Atomistry » Sodium » PDB 7zyq-8acy » 8a29
Atomistry »
  Sodium »
    PDB 7zyq-8acy »
      8a29 »

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

Go back to Sodium Binding Sites List in 8a29
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: Wed Oct 9 10:25:45 2024

Last articles

Fe in 9CUF
Fe in 9DEU
Fe in 9CCB
Fe in 9D86
Fe in 9DCO
Fe in 9EBM
Fe in 9EBK
Fe in 8ZQD
Fe in 8ZEH
Fe in 8ZET
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy