Magnesium in PDB 8r3s: Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate

Enzymatic activity of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate

All present enzymatic activity of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate:
2.2.1.1;

Protein crystallography data

The structure of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate, PDB code: 8r3s was solved by L.Ballut, N.Georges, N.Aghajari, L.Hecquet, F.Charmantray, B.Doumeche, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.86 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.9, 149.9, 253.3, 90, 90.2, 90
R / Rfree (%) 21.9 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate (pdb code 8r3s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate, PDB code: 8r3s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8r3s

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Magnesium binding site 1 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:49.5
occ:1.00
 OD2 A:ASP156 1.9 42.6 1.0
O A:ILE188 2.0 43.9 1.0
O2A A:TPP701 2.3 54.2 1.0
OD1 A:ASN186 2.4 54.4 1.0
ND2 A:ASN186 2.6 52.1 1.0
CG A:ASN186 2.8 47.8 1.0
O3B A:TPP701 3.0 59.3 1.0
CG A:ASP156 3.0 35.4 1.0
O1B A:TPP701 3.2 53.7 1.0
C A:ILE188 3.2 41.8 1.0
PB A:TPP701 3.4 77.3 1.0
PA A:TPP701 3.5 67.5 1.0
O3A A:TPP701 3.6 73.4 1.0
CB A:ASP156 3.7 34.1 1.0
N A:ILE188 3.8 40.1 1.0
OD1 A:ASP156 3.9 33.2 1.0
CA A:ILE188 4.1 41.3 1.0
CB A:ASN186 4.2 43.0 1.0
N A:SER189 4.2 40.9 1.0
O7 A:TPP701 4.3 59.1 1.0
N A:ASP156 4.3 32.8 1.0
CA A:SER189 4.4 43.0 1.0
N A:ASN186 4.5 40.5 1.0
N A:ASP187 4.5 42.7 1.0
C A:ASN186 4.6 42.8 1.0
O1A A:TPP701 4.6 50.4 1.0
CA A:ASN186 4.7 42.1 1.0
CA A:ASP156 4.7 32.8 1.0
CB A:ILE188 4.7 39.7 1.0
CD1 A:LEU194 4.7 35.2 1.0
O A:ASP184 4.8 37.5 1.0
O2B A:TPP701 4.9 55.4 1.0
C A:ASP187 4.9 38.4 1.0

Magnesium binding site 2 out of 10 in 8r3s

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Magnesium binding site 2 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:50.1
occ:1.00
 OD2 B:ASP156 1.9 38.0 1.0
OD1 B:ASN186 2.1 43.9 1.0
O B:ILE188 2.1 42.0 1.0
O1A B:TPP701 2.3 62.4 1.0
CG B:ASN186 2.8 40.3 1.0
ND2 B:ASN186 3.0 46.2 1.0
CG B:ASP156 3.1 36.1 1.0
PA B:TPP701 3.1 76.0 1.0
O1B B:TPP701 3.2 64.1 1.0
C B:ILE188 3.3 40.0 1.0
O2A B:TPP701 3.5 60.4 1.0
O3A B:TPP701 3.6 63.6 1.0
PB B:TPP701 3.7 88.9 1.0
CB B:ASP156 3.7 34.7 1.0
O2B B:TPP701 3.7 65.9 1.0
N B:ILE188 3.8 37.2 1.0
OD1 B:ASP156 4.1 35.1 1.0
CA B:ILE188 4.1 38.6 1.0
CB B:ASN186 4.2 37.8 1.0
N B:ASP156 4.3 30.3 1.0
N B:SER189 4.4 39.2 1.0
N B:ASP187 4.5 40.4 1.0
N B:ASN186 4.5 36.8 1.0
O B:ASP184 4.5 34.0 1.0
CA B:SER189 4.5 38.3 1.0
O7 B:TPP701 4.6 58.3 1.0
CA B:ASP156 4.7 33.2 1.0
C B:ASN186 4.7 38.1 1.0
CA B:ASN186 4.7 37.5 1.0
CB B:ILE188 4.7 38.2 1.0
CD1 B:LEU194 4.9 37.0 1.0
C B:ASP187 4.9 39.8 1.0

