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Sodium in PDB 8a4d: 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor

Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor:
2.2.1.7;

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d 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) 48.54 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.618, 137.618, 231.681, 90, 90, 90
R / Rfree (%) 17.6 / 24.1

Other elements in 8a4d:

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Magnesium (Mg) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor (pdb code 8a4d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8a4d

Go back to Sodium Binding Sites List in 8a4d
Sodium binding site 1 out of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


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 From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:40.4
occ:1.00
 O A:HOH1096 2.2 38.9 1.0
O A:HOH1042 2.3 37.5 1.0
HH12 A:ARG145 2.6 34.8 1.0
O D:HOH921 2.8 25.4 1.0
HG22 A:THR152 3.4 25.9 1.0
NH1 A:ARG145 3.4 29.1 1.0
HA A:THR152 3.5 27.6 1.0
HH22 A:ARG145 3.7 30.7 1.0
CZ A:ARG108 3.7 31.7 1.0
HD2 A:ARG108 3.8 29.7 1.0
HB A:THR152 3.8 28.5 1.0
NE A:ARG108 3.8 30.0 1.0
HH11 A:ARG145 3.9 34.8 1.0
NH2 A:ARG108 3.9 22.5 1.0
HB3 D:CYS382 4.0 26.9 1.0
HE A:ARG108 4.0 36.0 1.0
NH1 A:ARG108 4.0 31.6 1.0
HH21 A:ARG108 4.1 27.0 1.0
CG2 A:THR152 4.2 21.6 1.0
O D:CYS382 4.2 21.9 1.0
HH22 A:ARG108 4.2 27.0 1.0
HH11 A:ARG108 4.2 37.8 1.0
CB A:THR152 4.3 23.8 1.0
HH12 A:ARG108 4.3 37.8 1.0
NH2 A:ARG145 4.3 25.6 1.0
CA A:THR152 4.3 23.0 1.0
CD A:ARG108 4.3 24.8 1.0
CZ A:ARG145 4.4 22.6 1.0
OE2 D:GLU383 4.5 28.5 1.0
HG21 A:THR152 4.6 25.9 1.0
O A:HOH911 4.8 21.0 1.0
O A:THR152 4.8 20.7 1.0
HE2 A:MET168 4.9 25.7 1.0
HD3 A:ARG108 4.9 29.7 1.0
HG23 A:THR152 4.9 25.9 1.0
CB D:CYS382 5.0 22.4 1.0
O A:HOH1029 5.0 24.8 1.0
C D:CYS382 5.0 19.9 1.0

Sodium binding site 2 out of 5 in 8a4d

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Sodium binding site 2 out of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


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 From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na704

b:32.3
occ:1.00
 O C:ALA302 2.0 32.5 1.0
O C:HOH1011 2.5 32.5 1.0
O C:GLY299 2.6 31.4 1.0
O C:HOH1059 2.7 50.3 1.0
C C:ALA302 3.2 32.7 1.0
H C:ALA302 3.3 33.1 1.0
HA C:ILE303 3.5 43.9 1.0
C C:GLY299 3.7 26.5 1.0
HA2 C:GLY299 3.9 32.9 1.0
HG22 C:ILE303 3.9 39.4 1.0
N C:ALA302 4.0 27.7 1.0
HB3 C:ALA302 4.1 42.4 1.0
N C:ILE303 4.1 31.4 1.0
CA C:ALA302 4.1 30.9 1.0
HA C:TYR300 4.2 40.1 1.0
O C:HOH1058 4.2 44.4 1.0
CA C:ILE303 4.3 36.6 1.0
CA C:GLY299 4.4 27.5 1.0
O C:HOH1013 4.4 32.6 1.0
N C:TYR300 4.7 30.3 1.0
CB C:ALA302 4.7 35.4 1.0
CG2 C:ILE303 4.8 32.9 1.0
CA C:TYR300 4.8 33.5 1.0
O C:ILE298 4.8 30.9 1.0
HG23 C:ILE303 4.9 39.4 1.0
HA3 C:GLY299 4.9 32.9 1.0
H C:HIS301 4.9 38.5 1.0
H C:ILE303 4.9 37.6 1.0
HA C:ALA302 5.0 37.1 1.0

Sodium binding site 3 out of 5 in 8a4d

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Sodium binding site 3 out of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na705

