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Sodium in PDB 8a29: Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa

Enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa:
2.2.1.7;

Protein crystallography data

The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29 was solved by R.Hamid, S.Adam, A.Lacour, L.Monjas, A.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.444, 137.631, 232.082, 90, 90, 90
R / Rfree (%) 17.1 / 22.4

Other elements in 8a29:

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

Magnesium (Mg) 13 atoms
Calcium (Ca) 12 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa (pdb code 8a29). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8a29

Go back to Sodium Binding Sites List in 8a29
Sodium binding site 1 out of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:29.4
occ:1.00
 O A:ALA302 2.4 32.2 1.0
O A:GLY299 2.5 30.3 1.0
O A:HOH935 2.7 31.2 1.0
O A:HOH1088 2.7 47.3 1.0
HA A:ILE303 3.6 36.3 1.0
C A:ALA302 3.6 27.7 1.0
C A:GLY299 3.6 30.3 1.0
H A:ALA302 3.7 32.0 1.0
O A:HOH1068 3.8 39.0 1.0
HA2 A:GLY299 3.8 34.3 1.0
O A:HOH1091 4.0 43.1 1.0
HG22 A:ILE303 4.2 29.6 1.0
HA A:TYR300 4.3 36.1 1.0
CA A:GLY299 4.3 28.6 1.0
O A:HOH1113 4.3 33.9 1.0
CA A:ILE303 4.4 30.2 1.0
N A:ALA302 4.4 26.7 1.0
N A:ILE303 4.5 24.2 1.0
CA A:ALA302 4.6 28.4 1.0
O A:HOH968 4.6 39.9 1.0
HB3 A:ALA302 4.6 26.6 1.0
N A:TYR300 4.6 27.1 1.0
HA3 A:GLY299 4.8 34.3 1.0
HG23 A:ILE303 4.8 29.6 1.0
O A:ILE298 4.8 29.0 1.0
CA A:TYR300 4.9 30.1 1.0
CG2 A:ILE303 4.9 24.7 1.0

Sodium binding site 2 out of 5 in 8a29

Go back to Sodium Binding Sites List in 8a29
Sodium binding site 2 out of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:26.2
occ:1.00
 O C:HOH1057 2.2 36.5 1.0
O C:ALA302 2.2 26.1 1.0
O C:GLY299 2.4 26.4 1.0
O C:HOH1013 2.6 27.8 1.0
O C:HOH1054 2.8 48.8 1.0
C C:ALA302 3.4 33.6 1.0
H C:ALA302 3.5 30.1 1.0
C C:GLY299 3.5 23.6 1.0
HA C:ILE303 3.5 36.7 1.0
HG22 C:ILE303 3.8 37.0 1.0
HA2 C:GLY299 3.9 33.7 1.0
HA C:TYR300 4.0 36.2 1.0
N C:ALA302 4.3 25.1 1.0
CA C:GLY299 4.3 28.1 1.0
N C:ILE303 4.3 31.1 1.0
CA C:ILE303 4.3 30.6 1.0
O C:HOH1074 4.4 44.9 1.0
CA C:ALA302 4.4 33.1 1.0
O C:HOH1031 4.5 35.8 1.0
N C:TYR300 4.5 23.8 1.0
HB3 C:ALA302 4.6 41.2 1.0
CG2 C:ILE303 4.6 30.8 1.0
CA C:TYR300 4.7 30.2 1.0
HA3 C:GLY299 4.7 33.7 1.0
HG23 C:ILE303 4.8 37.0 1.0
O C:ILE298 4.9 32.6 1.0
H C:HIS301 4.9 28.5 1.0
O C:HOH1096 4.9 39.2 1.0
CB C:ALA302 5.0 34.3 1.0

