Magnesium in PDB 2o1x: 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans:
2.2.1.7;

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans, PDB code: 2o1x was solved by S.Xiang, G.Usunow, G.Lange, M.Busch, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.261, 154.062, 124.881, 90.00, 98.91, 90.00
R / Rfree (%)	20.9 / 27.2

The binding sites of Magnesium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans (pdb code 2o1x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans, PDB code: 2o1x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:9.8 occ:1.00 O22 A:TDP1001 1.9 5.4 1.0 ND2 A:ASN183 2.1 10.2 1.0 OD2 A:ASP154 2.1 10.0 1.0 O12 A:TDP1001 2.2 2.0 1.0 O A:MET185 2.5 13.2 1.0 CG A:ASN183 3.1 11.2 1.0 CG A:ASP154 3.3 10.2 1.0 P2 A:TDP1001 3.4 4.0 1.0 P1 A:TDP1001 3.5 2.3 1.0 OD1 A:ASN183 3.5 11.3 1.0 N A:ASP154 3.5 7.3 1.0 O A:ASN181 3.5 10.1 1.0 O11 A:TDP1001 3.7 3.3 1.0 C A:MET185 3.7 14.8 1.0 N A:ASN183 3.8 12.7 1.0 N A:MET185 4.0 15.0 1.0 OD1 A:ASP154 4.1 12.7 1.0 O23 A:TDP1001 4.2 4.2 1.0 CB A:ASN183 4.2 12.8 1.0 CB A:ASP154 4.3 8.9 1.0 CA A:GLY153 4.3 5.6 1.0 N A:GLY155 4.3 7.4 1.0 CA A:ASN183 4.4 13.4 1.0 C A:GLY153 4.4 6.5 1.0 CA A:ASP154 4.4 7.7 1.0 O13 A:TDP1001 4.4 2.1 1.0 CA A:MET185 4.4 15.2 1.0 N A:GLU184 4.5 14.9 1.0 O21 A:TDP1001 4.5 4.8 1.0 O5G A:TDP1001 4.5 2.4 1.0 C A:ASN183 4.5 14.3 1.0 C A:ASN181 4.7 9.7 1.0 C A:ASP182 4.8 13.1 1.0 N A:SER186 4.8 15.8 1.0 CB A:MET185 4.8 15.1 1.0 CA A:ASP182 4.8 12.4 1.0 C A:ASP154 4.9 7.7 1.0

Magnesium binding site 2 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:8.3 occ:1.00 O22 B:TDP1002 1.8 4.8 1.0 OD2 B:ASP154 2.0 11.1 1.0 O12 B:TDP1002 2.1 2.2 1.0 O B:MET185 2.3 16.0 1.0 CB B:ASN183 2.9 16.0 1.0 ND2 B:ASN183 2.9 15.2 1.0 CG B:ASP154 3.1 9.5 1.0 P2 B:TDP1002 3.2 3.7 1.0 CG B:ASN183 3.3 16.4 1.0 P1 B:TDP1002 3.5 2.5 1.0 OD1 B:ASP154 3.5 11.7 1.0 C B:MET185 3.5 17.4 1.0 O21 B:TDP1002 3.5 3.0 1.0 N B:ASN183 3.8 15.3 1.0 O11 B:TDP1002 3.8 3.4 1.0 CA B:ASN183 3.9 16.7 1.0 N B:MET185 4.0 18.4 1.0 O B:ASN181 4.0 9.6 1.0 CA B:MET185 4.2 18.2 1.0 N B:ASP154 4.2 5.5 1.0 O23 B:TDP1002 4.4 3.0 1.0 O13 B:TDP1002 4.4 2.1 1.0 CB B:MET185 4.4 18.1 1.0 N B:GLY155 4.4 6.7 1.0 CB B:ASP154 4.4 7.9 1.0 OD1 B:ASN183 4.5 18.4 1.0 O5G B:TDP1002 4.5 3.7 1.0 N B:SER186 4.6 17.9 1.0 C B:ASN183 4.6 18.4 1.0 N B:GLU184 4.7 18.3 1.0 CA B:ASP154 4.8 6.6 1.0 C B:ASP182 4.8 14.4 1.0 CA B:GLY153 4.8 3.8 1.0 C B:GLY153 4.9 4.2 1.0 CA B:SER186 4.9 17.6 1.0

