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Magnesium 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
Sodium (Na) 5 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 11 binding sites of Magnesium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 8a4d

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Magnesium binding site 1 out of 11 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 Magnesium with other atoms in the Mg 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:Mg702

b:37.9
occ:1.00
 OD1 A:ASN216 2.8 31.2 1.0
OD1 A:ASP187 2.8 29.1 1.0
O A:HOH861 2.9 28.1 1.0
O A:HOH1093 2.9 28.9 1.0
HD21 A:ASN216 3.2 39.5 1.0
H A:GLY188 3.4 26.2 1.0
CG A:ASN216 3.5 32.6 1.0
CG A:ASP187 3.5 29.7 1.0
ND2 A:ASN216 3.6 33.0 1.0
H A:ASP187 3.7 28.5 1.0
OD2 A:ASP187 3.7 21.9 1.0
OD2 A:ASP217 3.7 55.9 1.0
H A:ASN216 3.9 37.0 1.0
O A:HOH1107 4.0 29.8 1.0
N A:GLY188 4.2 21.9 1.0
N A:ASP187 4.2 23.8 1.0
HA3 A:GLY186 4.2 26.7 1.0
O A:HOH1112 4.4 24.6 1.0
HD22 A:ASN216 4.4 39.5 1.0
HA3 A:GLY188 4.6 30.0 1.0
N A:ASN216 4.7 30.9 1.0
CB A:ASP187 4.8 26.4 1.0
O A:ASN214 4.8 23.7 1.0
CB A:ASN216 4.8 31.2 1.0
CG A:ASP217 4.8 48.6 1.0
C A:GLY186 4.8 28.3 1.0
CA A:GLY186 4.8 22.3 1.0
HA2 A:GLY186 4.8 26.7 1.0
CA A:ASP187 4.9 25.3 1.0
CA A:GLY188 5.0 25.0 1.0
CE A:LYS286 5.0 38.6 1.0

Magnesium binding site 2 out of 11 in 8a4d

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Magnesium binding site 2 out of 11 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 Magnesium with other atoms in the Mg 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
A:Mg703

b:32.8
occ:1.00
 O A:GLY299 2.3 25.6 1.0
O A:ALA302 2.5 25.8 1.0
O A:HOH991 2.6 28.8 1.0
O A:HOH1007 2.8 34.6 1.0
O A:HOH1113 2.9 41.3 1.0
C A:GLY299 3.4 26.6 1.0
HA2 A:GLY299 3.6 29.4 1.0
HA A:ILE303 3.6 35.7 1.0
C A:ALA302 3.7 25.6 1.0
HG22 A:ILE303 3.8 31.2 1.0
H A:ALA302 3.8 30.2 1.0
CA A:GLY299 4.0 24.6 1.0
HA A:TYR300 4.3 30.5 1.0
HA3 A:GLY299 4.4 29.4 1.0
O A:HOH999 4.5 30.4 1.0
CA A:ILE303 4.5 29.8 1.0
N A:TYR300 4.5 21.5 1.0
N A:ILE303 4.5 25.9 1.0
N A:ALA302 4.6 25.2 1.0
CG2 A:ILE303 4.6 26.1 1.0
HB3 A:ALA302 4.7 39.6 1.0
O A:ILE298 4.7 28.4 1.0
CA A:ALA302 4.7 29.2 1.0
HG23 A:ILE303 4.8 31.2 1.0
CA A:TYR300 4.9 25.5 1.0

Magnesium binding site 3 out of 11 in 8a4d

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Magnesium binding site 3 out of 11 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 Magnesium with other atoms in the Mg 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
B:Mg702