Magnesium binding site 3 out of 10 in 8r3s

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Magnesium binding site 3 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:46.7
occ:1.00
 OD1 C:ASP156 1.9 38.4 1.0
OD1 C:ASN186 2.0 38.3 1.0
O C:ILE188 2.1 43.1 1.0
O2A C:TPP701 2.3 52.8 1.0
CG C:ASP156 2.7 33.1 1.0
CG C:ASN186 3.0 36.0 1.0
O2B C:TPP701 3.1 48.4 1.0
C C:ILE188 3.3 37.3 1.0
CB C:ASP156 3.3 31.3 1.0
ND2 C:ASN186 3.4 40.5 1.0
OD2 C:ASP156 3.5 31.3 1.0
O3B C:TPP701 3.5 59.0 1.0
PA C:TPP701 3.6 65.0 1.0
N C:ILE188 3.7 33.0 1.0
PB C:TPP701 3.8 78.9 1.0
O3A C:TPP701 3.9 60.6 1.0
CA C:ILE188 4.0 34.8 1.0
N C:ASP156 4.1 34.0 1.0
N C:SER189 4.3 35.2 1.0
O7 C:TPP701 4.3 49.4 1.0
CB C:ASN186 4.3 32.6 1.0
O C:ASP184 4.3 30.7 1.0
N C:ASN186 4.3 32.6 1.0
CA C:ASP156 4.3 30.9 1.0
N C:ASP187 4.4 35.2 1.0
CD1 C:LEU194 4.5 34.5 1.0
CA C:SER189 4.5 36.3 1.0
C C:ASN186 4.7 34.2 1.0
CA C:ASN186 4.7 31.1 1.0
CB C:ILE188 4.7 32.2 1.0
C C:ASP187 4.8 32.9 1.0
O1A C:TPP701 4.8 48.8 1.0

Magnesium binding site 4 out of 10 in 8r3s

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Magnesium binding site 4 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:43.1
occ:1.00
 OD2 D:ASP156 1.9 37.3 1.0
O D:ILE188 2.0 40.0 1.0
OD1 D:ASN186 2.0 38.9 1.0
O2A D:TPP701 2.1 51.6 1.0
CG D:ASN186 2.8 37.1 1.0
O2B D:TPP701 2.9 47.5 1.0
CG D:ASP156 3.0 34.5 1.0
ND2 D:ASN186 3.0 38.6 1.0
C D:ILE188 3.1 38.2 1.0
O3B D:TPP701 3.5 52.1 1.0
PA D:TPP701 3.5 63.3 1.0
N D:ILE188 3.6 35.8 1.0
CB D:ASP156 3.6 34.0 1.0
PB D:TPP701 3.6 71.3 1.0
O3A D:TPP701 3.8 54.8 1.0
CA D:ILE188 3.9 36.5 1.0
OD1 D:ASP156 4.0 32.7 1.0
CB D:ASN186 4.1 34.5 1.0
N D:SER189 4.2 37.3 1.0
O7 D:TPP701 4.2 56.9 1.0
N D:ASP156 4.3 31.9 1.0
CB D:ILE188 4.3 32.5 1.0
N D:ASP187 4.4 34.9 1.0
N D:ASN186 4.4 36.0 1.0
O D:ASP184 4.5 32.9 1.0
O1A D:TPP701 4.6 51.3 1.0
CA D:SER189 4.6 39.8 1.0
C D:ASN186 4.6 34.5 1.0
CA D:ASP156 4.6 31.5 1.0
CA D:ASN186 4.6 35.6 1.0
C D:ASP187 4.7 33.2 1.0
CG2 D:ILE188 4.8 33.1 1.0

Magnesium binding site 5 out of 10 in 8r3s

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Magnesium binding site 5 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:43.3
occ:1.00
 OD2 E:ASP156 1.9 34.2 1.0
O2A E:TPP701 2.0 50.0 1.0
O E:ILE188 2.0 40.1 1.0
OD1 E:ASN186 2.1 39.9 1.0
O1B E:TPP701 2.8 71.4 1.0
CG E:ASN186 2.9 34.3 1.0
CG E:ASP156 3.0 32.0 1.0
ND2 E:ASN186 3.1 39.4 1.0
C E:ILE188 3.2 37.0 1.0
PA E:TPP701 3.2 68.2 1.0
PB E:TPP701 3.4 75.0 1.0
O3A E:TPP701 3.4 63.8 1.0
O3B E:TPP701 3.5 48.4 1.0
CB E:ASP156 3.6 31.8 1.0
N E:ILE188 3.7 32.2 1.0
O7 E:TPP701 3.9 54.7 1.0
CA E:ILE188 3.9 36.8 1.0
OD1 E:ASP156 4.1 31.3 1.0
N E:ASP156 4.2 32.7 1.0
N E:SER189 4.2 36.2 1.0
CB E:ASN186 4.3 32.1 1.0
O1A E:TPP701 4.4 51.3 1.0
CB E:ILE188 4.4 35.8 1.0
CA E:SER189 4.5 38.3 1.0
CA E:ASP156 4.6 32.2 1.0
N E:ASP187 4.6 33.0 1.0
O E:ASP184 4.6 26.2 1.0
N E:ASN186 4.6 31.1 1.0
C E:ASN186 4.8 31.6 1.0
CA E:ASN186 4.8 31.1 1.0
C E:ASP187 4.9 32.3 1.0
CG2 E:ILE188 4.9 36.3 1.0
O2B E:TPP701 4.9 46.0 1.0

