Magnesium in PDB 6ouv: 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound

Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound:
2.2.1.7;

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound, PDB code: 6ouv was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.60 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.503, 125.279, 151.699, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 17.4

Other elements in 6ouv:

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound (pdb code 6ouv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound, PDB code: 6ouv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ouv

Go back to Magnesium Binding Sites List in 6ouv
Magnesium binding site 1 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound


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 (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:33.3
occ:1.00
 OD1 A:ASN183 2.0 35.9 1.0
O1A A:TDK701 2.0 35.3 1.0
OD1 A:ASP154 2.1 34.0 1.0
O A:MET185 2.1 34.1 1.0
O1B A:TDK701 2.1 33.3 1.0
O A:HOH828 2.2 30.0 1.0
CG A:ASN183 2.9 37.1 1.0
CG A:ASP154 3.2 36.9 1.0
C A:MET185 3.2 36.8 1.0
PB A:TDK701 3.2 33.0 1.0
PA A:TDK701 3.3 33.4 1.0
ND2 A:ASN183 3.3 36.6 1.0
O3A A:TDK701 3.5 31.2 1.0
OD2 A:ASP154 3.7 39.8 1.0
N A:MET185 3.8 33.8 1.0
O2B A:TDK701 3.9 36.9 1.0
CA A:MET185 4.0 34.8 1.0
N A:ASP154 4.0 33.7 1.0
N A:GLY155 4.1 33.4 1.0
O7 A:TDK701 4.1 33.3 1.0
N A:ASN183 4.2 36.5 1.0
O A:ASN181 4.2 36.6 1.0
CB A:ASN183 4.3 34.6 1.0
N A:SER186 4.3 30.6 1.0
CB A:MET185 4.3 35.0 1.0
CB A:ASP154 4.4 33.6 1.0
O2A A:TDK701 4.5 30.2 1.0
O3B A:TDK701 4.5 34.4 1.0
CA A:SER186 4.5 31.2 1.0
CA A:ASN183 4.6 36.8 1.0
CA A:ASP154 4.6 32.8 1.0
N A:GLU184 4.7 35.8 1.0
C A:ASN183 4.7 38.9 1.0
CA A:GLY153 4.7 32.1 1.0
C A:GLY153 4.8 29.9 1.0
C A:ASP154 4.8 33.8 1.0
C A:GLU184 4.9 38.1 1.0
CA A:GLY155 4.9 32.1 1.0
O A:SER186 5.0 35.1 1.0

Magnesium binding site 2 out of 2 in 6ouv

Go back to Magnesium Binding Sites List in 6ouv
Magnesium binding site 2 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound


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 (Dxps) From Deinococcus Radiodurans with Methylacetylphosphonate (Map) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:40.3
occ:1.00
 OD1 B:ASN183 2.0 40.3 1.0
OD1 B:ASP154 2.0 42.2 1.0
O1B B:TDK701 2.0 41.4 1.0
O B:MET185 2.1 43.6 1.0
O1A B:TDK701 2.1 37.9 1.0
O B:HOH838 2.1 40.4 1.0
CG B:ASN183 3.0 41.9 1.0
CG B:ASP154 3.2 41.6 1.0
PB B:TDK701 3.2 41.6 1.0
C B:MET185 3.3 44.4 1.0
PA B:TDK701 3.3 40.0 1.0
ND2 B:ASN183 3.3 39.7 1.0
O3A B:TDK701 3.5 38.9 1.0
OD2 B:ASP154 3.7 43.0 1.0
N B:MET185 3.9 44.7 1.0
O2B B:TDK701 3.9 40.1 1.0
N B:ASP154 3.9 38.2 1.0
CA B:MET185 4.0 41.5 1.0
N B:GLY155 4.0 38.4 1.0
O7 B:TDK701 4.2 37.8 1.0
N B:ASN183 4.2 43.7 1.0
O B:ASN181 4.2 42.4 1.0
CB B:ASN183 4.3 40.4 1.0
N B:SER186 4.3 41.4 1.0
CB B:MET185 4.4 41.8 1.0
CB B:ASP154 4.4 38.9 1.0
O3B B:TDK701 4.5 45.4 1.0
O2A B:TDK701 4.5 36.9 1.0
CA B:SER186 4.5 39.7 1.0
CA B:ASP154 4.6 37.5 1.0
CA B:ASN183 4.6 45.4 1.0
CA B:GLY153 4.7 38.0 1.0
C B:GLY153 4.7 38.1 1.0
N B:GLU184 4.7 41.5 1.0
C B:ASN183 4.7 45.7 1.0
C B:ASP154 4.8 38.5 1.0
CA B:GLY155 4.9 36.0 1.0
O B:SER186 4.9 40.4 1.0

Reference:

P.Y.Chen, A.A.Decolli, C.L.Freel Meyers, C.L.Drennan. X-Ray Crystallography-Based Structural Elucidation of Enzyme-Bound Intermediates Along the 1-Deoxy-D-Xylulose 5-Phosphate Synthase Reaction Coordinate. J.Biol.Chem. V. 294 12405 2019.
ISSN: ESSN 1083-351X
PubMed: 31239351
DOI: 10.1074/JBC.RA119.009321
Page generated: Mon Dec 14 23:44:53 2020

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