b:39.6
occ:1.00
 OD1 B:ASP187 2.4 37.6 1.0
OD1 B:ASN216 2.5 41.1 1.0
O B:HOH958 2.6 27.5 1.0
HD22 B:ASN216 2.9 53.6 1.0
CG B:ASN216 3.2 40.1 1.0
CG B:ASP187 3.2 31.9 1.0
ND2 B:ASN216 3.3 44.7 1.0
H B:GLY188 3.4 31.6 1.0
OD2 B:ASP187 3.5 32.2 1.0
H B:ASP187 3.6 33.4 1.0
O B:HOH1087 3.7 27.6 1.0
H B:ASN216 3.8 37.5 1.0
HD21 B:ASN216 4.1 53.6 1.0
OD1 B:ASP217 4.1 45.8 1.0
O B:HOH1062 4.1 36.5 1.0
N B:GLY188 4.2 26.4 1.0
N B:ASP187 4.2 27.9 1.0
O B:HOH1067 4.3 25.9 1.0
HA3 B:GLY186 4.3 28.3 1.0
CB B:ASN216 4.5 32.2 1.0
CB B:ASP187 4.5 25.9 1.0
N B:ASN216 4.6 31.3 1.0
HA3 B:GLY188 4.7 23.2 1.0
CE B:LYS286 4.7 54.0 1.0
O B:ASN214 4.7 27.0 1.0
CA B:ASP187 4.8 23.1 1.0
HB3 B:ASN216 4.8 38.5 1.0
HA2 B:GLY186 4.8 28.3 1.0
CA B:GLY186 4.9 23.6 1.0
C B:GLY186 4.9 25.7 1.0
NZ B:LYS286 4.9 61.6 1.0
C B:ASP187 4.9 27.4 1.0
HB3 B:ASP187 5.0 31.0 1.0
CA B:ASN216 5.0 39.4 1.0

Magnesium binding site 4 out of 11 in 8a4d

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Magnesium binding site 4 out of 11 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 Magnesium with other atoms in the Mg 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
C:Mg702

b:44.4
occ:1.00
 OD1 C:ASP187 2.6 41.2 1.0
O C:HOH858 2.7 39.2 1.0
OD2 C:ASP217 2.8 64.9 1.0
OD1 C:ASN216 2.9 50.2 1.0
O C:HOH982 3.1 52.2 1.0
H C:GLY188 3.2 34.3 1.0
CG C:ASP187 3.4 36.2 1.0
HD21 C:ASN216 3.6 50.0 1.0
H C:ASP187 3.6 45.2 1.0
CG C:ASN216 3.6 46.3 1.0
H C:ASN216 3.6 52.9 1.0
OD2 C:ASP187 3.7 52.4 1.0
O C:HOH1073 3.7 40.7 1.0
O C:HOH1079 3.9 32.7 1.0
ND2 C:ASN216 3.9 41.7 1.0
N C:GLY188 4.0 28.6 1.0
CG C:ASP217 4.0 64.8 1.0
N C:ASP187 4.1 37.8 1.0
H C:ASP217 4.2 73.4 1.0
HA3 C:GLY186 4.3 31.4 1.0
HB2 C:ASP217 4.5 71.8 1.0
N C:ASN216 4.5 44.1 1.0
HA3 C:GLY188 4.5 37.3 1.0
N C:ASP217 4.6 61.2 1.0
CB C:ASP187 4.6 33.5 1.0
HD22 C:ASN216 4.7 50.0 1.0
CA C:ASP187 4.7 32.4 1.0
O C:ASN214 4.7 26.2 1.0
O C:HOH1057 4.8 45.4 1.0
C C:ASP187 4.8 33.7 1.0
CB C:ASP217 4.8 59.9 1.0
CA C:GLY188 4.8 31.1 1.0
C C:GLY186 4.8 33.8 1.0
HA C:ASP215 4.8 40.0 1.0
CB C:ASN216 4.8 45.7 1.0
OD1 C:ASP217 4.9 72.3 1.0
CA C:GLY186 4.9 26.2 1.0
C C:ASN216 4.9 59.9 1.0
CA C:ASN216 5.0 47.5 1.0
HA2 C:GLY186 5.0 31.4 1.0

Magnesium binding site 5 out of 11 in 8a4d

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Magnesium binding site 5 out of 11 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 Magnesium with other atoms in the Mg 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
C:Mg703

b:37.0
occ:1.00
 HB3 C:ASP273 3.5 62.8 1.0
CB C:ASP273 4.4 52.4 1.0
CG C:ASP273 4.6 56.6 1.0
OD2 C:ASP273 4.7 53.0 1.0
HB2 C:ASP273 4.7 62.8 1.0
O C:ASP273 4.9 47.4 1.0

