:VMI701 3.5 17.3 1.0 O9 A:VMI701 3.8 17.8 1.0 O A:HOH819 3.8 36.7 1.0 N A:ASP144 4.0 14.8 1.0 N A:GLY145 4.0 16.7 1.0 O5 A:VMI701 4.1 17.5 1.0 N A:ASN173 4.1 14.9 1.0 O A:HOH1275 4.1 33.6 1.0 O A:HOH1202 4.2 33.7 1.0 O A:ASN171 4.3 15.1 1.0 CB A:ASN173 4.3 17.3 1.0 CB A:ASP144 4.4 16.7 1.0 O6 A:VMI701 4.5 16.2 1.0 O10 A:VMI701 4.5 18.9 1.0 CA A:ASN173 4.5 16.2 1.0 CA A:ASP144 4.6 14.4 1.0 C A:ASN173 4.6 21.8 1.0 N A:GLY174 4.7 18.2 1.0 CA A:GLY143 4.7 14.2 1.0 C A:GLY143 4.8 14.6 1.0 C A:ASP144 4.8 15.8 1.0 CA A:GLY145 4.9 17.4 1.0

Magnesium binding site 2 out of 2 in the Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Truncated 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Mycobacterium Tuberculosis with Butylacetylphosphonate (Bap) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg706 b:16.2 occ:1.00 O7 B:VMI701 2.0 16.4 1.0 O9 B:VMI701 2.1 17.1 1.0 OD1 B:ASN173 2.1 16.7 1.0 O B:HOH918 2.1 15.0 1.0 OD1 B:ASP144 2.1 15.4 1.0 O B:HOH1019 2.2 19.0 1.0 CG B:ASN173 3.0 18.4 1.0 CG B:ASP144 3.1 16.9 1.0 P3 B:VMI701 3.2 16.8 1.0 P2 B:VMI701 3.2 15.3 1.0 ND2 B:ASN173 3.4 16.2 1.0 O8 B:VMI701 3.5 17.0 1.0 OD2 B:ASP144 3.5 18.6 1.0 O10 B:VMI701 3.7 17.6 1.0 O B:HOH959 3.9 31.7 1.0 N B:ASP144 4.0 13.9 1.0 O B:HOH1279 4.0 38.4 1.0 O5 B:VMI701 4.0 19.1 1.0 O B:HOH1215 4.1 34.2 1.0 N B:ASN173 4.1 15.8 1.0 N B:GLY145 4.1 15.3 1.0 O B:ASN171 4.3 15.9 1.0 CB B:ASN173 4.3 15.4 1.0 CB B:ASP144 4.4 16.3 1.0 O6 B:VMI701 4.4 14.7 1.0 O11 B:VMI701 4.5 17.0 1.0 CA B:ASN173 4.6 16.2 1.0 C B:ASN173 4.7 18.1 1.0 CA B:ASP144 4.7 14.4 1.0 CA B:GLY143 4.7 16.0 1.0 C B:GLY143 4.7 15.8 1.0 N B:GLY174 4.8 19.3 1.0 C B:ASP144 4.9 14.1 1.0

V.O.Gawriljuk, R.Oerlemans, R.M.Gierse, R.Jotwani, A.K.H.Hirsch, M.R.Groves. Structure of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Synthase in Complex with Butylacetylphosphonate Crystals V. 13 2023.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST13050737