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Magnesium in PDB 5a65: Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.

Enzymatic activity of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.

All present enzymatic activity of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.:
3.6.1.28;

Protein crystallography data

The structure of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions., PDB code: 5a65 was solved by J.Martinez, V.Truffault, M.Hothorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 1.98
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.483, 105.483, 111.805, 90.00, 90.00, 90.00
R / Rfree (%) 20.784 / 25.818

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions. (pdb code 5a65). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions., PDB code: 5a65:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5a65

Go back to Magnesium Binding Sites List in 5a65
Magnesium binding site 1 out of 4 in the Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:40.9
occ:1.00
 OE2 A:GLU159 2.0 40.0 1.0
O2 A:PO41001 2.0 40.4 1.0
O A:HOH2047 2.1 35.5 1.0
O A:HOH2005 2.2 35.9 1.0
OE1 A:GLU157 2.2 39.9 1.0
O A:HOH2006 2.2 36.5 1.0
CD A:GLU159 3.2 42.1 1.0
P A:PO41001 3.2 49.2 1.0
CD A:GLU157 3.2 35.4 1.0
O3 A:PO41001 3.5 40.9 1.0
MG A:MG501 3.6 38.8 1.0
OE2 A:GLU157 3.6 34.9 1.0
O1 A:PO41001 3.8 39.6 1.0
CG A:GLU159 3.8 39.1 1.0
O A:HOH2008 3.8 55.9 1.0
OD2 A:ASP145 3.9 37.7 1.0
OE1 A:GLU159 4.2 47.7 1.0
OE1 A:GLU9 4.2 46.2 1.0
O2B A:TPP1000 4.2 43.9 1.0
OE2 A:GLU7 4.3 52.6 1.0
O4 A:PO41001 4.4 50.1 1.0
O A:HOH2036 4.4 45.0 1.0
O A:HOH2004 4.4 46.7 1.0
CG A:GLU157 4.5 32.5 1.0
O3B A:TPP1000 4.7 46.3 1.0
CB A:GLU157 4.8 31.3 1.0
CD A:GLU9 4.9 46.3 1.0
CD A:GLU7 5.0 49.7 1.0
CG A:ASP145 5.0 34.6 1.0

Magnesium binding site 2 out of 4 in 5a65

Go back to Magnesium Binding Sites List in 5a65
Magnesium binding site 2 out of 4 in the Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:38.8
occ:1.00
 O A:HOH2004 1.9 46.7 1.0
O A:HOH2050 1.9 39.5 1.0
O3 A:PO41001 2.0 40.9 1.0
OD2 A:ASP145 2.2 37.7 1.0
OE2 A:GLU159 2.2 40.0 1.0
OE1 A:GLU159 2.3 47.7 1.0
CD A:GLU159 2.6 42.1 1.0
CG A:ASP145 3.2 34.6 1.0
P A:PO41001 3.3 49.2 1.0
O2 A:PO41001 3.5 40.4 1.0
MG A:MG500 3.6 40.9 1.0
O A:HOH2047 3.6 35.5 1.0
OD1 A:ASP145 3.6 36.1 1.0
NH1 A:ARG125 3.7 38.7 1.0
CG A:GLU159 4.1 39.1 1.0
O4 A:PO41001 4.2 50.1 1.0
OE2 A:GLU7 4.2 52.6 1.0
O1 A:PO41001 4.3 39.6 1.0
O A:HOH2074 4.3 63.8 1.0
O A:HOH2003 4.4 53.1 1.0
CB A:ASP145 4.5 32.6 1.0
CZ A:ARG125 4.6 35.8 1.0
CG2 A:THR143 4.6 37.6 1.0
O A:HOH2005 4.8 35.9 1.0
NH2 A:ARG125 4.9 34.9 1.0

Magnesium binding site 3 out of 4 in 5a65

Go back to Magnesium Binding Sites List in 5a65
Magnesium binding site 3 out of 4 in the Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:38.4
occ:1.00
 O2 B:PO41001 2.0 43.8 1.0
O B:HOH2001 2.1 37.8 1.0
O B:HOH2031 2.1 29.8 1.0
OE2 B:GLU159 2.2 44.5 1.0
O B:HOH2038 2.2 36.9 1.0
OE1 B:GLU157 2.2 38.2 1.0
CD B:GLU157 3.2 36.6 1.0
P B:PO41001 3.2 49.5 1.0
CD B:GLU159 3.3 42.8 1.0
OE2 B:GLU157 3.6 42.1 1.0
O1 B:PO41001 3.6 45.3 1.0
O4 B:PO41001 3.7 43.6 1.0
O B:HOH2003 3.8 56.2 1.0
CG B:GLU159 3.8 40.3 1.0
MG B:MG501 3.8 55.4 1.0
OD2 B:ASP145 3.9 39.4 1.0
O2B B:TPP1000 4.1 40.4 1.0
OE1 B:GLU9 4.1 48.7 1.0
O B:HOH2002 4.3 46.6 1.0
OE1 B:GLU159 4.3 42.1 1.0
O3 B:PO41001 4.4 49.7 1.0
CG B:GLU157 4.5 33.8 1.0
OE2 B:GLU7 4.5 55.3 1.0
O B:HOH2030 4.6 59.8 1.0
O B:HOH2021 4.8 53.6 1.0
CD B:GLU9 4.8 48.5 1.0
CB B:GLU157 4.8 32.2 1.0
O3B B:TPP1000 4.8 50.3 1.0
CD B:GLU7 5.0 55.3 1.0
CB B:GLU9 5.0 42.0 1.0

Magnesium binding site 4 out of 4 in 5a65

Go back to Magnesium Binding Sites List in 5a65
Magnesium binding site 4 out of 4 in the Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mouse Thiamine Triphosphatase in Complex with Thiamine Diphosphate, Orthophosphate and Magnesium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:55.4
occ:1.00
 O B:HOH2032 2.0 45.8 1.0
O1 B:PO41001 2.0 45.3 1.0
O B:HOH2002 2.1 46.6 1.0
OD2 B:ASP145 2.2 39.4 1.0
OE2 B:GLU159 2.4 44.5 1.0
OE1 B:GLU159 2.7 42.1 1.0
CD B:GLU159 2.9 42.8 1.0
CG B:ASP145 3.2 36.4 1.0
P B:PO41001 3.2 49.5 1.0
O2 B:PO41001 3.5 43.8 1.0
NH1 B:ARG125 3.6 38.8 1.0
OD1 B:ASP145 3.6 36.4 1.0
O B:HOH2031 3.7 29.8 1.0
MG B:MG500 3.8 38.4 1.0
O B:HOH2053 3.9 74.5 1.0
O3 B:PO41001 4.1 49.7 1.0
O4 B:PO41001 4.2 43.6 1.0
CG B:GLU159 4.4 40.3 1.0
OE2 B:GLU7 4.5 55.3 1.0
CZ B:ARG125 4.6 37.0 1.0
CB B:ASP145 4.6 35.5 1.0
CG2 B:THR143 4.8 40.4 1.0
NH2 B:ARG125 5.0 36.9 1.0

Reference:

J.Martinez, V.Truffault, M.Hothorn. Structural Determinants For Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. J.Biol.Chem. V. 290 23348 2015.
ISSN: ISSN 0021-9258
PubMed: 26221030
DOI: 10.1074/JBC.M115.674473
Page generated: Mon Dec 14 19:59:33 2020

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