Magnesium binding site 6 out of 11 in 8a4d

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Magnesium binding site 6 out of 11 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg702

b:50.0
occ:1.00
 OD1 D:ASP187 2.5 50.5 1.0
O D:HOH847 2.7 47.2 1.0
OD2 D:ASP217 2.8 78.1 1.0
H D:GLY188 2.8 33.3 1.0
OD1 D:ASN216 3.0 84.3 1.0
O D:HOH1079 3.0 37.0 1.0
H D:ASP187 3.1 38.3 1.0
O D:HOH1064 3.1 45.8 1.0
CG D:ASP187 3.4 39.0 1.0
HD21 D:ASN216 3.6 95.8 1.0
N D:ASP187 3.6 32.0 1.0
HA3 D:GLY186 3.6 37.6 1.0
N D:GLY188 3.7 27.8 1.0
OD2 D:ASP187 3.9 52.2 1.0
CG D:ASN216 3.9 81.0 1.0
CG D:ASP217 4.0 90.3 1.0
ND2 D:ASN216 4.1 79.9 1.0
H D:ASP217 4.2 95.5 1.0
HA3 D:GLY188 4.2 32.6 1.0
H D:ASN216 4.2 83.7 1.0
CA D:GLY186 4.3 31.4 1.0
C D:GLY186 4.3 30.9 1.0
CA D:ASP187 4.4 31.6 1.0
HB2 D:ASP217 4.4 108.8 1.0
HA2 D:GLY186 4.4 37.6 1.0
CB D:ASP187 4.5 35.4 1.0
C D:ASP187 4.5 31.3 1.0
CA D:GLY188 4.5 27.2 1.0
O D:ASN214 4.6 40.5 1.0
CB D:ASP217 4.8 90.7 1.0
H D:ALA189 4.8 34.5 1.0
OD1 D:ASP217 4.8 94.7 1.0
N D:ASP217 4.9 79.6 1.0
HB3 D:ASP187 4.9 42.4 1.0
HD22 D:ASN216 4.9 95.8 1.0

Magnesium binding site 7 out of 11 in 8a4d

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Magnesium binding site 7 out of 11 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 Magnesium with other atoms in the Mg binding site number 7 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
E:Mg702

b:42.2
occ:1.00
 OD2 E:ASP217 2.4 68.2 1.0
OD1 E:ASP187 2.6 36.4 1.0
OD1 E:ASN216 2.9 52.3 1.0
H E:GLY188 3.2 35.6 1.0
CG E:ASP187 3.3 35.3 1.0
CG E:ASP217 3.5 75.1 1.0
OD2 E:ASP187 3.5 43.6 1.0
H E:ASP187 3.6 28.9 1.0
CG E:ASN216 3.7 52.0 1.0
O E:HOH1102 3.8 31.9 1.0
H E:ASN216 3.8 53.7 1.0
HD22 E:ASN216 3.8 82.2 1.0
N E:GLY188 3.9 29.7 1.0
O E:HOH1075 4.0 37.3 1.0
ND2 E:ASN216 4.1 68.5 1.0
N E:ASP187 4.1 24.1 1.0
OD1 E:ASP217 4.2 79.4 1.0
HA3 E:GLY186 4.3 27.9 1.0
HB2 E:ASP217 4.3 91.3 1.0
HA3 E:GLY188 4.3 29.9 1.0
N E:ASN216 4.5 44.8 1.0
CB E:ASP217 4.6 76.1 1.0
CB E:ASP187 4.6 32.9 1.0
CA E:ASP187 4.7 27.7 1.0
CA E:GLY188 4.7 25.0 1.0
C E:ASP187 4.7 34.5 1.0
C E:GLY186 4.8 26.7 1.0
O E:ASN214 4.8 29.3 1.0
HD21 E:ASN216 4.8 82.2 1.0
C E:ASN216 4.8 57.1 1.0
CB E:ASN216 4.8 49.8 1.0
HA2 E:GLY186 4.9 27.9 1.0
N E:ASP217 4.9 69.4 1.0
CA E:GLY186 4.9 23.3 1.0
H E:ASP217 4.9 83.3 1.0
CA E:ASN216 5.0 46.1 1.0
HA E:ASP215 5.0 31.1 1.0