Sodium binding site 3 out of 5 in 8a29

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Sodium binding site 3 out of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:54.4
occ:1.00
 O D:HOH987 2.2 52.0 1.0
O D:ALA302 2.3 46.6 1.0
O D:GLY299 2.5 55.4 1.0
O D:HOH1070 2.5 47.9 1.0
O D:HOH1077 2.6 54.7 1.0
O D:HOH993 2.7 44.9 1.0
C D:ALA302 3.5 41.0 1.0
H D:ALA302 3.6 49.8 1.0
C D:GLY299 3.6 52.3 1.0
HA D:ILE303 3.7 56.7 1.0
HA2 D:GLY299 3.8 65.8 1.0
CA D:GLY299 4.3 54.8 1.0
N D:ALA302 4.3 41.5 1.0
HA D:TYR300 4.4 65.1 1.0
N D:ILE303 4.4 43.3 1.0
HG22 D:ILE303 4.4 53.5 1.0
CA D:ALA302 4.5 46.0 1.0
HB3 D:ALA302 4.5 46.7 1.0
CA D:ILE303 4.5 47.2 1.0
HA3 D:GLY299 4.7 65.8 1.0
N D:TYR300 4.7 54.5 1.0
O D:HOH1122 4.8 58.2 1.0
CA D:TYR300 5.0 54.3 1.0
CB D:ALA302 5.0 38.9 1.0
O D:ILE298 5.0 52.9 1.0

Sodium binding site 4 out of 5 in 8a29

Go back to Sodium Binding Sites List in 8a29
Sodium binding site 4 out of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na705

b:24.6
occ:1.00
 O E:HOH1051 2.2 39.9 1.0
OD2 E:ASP488 2.3 23.5 1.0
O E:HOH1045 2.4 42.8 1.0
O E:HOH1086 2.6 34.0 1.0
OD2 E:ASP486 2.6 31.6 1.0
OD1 E:ASP486 2.6 27.0 1.0
CG E:ASP486 3.0 29.6 1.0
HB2 E:ASP488 3.2 27.3 1.0
CG E:ASP488 3.4 26.4 1.0
CB E:ASP488 3.8 22.8 1.0
H E:ASP488 4.1 27.7 1.0
HB3 E:ASP488 4.4 27.3 1.0
OD1 E:ASP488 4.5 22.2 1.0
O E:HOH809 4.5 25.2 1.0
CB E:ASP486 4.5 25.6 1.0
HD2 E:PRO487 4.8 33.0 1.0
N E:ASP488 4.8 23.1 1.0
HB2 E:ASP486 4.9 30.7 1.0
HB3 E:ASP486 4.9 30.7 1.0
CA E:ASP488 5.0 26.7 1.0

Sodium binding site 5 out of 5 in 8a29

Go back to Sodium Binding Sites List in 8a29
Sodium binding site 5 out of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:37.3
occ:1.00
 O F:HOH1127 2.4 34.6 1.0
O F:HOH1159 2.4 37.8 1.0
HB2 F:GLN490 2.8 34.1 1.0
HE2 F:LYS459 2.9 29.5 1.0
HG2 F:LYS459 2.9 22.3 1.0
O F:GLN490 3.2 20.4 1.0
O F:PRO491 3.4 19.7 1.0
HG12 F:VAL492 3.4 24.2 1.0
CB F:GLN490 3.6 28.4 1.0
HB3 F:GLN490 3.6 34.1 1.0
C F:GLN490 3.7 25.4 1.0
HG13 F:VAL492 3.7 24.2 1.0
CE F:LYS459 3.8 24.6 1.0
CG F:LYS459 3.8 18.6 1.0
CG1 F:VAL492 4.0 20.1 1.0
C F:PRO491 4.0 22.8 1.0
HD3 F:LYS459 4.0 27.9 1.0
CD F:LYS459 4.1 23.2 1.0
H F:GLN490 4.2 29.8 1.0
CA F:GLN490 4.2 22.6 1.0
HE3 F:LYS459 4.2 29.5 1.0
N F:PRO491 4.3 24.5 1.0
HG3 F:LYS459 4.4 22.3 1.0
HG11 F:VAL492 4.5 24.2 1.0
HB3 F:LYS459 4.5 23.1 1.0
HZ3 F:LYS459 4.6 29.2 1.0
CA F:PRO491 4.6 22.8 1.0
HA F:VAL492 4.6 21.3 1.0
N F:GLN490 4.7 24.8 1.0
N F:VAL492 4.7 17.6 1.0
HA F:PRO491 4.7 27.4 1.0
NZ F:LYS459 4.7 24.4 1.0
O F:HOH844 4.7 24.8 1.0
CB F:LYS459 4.8 19.2 1.0
O F:HOH851 4.8 26.5 1.0
CG F:GLN490 4.8 30.0 1.0
HG3 F:GLN490 4.8 36.0 1.0
HZ1 F:LYS459 5.0 29.2 1.0

Reference:

R.Hamid, S.Adam, A.Lacour, L.Monjas, A.Hirsch. Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding To Be Published.
Page generated: Fri Jul 28 03:00:47 2023

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