Magnesium binding site 6 out of 10 in 8r3s

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Magnesium binding site 6 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:52.8
occ:1.00
 OD1 F:ASN186 1.9 44.2 1.0
OD1 F:ASP156 2.0 47.6 1.0
O2A F:TPP701 2.2 57.7 1.0
O F:ILE188 2.3 44.8 1.0
CG F:ASN186 2.8 41.4 1.0
O3B F:TPP701 2.9 58.9 1.0
CG F:ASP156 3.0 37.0 1.0
O1B F:TPP701 3.1 63.4 1.0
ND2 F:ASN186 3.1 45.0 1.0
PB F:TPP701 3.3 86.0 1.0
PA F:TPP701 3.4 73.0 1.0
C F:ILE188 3.5 40.5 1.0
O3A F:TPP701 3.5 68.4 1.0
CB F:ASP156 3.6 36.8 1.0
OD2 F:ASP156 3.9 31.2 1.0
N F:ILE188 3.9 40.8 1.0
N F:ASP156 4.1 32.3 1.0
CA F:ILE188 4.2 39.4 1.0
CB F:ASN186 4.3 38.0 1.0
O7 F:TPP701 4.3 69.9 1.0
O F:ASP184 4.3 39.8 1.0
N F:ASN186 4.4 40.0 1.0
O1A F:TPP701 4.5 53.6 1.0
CA F:ASP156 4.5 32.8 1.0
N F:SER189 4.5 39.7 1.0
CB F:ILE188 4.6 38.1 1.0
N F:ASP187 4.7 38.0 1.0
CA F:ASN186 4.7 38.6 1.0
CA F:SER189 4.8 41.6 1.0
C F:ASN186 4.8 37.6 1.0
O2B F:TPP701 4.8 63.6 1.0

Magnesium binding site 7 out of 10 in 8r3s

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Magnesium binding site 7 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg702

b:54.5
occ:1.00
 OD1 G:ASP156 1.9 46.7 1.0
O G:ILE188 2.1 50.7 1.0
ND2 G:ASN186 2.3 49.3 1.0
OD1 G:ASN186 2.4 44.9 1.0
O3B G:TPP701 2.4 57.5 1.0
CG G:ASN186 2.5 44.7 1.0
CG G:ASP156 2.7 45.0 1.0
OD2 G:ASP156 3.1 43.0 1.0
C G:ILE188 3.2 46.6 1.0
N G:ILE188 3.2 40.2 1.0
N G:ASP187 3.7 41.7 1.0
CA G:ILE188 3.7 41.9 1.0
CB G:ASN186 3.8 42.4 1.0
PB G:TPP701 3.9 81.0 1.0
CB G:ASP156 3.9 42.9 1.0
N G:ASN186 3.9 39.5 1.0
O1A G:TPP701 3.9 55.8 1.0
C G:ASN186 4.0 40.6 1.0
CA G:ASN186 4.1 40.7 1.0
C G:ASP187 4.2 40.9 1.0
N G:SER189 4.3 49.1 1.0
O3A G:TPP701 4.3 64.8 1.0
O2B G:TPP701 4.4 64.4 1.0
CA G:ASP187 4.4 40.2 1.0
CB G:ILE188 4.4 41.6 1.0
O G:ASP184 4.4 38.0 1.0
PA G:TPP701 4.5 70.3 1.0
N G:ASP156 4.6 42.8 1.0
O2A G:TPP701 4.7 65.4 1.0
O G:ASN186 4.7 38.0 1.0
CA G:SER189 4.7 51.7 1.0
CA G:ASP156 4.9 41.4 1.0
O1B G:TPP701 4.9 60.9 1.0
CG2 G:ILE188 4.9 44.4 1.0

Magnesium binding site 8 out of 10 in 8r3s

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Magnesium binding site 8 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg702