Magnesium binding site 8 out of 11 in 8a4d

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Magnesium binding site 8 out of 11 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 Magnesium with other atoms in the Mg binding site number 8 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
E:Mg703

b:26.2
occ:1.00
 O E:HOH1093 2.3 36.3 1.0
OD2 E:ASP488 2.4 25.6 1.0
OD2 E:ASP486 2.5 30.7 1.0
O E:HOH1054 2.6 45.6 1.0
OD1 E:ASP486 2.9 26.7 1.0
CG E:ASP486 3.1 30.4 1.0
HB2 E:ASP488 3.3 26.9 1.0
CG E:ASP488 3.5 22.9 1.0
CB E:ASP488 3.9 22.5 1.0
O E:HOH803 4.2 24.5 1.0
H E:ASP488 4.3 33.1 1.0
HB3 E:ASP488 4.3 26.9 1.0
CB E:ASP486 4.6 28.3 1.0
OD1 E:ASP488 4.6 17.1 1.0
HD2 E:PRO487 4.6 26.4 1.0
HB2 E:ASP486 4.9 33.9 1.0
O E:HOH1091 4.9 33.9 1.0
N E:ASP488 5.0 27.6 1.0
HB3 E:ASP486 5.0 33.9 1.0

Magnesium binding site 9 out of 11 in 8a4d

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Magnesium binding site 9 out of 11 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 Magnesium with other atoms in the Mg binding site number 9 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:Mg703

b:22.8
occ:1.00
 OD2 F:ASP488 2.2 32.7 1.0
OD2 F:ASP486 2.4 27.3 1.0
O F:HOH1091 2.6 36.8 1.0
O F:HOH1048 2.6 40.1 1.0
O F:HOH1108 2.7 49.7 1.0
OD1 F:ASP486 2.8 26.1 1.0
HB2 F:ASP488 2.9 31.0 1.0
CG F:ASP486 3.0 31.5 1.0
CG F:ASP488 3.1 26.6 1.0
CB F:ASP488 3.5 25.9 1.0
H F:ASP488 4.0 26.9 1.0
HB3 F:ASP488 4.0 31.0 1.0
OD1 F:ASP488 4.2 25.6 1.0
O F:HOH802 4.3 27.3 1.0
HD2 F:PRO487 4.5 29.6 1.0
CB F:ASP486 4.5 27.8 1.0
N F:ASP488 4.7 22.5 1.0
O F:HOH1129 4.7 44.1 1.0
O F:HOH1105 4.7 33.0 1.0
CA F:ASP488 4.7 26.9 1.0
HB2 F:ASP486 4.8 33.3 1.0
HB3 F:ASP486 4.9 33.3 1.0

Magnesium binding site 10 out of 11 in 8a4d

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Magnesium binding site 10 out of 11 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 Magnesium with other atoms in the Mg binding site number 10 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:Mg704

b:46.8
occ:1.00
 O F:HOH849 2.4 36.5 1.0
OD2 F:ASP217 2.6 79.2 1.0
OD1 F:ASN216 2.8 50.8 1.0
OD2 F:ASP187 2.9 44.1 1.0
H F:GLY188 3.2 30.8 1.0
OD1 F:ASP187 3.3 45.0 1.0
CG F:ASP187 3.3 39.1 1.0
O F:HOH1096 3.3 31.7 1.0
H F:ASP187 3.3 43.1 1.0
HD22 F:ASN216 3.5 48.3 1.0
CG F:ASN216 3.7 47.9 1.0
CG F:ASP217 3.8 84.0 1.0
H F:ASN216 3.9 53.1 1.0
N F:ASP187 3.9 36.0 1.0
ND2 F:ASN216 3.9 40.3 1.0
HA3 F:GLY186 4.0 34.4 1.0
N F:GLY188 4.0 25.7 1.0
O F:HOH1078 4.1 36.8 1.0
OD1 F:ASP217 4.4 90.1 1.0
O F:HOH1089 4.4 47.8 1.0
HA3 F:GLY188 4.5 36.5 1.0
CB F:ASP187 4.5 34.1 1.0
H F:ASP217 4.6 92.1 1.0
O F:ASN214 4.6 34.3 1.0
CA F:ASP187 4.6 33.5 1.0
CA F:GLY186 4.7 28.7 1.0
N F:ASN216 4.7 44.3 1.0
C F:GLY186 4.7 30.7 1.0
HA2 F:GLY186 4.7 34.4 1.0
HB2 F:ASP217 4.7 84.6 1.0
HD21 F:ASN216 4.8 48.3 1.0
C F:ASP187 4.8 29.5 1.0
N F:ASP217 4.8 76.8 1.0
CA F:GLY188 4.9 30.5 1.0
CB F:ASP217 4.9 70.5 1.0
HA F:ASP215 5.0 38.2 1.0
CB F:ASN216 5.0 46.6 1.0

Reference:

R.Hamid, R.Hamid, A.Hirsch. N/A N/A.
Page generated: Thu Jul 27 22:07:50 2023

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