Magnesium binding site 3 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2003 b:33.9 occ:1.00 OD2 C:ASP154 1.9 73.2 1.0 OD1 C:ASN183 2.0 88.2 1.0 O12 C:TDP1003 2.2 50.5 1.0 O22 C:TDP1003 2.5 53.0 1.0 CG C:ASP154 3.0 73.3 1.0 CG C:ASN183 3.1 90.5 1.0 P2 C:TDP1003 3.3 52.7 1.0 O23 C:TDP1003 3.3 52.5 1.0 OD1 C:ASP154 3.4 73.9 1.0 P1 C:TDP1003 3.6 50.7 1.0 ND2 C:ASN183 3.6 90.7 1.0 O C:MET185 3.7 87.7 1.0 O11 C:TDP1003 3.7 51.8 1.0 C C:MET185 3.8 85.7 1.0 N C:SER186 3.8 82.2 1.0 CA C:SER186 3.9 80.4 1.0 N C:ASP154 3.9 69.9 1.0 N C:ASN183 4.0 91.2 1.0 CB C:SER186 4.1 76.8 1.0 N C:GLY155 4.1 65.2 1.0 CB C:ASP154 4.3 72.2 1.0 O C:ASN181 4.3 81.5 1.0 CB C:ASN183 4.4 94.2 1.0 O13 C:TDP1003 4.5 51.8 1.0 N C:MET185 4.5 89.7 1.0 CA C:GLY153 4.5 69.3 1.0 CA C:ASP154 4.6 69.1 1.0 CA C:ASN183 4.6 94.5 1.0 C C:GLY153 4.6 67.9 1.0 O5G C:TDP1003 4.6 51.0 1.0 CA C:MET185 4.7 87.3 1.0 C C:ASP154 4.8 66.1 1.0 O21 C:TDP1003 4.8 51.9 1.0 C C:ASN183 4.9 94.4 1.0 CA C:GLY155 5.0 62.4 1.0 C C:ASP182 5.0 92.0 1.0

Magnesium binding site 4 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2004 b:36.0 occ:1.00 OD2 D:ASP154 1.7 70.9 1.0 OD1 D:ASN183 1.9 85.9 1.0 O12 D:TDP1004 2.3 47.8 1.0 O D:MET185 2.4 87.7 1.0 CG D:ASP154 2.9 73.0 1.0 O22 D:TDP1004 3.0 47.9 1.0 CG D:ASN183 3.0 90.2 1.0 OD1 D:ASP154 3.4 72.7 1.0 O21 D:TDP1004 3.4 48.4 1.0 O11 D:TDP1004 3.5 48.1 1.0 P1 D:TDP1004 3.6 48.6 1.0 N D:ASP154 3.6 69.8 1.0 P2 D:TDP1004 3.6 48.6 1.0 C D:MET185 3.6 88.4 1.0 ND2 D:ASN183 3.7 90.2 1.0 N D:GLY155 3.8 64.3 1.0 N D:ASN183 3.9 93.5 1.0 O D:ASN181 3.9 80.8 1.0 CB D:ASP154 4.0 73.7 1.0 N D:MET185 4.1 94.9 1.0 CA D:ASP154 4.2 69.5 1.0 CB D:ASN183 4.2 95.5 1.0 N D:GLU184 4.2 96.7 1.0 C D:GLY153 4.3 66.7 1.0 CA D:GLY153 4.3 67.5 1.0 O13 D:TDP1004 4.3 48.1 1.0 CA D:ASN183 4.4 97.5 1.0 C D:ASP154 4.5 66.0 1.0 CA D:MET185 4.5 93.0 1.0 C D:ASN183 4.5 98.2 1.0 N D:SER186 4.6 86.1 1.0 CA D:SER186 4.7 82.0 1.0 CA D:GLY155 4.7 60.8 1.0 CB D:SER186 4.7 80.3 1.0 O5G D:TDP1004 4.8 47.9 1.0 C D:GLU184 4.8 95.2 1.0 C D:ASP182 4.9 95.1 1.0 CA D:ASP182 4.9 90.9 1.0 CA D:GLU184 4.9 97.2 1.0 C D:ASN181 5.0 84.4 1.0

S.Xiang, G.Usunow, G.Lange, M.Busch, L.Tong. Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase, A Crucial Enzyme For Isoprenoids Biosynthesis. J.Biol.Chem. V. 282 2676 2007.
ISSN: ISSN 0021-9258
PubMed: 17135236
DOI: 10.1074/JBC.M610235200