b:52.2
occ:1.00
 OD1 H:ASN186 1.9 47.5 1.0
O1A H:TPP701 2.1 58.2 1.0
OD2 H:ASP156 2.1 53.3 1.0
O H:ILE188 2.2 47.7 1.0
CG H:ASN186 2.9 47.1 1.0
PA H:TPP701 3.0 68.7 1.0
O1B H:TPP701 3.2 64.1 1.0
ND2 H:ASN186 3.2 52.7 1.0
CG H:ASP156 3.3 48.5 1.0
C H:ILE188 3.4 46.4 1.0
O2A H:TPP701 3.4 82.7 1.0
O3A H:TPP701 3.4 63.4 1.0
PB H:TPP701 3.7 92.1 1.0
O2B H:TPP701 3.8 70.8 1.0
N H:ILE188 3.9 43.1 1.0
CB H:ASP156 4.0 40.4 1.0
CA H:ILE188 4.2 43.0 1.0
CB H:ASN186 4.2 41.2 1.0
OD1 H:ASP156 4.3 42.1 1.0
N H:ASN186 4.4 37.5 1.0
N H:ASP156 4.4 37.4 1.0
O7 H:TPP701 4.4 58.7 1.0
N H:SER189 4.4 48.7 1.0
O H:ASP184 4.6 34.9 1.0
CB H:ILE188 4.6 41.7 1.0
N H:ASP187 4.6 40.8 1.0
CA H:SER189 4.6 49.1 1.0
CA H:ASN186 4.7 39.1 1.0
C H:ASN186 4.8 41.7 1.0
CA H:ASP156 4.9 36.4 1.0
CG2 H:ILE188 4.9 43.3 1.0

Magnesium binding site 9 out of 10 in 8r3s

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Magnesium binding site 9 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg702

b:53.9
occ:1.00
 OD1 I:ASN186 1.9 47.0 1.0
OD2 I:ASP156 2.1 42.6 1.0
O2A I:TPP701 2.2 56.2 1.0
O I:ILE188 2.3 46.4 1.0
CG I:ASN186 2.5 44.8 1.0
ND2 I:ASN186 2.6 48.5 1.0
O3B I:TPP701 2.8 68.0 1.0
CG I:ASP156 3.3 38.9 1.0
O1B I:TPP701 3.3 59.0 1.0
PB I:TPP701 3.4 86.9 1.0
PA I:TPP701 3.4 66.3 1.0
C I:ILE188 3.5 44.6 1.0
O3A I:TPP701 3.6 62.5 1.0
CB I:ASP156 3.9 36.1 1.0
N I:ILE188 4.0 40.2 1.0
CB I:ASN186 4.0 40.2 1.0
N I:ASP156 4.2 35.9 1.0
O7 I:TPP701 4.3 61.9 1.0
OD1 I:ASP156 4.3 39.3 1.0
CA I:ILE188 4.3 44.0 1.0
O I:ASP184 4.3 39.9 1.0
N I:ASN186 4.4 38.9 1.0
N I:SER189 4.5 44.1 1.0
O1A I:TPP701 4.6 56.6 1.0
CA I:ASN186 4.6 40.7 1.0
CA I:ASP156 4.7 36.5 1.0
N I:ASP187 4.7 42.8 1.0
CA I:SER189 4.8 46.5 1.0
C I:ASN186 4.8 41.5 1.0
CB I:ILE188 4.8 44.6 1.0
O2B I:TPP701 4.9 68.1 1.0
CB I:SER155 4.9 40.7 1.0

Magnesium binding site 10 out of 10 in 8r3s

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Magnesium binding site 10 out of 10 in the Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Transketolase From Staphylococcus Aureus in Complex with Thiamin Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg702

b:58.7
occ:1.00
 OD2 J:ASP156 2.0 43.8 1.0
OD1 J:ASN186 2.0 50.9 1.0
O3B J:TPP701 2.5 56.5 1.0
O J:ILE188 2.5 45.5 1.0
O2A J:TPP701 2.6 56.1 1.0
O1A J:TPP701 2.8 67.6 1.0
CG J:ASN186 2.8 42.5 1.0
PA J:TPP701 2.9 69.4 1.0
ND2 J:ASN186 3.0 41.4 1.0
PB J:TPP701 3.1 73.0 1.0
O3A J:TPP701 3.1 60.1 1.0
CG J:ASP156 3.2 38.9 1.0
O1B J:TPP701 3.3 53.3 1.0
C J:ILE188 3.7 44.5 1.0
CB J:ASP156 3.9 38.1 1.0
N J:ASP156 4.2 36.9 1.0
OD1 J:ASP156 4.2 36.9 1.0
CB J:ASN186 4.3 38.6 1.0
O7 J:TPP701 4.5 60.4 1.0
N J:ILE188 4.5 42.9 1.0
O2B J:TPP701 4.6 60.7 1.0
CA J:ILE188 4.6 42.8 1.0
N J:SER189 4.7 44.2 1.0
O J:ASP184 4.7 35.5 1.0
CA J:ASP156 4.7 36.3 1.0
N J:ASN186 4.7 37.3 1.0
CA J:SER189 4.7 47.4 1.0
CB J:SER155 4.9 38.2 1.0
CD1 J:ILE247 4.9 34.5 1.0
CA J:ASN186 4.9 38.9 1.0

Reference:

N.R.Georges, L.Ballut, N.Aghajari, L.Hecquet, F.Charmantray, B.Doumeche. Are Transketolases Relevant Targets Fighting Human Pathogens? A Comparative Biochemical, Bioinformatic and Structural Study To Be Published.
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