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Magnesium in PDB 8a5k: Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding

Enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding

All present enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding:
2.2.1.7;

Protein crystallography data

The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding, PDB code: 8a5k 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) 46.92 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.819, 137.065, 231.445, 90, 90, 90
R / Rfree (%) 18.3 / 23.8

Other elements in 8a5k:

The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding (pdb code 8a5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding, PDB code: 8a5k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8a5k

Go back to Magnesium Binding Sites List in 8a5k
Magnesium binding site 1 out of 6 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:21.8
occ:1.00
 O2B A:TPP701 2.1 28.9 1.0
O A:MET218 2.1 37.5 1.0
O A:HOH911 2.1 25.6 1.0
OD1 A:ASP187 2.2 28.4 1.0
OD1 A:ASN216 2.3 29.9 1.0
O1A A:TPP701 2.4 33.0 1.0
CG A:ASN216 3.2 30.4 1.0
PB A:TPP701 3.2 32.0 1.0
C A:MET218 3.3 44.1 1.0
CG A:ASP187 3.3 28.6 1.0
PA A:TPP701 3.4 35.2 1.0
ND2 A:ASN216 3.5 28.9 1.0
O3A A:TPP701 3.5 34.0 1.0
OD2 A:ASP187 3.8 34.1 1.0
O1B A:TPP701 3.9 32.1 1.0
N A:ASP187 3.9 28.4 1.0
N A:GLY188 4.0 26.5 1.0
N A:MET218 4.0 41.5 1.0
CA A:MET218 4.0 42.3 1.0
O7 A:TPP701 4.2 33.4 1.0
CB A:MET218 4.3 42.6 1.0
N A:ASN216 4.3 27.2 1.0
N A:SER219 4.3 44.2 1.0
O A:ASN214 4.4 29.3 1.0
CB A:ASP187 4.5 25.4 1.0
CB A:ASN216 4.5 25.7 1.0
O2A A:TPP701 4.5 30.4 1.0
O3B A:TPP701 4.5 37.6 1.0
CA A:SER219 4.6 37.7 1.0
CA A:ASP187 4.6 28.3 1.0
CA A:GLY186 4.6 25.9 1.0
C A:GLY186 4.6 28.3 1.0
C A:ASP187 4.8 28.0 1.0
CA A:ASN216 4.8 31.6 1.0
CA A:GLY188 4.8 27.0 1.0
N A:ASP217 4.8 42.1 1.0
O A:SER219 4.9 45.6 1.0
C A:ASN216 4.9 37.7 1.0

Magnesium binding site 2 out of 6 in 8a5k

Go back to Magnesium Binding Sites List in 8a5k
Magnesium binding site 2 out of 6 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:18.1
occ:1.00
 O B:MET218 2.0 31.2 1.0
OD1 B:ASP187 2.1 24.3 1.0
O3B B:TPP701 2.2 26.2 1.0
O B:HOH827 2.3 22.1 1.0
OD1 B:ASN216 2.3 25.6 1.0
O1A B:TPP701 2.4 27.1 1.0
C B:MET218 3.1 31.6 1.0
CG B:ASP187 3.2 25.7 1.0
CG B:ASN216 3.2 27.3 1.0
PB B:TPP701 3.3 26.7 1.0
PA B:TPP701 3.5 22.8 1.0
ND2 B:ASN216 3.6 21.7 1.0
OD2 B:ASP187 3.7 28.9 1.0
N B:MET218 3.7 33.3 1.0
O3A B:TPP701 3.8 26.1 1.0
CA B:MET218 3.9 32.1 1.0
O1B B:TPP701 3.9 21.1 1.0
N B:ASP187 4.0 25.5 1.0
N B:GLY188 4.0 23.6 1.0
O7 B:TPP701 4.1 31.4 1.0
N B:SER219 4.1 33.2 1.0
CB B:MET218 4.3 30.6 1.0
CA B:SER219 4.4 30.4 1.0
O B:ASN214 4.4 25.2 1.0
CB B:ASP187 4.4 23.2 1.0
N B:ASN216 4.4 24.5 1.0
O2B B:TPP701 4.5 23.0 1.0
CA B:ASP187 4.6 25.3 1.0
CB B:ASN216 4.6 24.9 1.0
O2A B:TPP701 4.6 27.8 1.0
N B:ASP217 4.7 32.0 1.0
CA B:GLY186 4.7 24.6 1.0
C B:GLY186 4.7 23.4 1.0
C B:ASP187 4.8 24.6 1.0
O B:SER219 4.8 33.1 1.0
C B:ASN216 4.8 31.2 1.0
CA B:ASN216 4.8 27.6 1.0
H72 B:TPP701 4.9 38.5 1.0
C B:ASP217 4.9 32.8 1.0
CA B:GLY188 4.9 23.4 1.0

