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Sodium in PDB 8a45: Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate

Enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate

All present enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate:
2.2.1.7;

Protein crystallography data

The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate, PDB code: 8a45 was solved by R.Hamid, A.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.12, 138.013, 231.626, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Other elements in 8a45:

The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Calcium (Ca) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate (pdb code 8a45). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate, PDB code: 8a45:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8a45

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Sodium binding site 1 out of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:25.8
occ:1.00
 O A:HOH1119 2.2 37.5 1.0
O A:GLY299 2.3 28.8 1.0
O A:ALA302 2.3 26.8 1.0
O A:HOH1048 2.4 29.7 1.0
O A:HOH1112 2.6 40.7 1.0
C A:GLY299 3.3 30.6 1.0
HA2 A:GLY299 3.4 37.4 1.0
H A:ALA302 3.5 31.8 1.0
C A:ALA302 3.6 28.0 1.0
HA A:ILE303 3.7 31.9 1.0
CA A:GLY299 3.9 31.1 1.0
HG22 A:ILE303 4.1 33.8 1.0
HA A:TYR300 4.1 34.4 1.0
N A:ALA302 4.3 26.5 1.0
HA3 A:GLY299 4.3 37.4 1.0
N A:TYR300 4.4 27.8 1.0
N A:ILE303 4.5 25.8 1.0
HB3 A:ALA302 4.5 33.0 1.0
CA A:ILE303 4.5 26.5 1.0
CA A:ALA302 4.5 27.3 1.0
O A:ILE298 4.6 31.9 1.0
CA A:TYR300 4.7 28.6 1.0
O A:HOH1133 4.7 50.2 1.0
H A:HIS301 4.7 34.0 1.0
HG23 A:ILE303 4.8 33.8 1.0
CG2 A:ILE303 4.8 28.1 1.0
N A:HIS301 5.0 28.3 1.0

Sodium binding site 2 out of 4 in 8a45

Go back to Sodium Binding Sites List in 8a45
Sodium binding site 2 out of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:24.4
occ:1.00
 O B:HOH863 2.2 36.4 1.0
O B:GLY299 2.3 27.5 1.0
O B:ALA302 2.3 30.0 1.0
O B:HOH1057 2.4 40.4 1.0
O B:HOH1079 2.5 37.1 1.0
O B:HOH1059 2.6 28.1 1.0
C B:GLY299 3.4 26.3 1.0
C B:ALA302 3.6 30.4 1.0
HA B:ILE303 3.6 37.5 1.0
H B:ALA302 3.6 31.9 1.0
HA2 B:GLY299 3.7 32.0 1.0
O B:HOH1135 3.9 36.2 1.0
HG22 B:ILE303 4.0 37.1 1.0
CA B:GLY299 4.1 26.6 1.0
HA B:TYR300 4.2 33.8 1.0
N B:ALA302 4.4 26.5 1.0
CA B:ILE303 4.4 31.2 1.0
N B:ILE303 4.4 25.6 1.0
O B:HOH1120 4.4 46.9 1.0
HA3 B:GLY299 4.5 32.0 1.0
O B:HOH1029 4.5 36.0 1.0
N B:TYR300 4.5 24.9 1.0
HB3 B:ALA302 4.5 32.8 1.0
CA B:ALA302 4.5 27.5 1.0
CA B:TYR300 4.8 28.1 1.0
CG2 B:ILE303 4.9 30.9 1.0
O B:ILE298 4.9 26.6 1.0
H B:HIS301 4.9 35.1 1.0
HG23 B:ILE303 4.9 37.1 1.0

Sodium binding site 3 out of 4 in 8a45

Go back to Sodium Binding Sites List in 8a45
Sodium binding site 3 out of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na703

b:23.6
occ:1.00
 O C:HOH1087 2.2 33.4 1.0
O C:ALA302 2.3 27.5 1.0
O C:GLY299 2.4 28.8 1.0
O C:HOH1101 2.4 36.0 1.0
O C:HOH1059 2.5 28.5 1.0
C C:ALA302 3.5 31.2 1.0
C C:GLY299 3.5 26.6 1.0
HA C:ILE303 3.5 39.5 1.0
H C:ALA302 3.6 31.1 1.0
HA2 C:GLY299 3.9 30.1 1.0
HG22 C:ILE303 3.9 36.3 1.0
HA C:TYR300 4.0 33.0 1.0
O C:HOH1161 4.2 40.0 1.0
CA C:GLY299 4.3 25.0 1.0
N C:ALA302 4.3 25.9 1.0
CA C:ILE303 4.4 32.9 1.0
N C:ILE303 4.4 31.1 1.0
N C:TYR300 4.5 25.6 1.0
CA C:ALA302 4.5 25.6 1.0
HB3 C:ALA302 4.5 34.2 1.0
CA C:TYR300 4.6 27.5 1.0
HA3 C:GLY299 4.6 30.1 1.0
O C:HOH1030 4.7 32.1 1.0
CG2 C:ILE303 4.8 30.2 1.0
H C:HIS301 4.8 31.1 1.0
HG23 C:ILE303 5.0 36.3 1.0

Sodium binding site 4 out of 4 in 8a45

Go back to Sodium Binding Sites List in 8a45
Sodium binding site 4 out of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na704

b:31.8
occ:1.00
 O E:ALA302 2.2 30.2 1.0
O E:HOH1068 2.2 39.8 1.0
O E:HOH1052 2.4 33.3 1.0
O E:GLY299 2.4 27.7 1.0
O E:HOH1038 2.5 38.7 1.0
H E:ALA302 3.4 35.4 1.0
C E:ALA302 3.4 31.9 1.0
C E:GLY299 3.5 32.0 1.0
HA E:ILE303 3.6 40.0 1.0
HA2 E:GLY299 3.7 39.3 1.0
N E:ALA302 4.1 29.4 1.0
HA E:TYR300 4.1 37.4 1.0
HG22 E:ILE303 4.2 40.0 1.0
HB3 E:ALA302 4.2 33.9 1.0
CA E:GLY299 4.2 32.7 1.0
CA E:ALA302 4.3 31.4 1.0
N E:ILE303 4.3 31.4 1.0
CA E:ILE303 4.4 33.2 1.0
O E:HOH1041 4.5 37.1 1.0
N E:TYR300 4.5 32.0 1.0
HA3 E:GLY299 4.6 39.3 1.0
CA E:TYR300 4.7 31.1 1.0
CB E:ALA302 4.7 28.2 1.0
H E:HIS301 4.8 32.8 1.0
O E:ILE298 4.9 32.6 1.0
CG2 E:ILE303 4.9 33.3 1.0
HG23 E:ILE303 5.0 40.0 1.0
N E:HIS301 5.0 27.3 1.0

Reference:

R.Hamid, A.Hirsch. Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate To Be Published.
Page generated: Mon Aug 18 13:04:26 2025

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