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Sodium 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:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 6ouv

Go back to Sodium Binding Sites List in 6ouv
Sodium 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 Sodium with other atoms in the Na 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:Na703

b:33.4
occ:1.00
 O A:HOH975 2.3 30.3 1.0
O A:HIS470 2.3 33.2 1.0
O A:HOH887 2.4 31.5 1.0
O A:GLY472 2.5 31.4 1.0
OD1 A:ASN416 2.6 35.6 1.0
O A:ALA467 3.1 29.1 1.0
CG A:ASN416 3.4 33.9 1.0
C A:HIS470 3.5 35.8 1.0
N A:GLY472 3.5 31.1 1.0
C A:GLY472 3.6 29.8 1.0
CA A:ASN416 3.6 27.6 1.0
CB A:ASN416 3.7 28.8 1.0
C A:ASP471 3.7 33.2 1.0
CE1 A:PHE474 3.9 31.2 1.0
CD1 A:PHE474 3.9 31.2 1.0
NH1 A:ARG389 4.0 36.4 1.0
CA A:ASP471 4.1 33.5 0.5
CA A:ASP471 4.1 33.5 0.5
CA A:GLY472 4.1 30.6 1.0
O A:ASP471 4.2 33.0 1.0
C A:ASN416 4.3 31.8 1.0
N A:ASP471 4.3 34.5 1.0
C A:ALA467 4.3 31.4 1.0
O A:HOH1007 4.4 30.3 1.0
ND2 A:ASN416 4.6 33.5 1.0
N A:HIS470 4.6 33.9 1.0
CA A:HIS470 4.7 33.9 1.0
N A:PRO473 4.7 28.9 1.0
N A:VAL417 4.7 31.2 1.0
N A:ASN416 4.7 29.1 1.0
OG1 A:THR418 4.8 30.4 1.0
O A:ASN416 4.8 33.5 1.0
O A:LEU415 4.9 30.4 1.0
CA A:PRO473 5.0 28.8 1.0

Sodium binding site 2 out of 2 in 6ouv

Go back to Sodium Binding Sites List in 6ouv
Sodium 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 Sodium with other atoms in the Na 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:Na703

b:33.5
occ:1.00
 O B:HIS470 2.3 33.6 1.0
O B:HOH920 2.3 28.6 1.0
O B:HOH980 2.4 31.8 1.0
O B:GLY472 2.5 30.1 1.0
OD1 B:ASN416 2.6 32.9 1.0
O B:ALA467 3.0 30.8 1.0
CG B:ASN416 3.4 30.8 1.0
C B:HIS470 3.5 36.9 1.0
N B:GLY472 3.5 29.7 1.0
C B:GLY472 3.6 28.9 1.0
CA B:ASN416 3.6 28.0 1.0
CB B:ASN416 3.7 27.8 1.0
C B:ASP471 3.7 31.7 1.0
CE1 B:PHE474 3.8 33.1 1.0
CD1 B:PHE474 3.8 30.3 1.0
NH1 B:ARG389 3.9 35.8 1.0
CA B:ASP471 4.1 33.9 0.5
CA B:ASP471 4.1 33.9 0.5
CA B:GLY472 4.1 26.8 1.0
C B:ALA467 4.2 29.1 1.0
C B:ASN416 4.3 29.8 1.0
N B:ASP471 4.3 34.7 1.0
O B:ASP471 4.3 31.4 1.0
O B:HOH976 4.4 33.9 1.0
ND2 B:ASN416 4.6 29.7 1.0
N B:HIS470 4.6 31.6 1.0
CA B:HIS470 4.7 33.4 1.0
N B:PRO473 4.7 28.8 1.0
N B:VAL417 4.7 30.3 1.0
N B:ASN416 4.8 28.0 1.0
O B:ASN416 4.8 31.6 1.0
OG1 B:THR418 4.8 31.1 1.0
O B:LEU415 4.9 26.4 1.0
CA B:ALA467 5.0 30.7 1.0
CA B:PRO473 5.0 28.3 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 Aug 18 06:31:51 2025

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