Magnesium binding site 3 out of 6 in 8a5k

Go back to Magnesium Binding Sites List in 8a5k
Magnesium binding site 3 out of 6 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:18.1
occ:1.00
 O C:MET218 2.0 34.7 1.0
O3B C:TPP701 2.0 26.6 1.0
OD1 C:ASN216 2.3 28.1 1.0
OD1 C:ASP187 2.3 27.3 1.0
O C:HOH889 2.4 22.7 1.0
O1A C:TPP701 2.4 26.8 1.0
C C:MET218 3.1 34.7 1.0
CG C:ASN216 3.2 27.8 1.0
CG C:ASP187 3.4 26.6 1.0
PB C:TPP701 3.4 26.4 1.0
PA C:TPP701 3.5 23.2 1.0
ND2 C:ASN216 3.6 26.0 1.0
N C:MET218 3.6 34.5 1.0
CA C:MET218 3.8 33.9 1.0
O3A C:TPP701 3.9 24.2 1.0
OD2 C:ASP187 3.9 32.6 1.0
N C:ASP187 4.0 20.7 1.0
N C:GLY188 4.0 22.6 1.0
O1B C:TPP701 4.0 22.9 1.0
O7 C:TPP701 4.1 28.1 1.0
CB C:MET218 4.1 33.2 1.0
N C:SER219 4.2 33.2 1.0
N C:ASN216 4.3 27.4 1.0
O C:ASN214 4.4 23.9 1.0
CB C:ASN216 4.5 25.5 1.0
CB C:ASP187 4.6 24.5 1.0
O2A C:TPP701 4.6 25.5 1.0
O2B C:TPP701 4.6 24.6 1.0
CA C:SER219 4.6 33.1 1.0
CA C:ASP187 4.7 24.1 1.0
N C:ASP217 4.7 35.1 1.0
CA C:ASN216 4.7 30.9 1.0
C C:ASN216 4.7 31.2 1.0
C C:ASP187 4.8 22.3 1.0
C C:GLY186 4.8 23.9 1.0
CA C:GLY186 4.8 23.0 1.0
C C:ASP217 4.9 39.6 1.0
O C:SER219 4.9 33.8 1.0
CA C:GLY188 4.9 24.7 1.0

Magnesium binding site 4 out of 6 in 8a5k

Go back to Magnesium Binding Sites List in 8a5k
Magnesium binding site 4 out of 6 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:22.0
occ:1.00
 O D:MET218 2.0 40.7 1.0
O3B D:TPP701 2.2 35.1 1.0
O D:HOH877 2.2 33.2 1.0
O2A D:TPP701 2.3 33.1 1.0
OD1 D:ASP187 2.3 33.5 1.0
OD1 D:ASN216 2.4 36.1 1.0
CG D:ASN216 3.2 36.0 1.0
C D:MET218 3.2 41.2 1.0
CG D:ASP187 3.2 33.6 1.0
PA D:TPP701 3.3 35.0 1.0
PB D:TPP701 3.3 29.3 1.0
ND2 D:ASN216 3.4 33.5 1.0
O3A D:TPP701 3.5 32.9 1.0
OD2 D:ASP187 3.6 30.9 1.0
N D:MET218 3.9 45.6 1.0
CA D:MET218 4.0 44.7 1.0
N D:ASP187 4.0 32.5 1.0
O1B D:TPP701 4.0 33.6 1.0
N D:GLY188 4.0 28.4 1.0
O7 D:TPP701 4.1 40.1 1.0
N D:SER219 4.2 43.6 1.0
CB D:MET218 4.3 40.2 1.0
O D:ASN214 4.4 29.9 1.0
O1A D:TPP701 4.4 33.6 1.0
N D:ASN216 4.5 35.5 1.0
CA D:SER219 4.5 43.4 1.0
CB D:ASP187 4.5 30.1 1.0
CB D:ASN216 4.6 34.7 1.0
O2B D:TPP701 4.6 29.1 1.0
CA D:ASP187 4.7 30.1 1.0
CA D:GLY186 4.8 28.3 1.0
C D:GLY186 4.8 30.1 1.0
C D:ASP187 4.8 31.2 1.0
CA D:ASN216 4.9 37.1 1.0
N D:ASP217 4.9 49.1 1.0
C D:ASN216 4.9 37.6 1.0
O D:SER219 4.9 45.3 1.0
CA D:GLY188 4.9 30.2 1.0