b:26.3
occ:1.00
 H C:VAL592 2.1 22.8 1.0
O C:HOH880 2.6 20.3 1.0
O C:HOH904 2.8 15.3 1.0
O C:HOH978 2.8 15.5 1.0
N C:VAL592 2.9 19.1 1.0
HA C:TYR591 3.0 20.7 1.0
HB C:VAL592 3.0 20.0 1.0
HG C:SER434 3.1 18.4 1.0
HG23 C:VAL592 3.1 24.3 1.0
HB3 C:PRO429 3.3 29.1 1.0
CB C:VAL592 3.6 16.7 1.0
HD1 C:TYR591 3.7 25.7 1.0
HB2 C:ALA432 3.7 27.2 1.0
O C:HOH962 3.7 18.2 1.0
CG2 C:VAL592 3.7 20.3 1.0
OG C:SER434 3.8 15.4 1.0
HA C:PRO429 3.8 27.4 1.0
CA C:VAL592 3.8 20.8 1.0
CA C:TYR591 3.8 17.3 1.0
HB3 C:ALA432 3.8 27.2 1.0
C C:TYR591 3.8 21.5 1.0
HB1 C:ALA432 3.8 27.2 1.0
HD23 C:LEU423 3.9 27.9 1.0
CB C:ALA432 4.0 22.7 1.0
HG21 C:VAL592 4.0 24.3 1.0
O C:TYR590 4.0 18.7 1.0
O C:VAL592 4.1 24.9 1.0
CB C:PRO429 4.2 24.3 1.0
HD21 C:LEU423 4.3 27.9 1.0
CD2 C:LEU423 4.4 23.3 1.0
HB3 C:TYR591 4.4 26.1 1.0
HD22 C:LEU423 4.4 27.9 1.0
C C:VAL592 4.5 19.9 1.0
CA C:PRO429 4.5 22.9 1.0
CD1 C:TYR591 4.5 21.4 1.0
HG22 C:VAL592 4.6 24.3 1.0
HA C:VAL592 4.6 24.9 1.0
HB2 C:PRO429 4.6 29.1 1.0
CB C:TYR591 4.6 21.8 1.0
N C:TYR591 4.8 18.9 1.0
C C:TYR590 4.8 19.3 1.0
CB C:SER434 5.0 17.4 1.0
CG1 C:VAL592 5.0 17.2 1.0
O C:TYR591 5.0 23.3 1.0

Sodium binding site 4 out of 5 in 8a4d

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Sodium binding site 4 out of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na703

b:26.7
occ:1.00
 OD2 D:ASP455 2.6 23.1 1.0
O D:HOH979 2.7 27.1 1.0
OE2 D:GLU456 2.8 17.8 1.0
O D:HOH806 2.8 23.7 1.0
HB3 D:ASP455 3.1 25.7 1.0
HG2 D:GLU456 3.1 22.9 1.0
HH22 D:ARG500 3.3 33.4 1.0
CG D:ASP455 3.6 23.5 1.0
CD D:GLU456 3.7 20.2 1.0
HZ2 D:LYS459 3.8 32.3 1.0
HZ1 D:LYS459 3.8 32.3 1.0
CB D:ASP455 3.8 21.5 1.0
HH12 D:ARG500 3.8 26.2 1.0
CG D:GLU456 3.8 19.1 1.0
NH2 D:ARG500 4.0 27.9 1.0
HD2 D:LYS459 4.1 30.6 1.0
NZ D:LYS459 4.2 27.0 1.0
HH21 D:ARG533 4.2 18.8 1.0
O D:HOH902 4.3 29.5 1.0
H D:GLU456 4.4 25.3 1.0
N D:GLU456 4.4 21.1 1.0
HB2 D:ASP455 4.4 25.7 1.0
HA D:GLU456 4.4 26.9 1.0
HG3 D:GLU456 4.4 22.9 1.0
OD1 D:ASP453 4.4 16.0 1.0
NH1 D:ARG500 4.5 21.9 1.0
HH21 D:ARG500 4.5 33.4 1.0
C D:ASP455 4.5 20.4 1.0
O D:HOH1089 4.6 31.8 1.0
OD2 D:ASP453 4.6 21.0 1.0
CZ D:ARG500 4.7 27.2 1.0
OD1 D:ASP455 4.7 25.6 1.0
CA D:GLU456 4.8 22.4 1.0
CA D:ASP455 4.8 18.4 1.0
CD D:LYS459 4.8 25.6 1.0
HZ3 D:LYS459 4.8 32.3 1.0
OE1 D:GLU456 4.9 17.3 1.0
CB D:GLU456 4.9 20.4 1.0
HD3 D:LYS459 4.9 30.6 1.0
O D:ASP455 5.0 19.6 1.0
NH2 D:ARG533 5.0 15.8 1.0
CG D:ASP453 5.0 20.1 1.0

Sodium binding site 5 out of 5 in 8a4d

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Sodium binding site 5 out of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na707

b:42.9
occ:1.00
 O F:ALA302 2.2 32.3 1.0
O F:HOH1107 2.6 48.5 1.0
O F:GLY299 2.7 34.1 1.0
O F:HOH1013 2.7 34.2 1.0
HA F:ILE303 3.3 43.7 1.0
C F:ALA302 3.4 34.4 1.0
H F:ALA302 3.7 37.3 1.0
C F:GLY299 3.8 30.7 1.0
HA2 F:GLY299 3.9 37.9 1.0
HG22 F:ILE303 3.9 37.7 1.0
O F:HOH998 3.9 40.3 1.0
CA F:ILE303 4.1 36.4 1.0
N F:ILE303 4.2 41.0 1.0
CA F:GLY299 4.4 31.6 1.0
N F:ALA302 4.4 31.1 1.0
CA F:ALA302 4.5 37.0 1.0
HA F:TYR300 4.5 37.6 1.0
HB3 F:ALA302 4.6 41.3 1.0
CG2 F:ILE303 4.7 31.4 1.0
HA3 F:GLY299 4.7 37.9 1.0
N F:TYR300 4.8 34.8 1.0
HG23 F:ILE303 4.9 37.7 1.0

Reference:

R.Hamid, R.Hamid, A.Hirsch. N/A N/A.
Page generated: Fri Jul 28 03:00:47 2023

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