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Sodium in PDB 6ouw: 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound

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

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

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound, PDB code: 6ouw 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) 49.39 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.750, 85.540, 60.572, 90.00, 114.77, 90.00
R / Rfree (%) 15.8 / 19.6

Other elements in 6ouw:

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

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound (pdb code 6ouw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound, PDB code: 6ouw:

Sodium binding site 1 out of 1 in 6ouw

Go back to Sodium Binding Sites List in 6ouw
Sodium binding site 1 out of 1 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:52.7
occ:1.00
 O A:HOH882 2.4 42.7 1.0
O A:GLY472 2.4 42.3 1.0
O A:HIS470 2.4 48.6 1.0
O A:HOH814 2.4 50.3 1.0
OD1 A:ASN416 2.9 49.9 1.0
O A:ALA467 3.2 43.2 1.0
CA A:ASN416 3.4 42.8 1.0
CB A:ASN416 3.5 42.0 1.0
N A:GLY472 3.5 38.2 1.0
C A:GLY472 3.5 42.4 1.0
CG A:ASN416 3.6 50.0 1.0
C A:HIS470 3.6 46.4 1.0
C A:ASP471 3.7 41.5 1.0
NH1 A:ARG389 3.8 43.7 1.0
CE1 A:PHE474 3.8 42.1 1.0
CD1 A:PHE474 3.9 38.1 1.0
CA A:ASP471 4.1 41.0 1.0
CA A:GLY472 4.1 39.0 1.0
C A:ASN416 4.1 43.3 1.0
O A:HOH890 4.2 46.0 1.0
O A:ASP471 4.2 43.6 1.0
N A:ASP471 4.3 42.4 1.0
C A:ALA467 4.4 43.4 1.0
N A:VAL417 4.5 42.1 1.0
N A:ASN416 4.6 41.0 1.0
N A:PRO473 4.6 43.9 1.0
O A:ASN416 4.7 38.9 1.0
N A:HIS470 4.7 47.2 1.0
O A:LEU415 4.8 39.8 1.0
CA A:HIS470 4.8 45.8 1.0
ND2 A:ASN416 4.8 32.5 1.0
OG1 A:THR418 4.9 40.3 1.0
CA A:PRO473 4.9 38.8 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: Tue Oct 8 12:37:33 2024

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