Magnesium binding site 5 out of 6 in 8a5k

Go back to Magnesium Binding Sites List in 8a5k
Magnesium binding site 5 out of 6 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:22.9
occ:1.00
 O E:MET218 2.0 34.7 1.0
OD1 E:ASN216 2.1 27.8 1.0
OD2 E:ASP187 2.2 34.0 1.0
O1B E:TPP701 2.3 29.9 1.0
O1A E:TPP701 2.3 29.8 1.0
O E:HOH841 2.4 25.8 1.0
CG E:ASN216 3.0 30.8 1.0
C E:MET218 3.1 39.2 1.0
CG E:ASP187 3.2 32.1 1.0
ND2 E:ASN216 3.4 30.8 1.0
PA E:TPP701 3.5 29.1 1.0
PB E:TPP701 3.6 32.1 1.0
OD1 E:ASP187 3.6 33.0 1.0
N E:MET218 3.7 36.9 1.0
CA E:MET218 3.9 37.6 1.0
O3A E:TPP701 3.9 31.1 1.0
N E:ASP187 4.0 25.6 1.0
N E:GLY188 4.0 28.5 1.0
O2B E:TPP701 4.1 30.6 1.0
O7 E:TPP701 4.1 37.1 1.0
N E:SER219 4.2 44.2 1.0
N E:ASN216 4.2 29.8 1.0
CB E:ASN216 4.3 31.1 1.0
O E:ASN214 4.4 28.4 1.0
CB E:MET218 4.4 41.6 1.0
CA E:SER219 4.4 42.8 1.0
CB E:ASP187 4.5 27.7 1.0
CA E:ASN216 4.6 33.6 1.0
O2A E:TPP701 4.6 27.3 1.0
CA E:ASP187 4.6 27.4 1.0
C E:ASN216 4.6 35.6 1.0
N E:ASP217 4.6 34.3 1.0
C E:GLY186 4.7 24.9 1.0
CA E:GLY186 4.7 25.7 1.0
O3B E:TPP701 4.7 28.9 1.0
C E:ASP187 4.8 31.5 1.0
CA E:GLY188 4.9 27.9 1.0
C E:ASP217 4.9 39.2 1.0
O E:SER219 5.0 45.3 1.0

Magnesium binding site 6 out of 6 in 8a5k

Go back to Magnesium Binding Sites List in 8a5k
Magnesium binding site 6 out of 6 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:23.2
occ:1.00
 OD1 F:ASP187 2.0 35.9 1.0
O1B F:TPP701 2.1 32.4 1.0
O1A F:TPP701 2.2 32.6 1.0
O F:MET218 2.2 39.5 1.0
OD1 F:ASN216 2.3 34.4 1.0
O F:HOH833 2.3 27.5 1.0
CG F:ASP187 3.0 33.0 1.0
C F:MET218 3.2 39.9 1.0
CG F:ASN216 3.2 35.6 1.0
PA F:TPP701 3.4 32.9 1.0
OD2 F:ASP187 3.4 36.3 1.0
PB F:TPP701 3.5 34.9 1.0
N F:MET218 3.6 45.2 1.0
ND2 F:ASN216 3.7 33.0 1.0
CA F:MET218 3.9 40.4 1.0
O3A F:TPP701 3.9 31.9 1.0
N F:GLY188 4.0 29.8 1.0
N F:ASP187 4.0 28.7 1.0
O2B F:TPP701 4.1 32.1 1.0
O7 F:TPP701 4.2 36.1 1.0
CB F:MET218 4.2 39.2 1.0
N F:ASN216 4.2 37.3 1.0
N F:SER219 4.3 40.5 1.0
CB F:ASP187 4.3 33.5 1.0
O F:ASN214 4.3 32.3 1.0
O2A F:TPP701 4.5 29.2 1.0
CB F:ASN216 4.5 35.7 1.0
N F:ASP217 4.6 45.4 1.0
CA F:ASP187 4.6 31.2 1.0
C F:ASN216 4.6 42.4 1.0
CA F:SER219 4.6 38.7 1.0
O3B F:TPP701 4.6 31.1 1.0
CA F:ASN216 4.7 39.4 1.0
C F:ASP187 4.7 31.7 1.0
C F:ASP217 4.8 52.3 1.0
C F:GLY186 4.8 28.9 1.0
CA F:GLY186 4.8 29.4 1.0
CA F:GLY188 4.8 30.4 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.
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