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Magnesium in PDB 4a5a: Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

Enzymatic activity of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

All present enzymatic activity of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp:
3.6.1.5;

Protein crystallography data

The structure of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp, PDB code: 4a5a was solved by U.Krug, M.Zebisch, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.953, 150.668, 486.988, 90.00, 90.00, 90.00
R / Rfree (%) 23.369 / 28.411

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp (pdb code 4a5a). 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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp, PDB code: 4a5a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4a5a

Go back to Magnesium Binding Sites List in 4a5a
Magnesium binding site 1 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp


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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:30.4
occ:1.00
 O2G A:ANP700 2.0 58.6 1.0
O2B A:ANP700 2.4 52.6 1.0
PG A:ANP700 3.4 53.0 1.0
O2A A:ANP700 3.6 58.0 1.0
OE2 A:GLU236 3.6 36.7 1.0
OE2 A:GLU277 3.7 43.5 1.0
PB A:ANP700 3.8 47.8 1.0
NE1 A:TRP600 3.9 35.2 1.0
N3B A:ANP700 4.0 51.3 1.0
O1G A:ANP700 4.2 52.8 1.0
OD2 A:ASP70 4.2 47.1 1.0
CD1 A:TRP600 4.3 34.7 1.0
NH2 A:ARG77 4.3 50.0 1.0
OG1 A:THR188 4.3 31.2 1.0
O3G A:ANP700 4.5 54.3 1.0
OD1 A:ASP70 4.5 46.8 1.0
O3A A:ANP700 4.6 51.8 1.0
PA A:ANP700 4.7 56.1 1.0
CG A:ASP70 4.8 44.4 1.0
CD A:GLU236 4.8 34.7 1.0
CD A:GLU277 4.9 42.0 1.0
O1B A:ANP700 5.0 47.6 1.0
CA A:GLY279 5.0 35.3 1.0

Magnesium binding site 2 out of 4 in 4a5a

Go back to Magnesium Binding Sites List in 4a5a
Magnesium binding site 2 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp


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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:39.6
occ:1.00
 O2G B:ANP700 1.9 81.2 1.0
O2B B:ANP700 2.4 68.8 1.0
PG B:ANP700 3.4 78.9 1.0
O2A B:ANP700 3.5 93.7 1.0
OE2 B:GLU236 3.7 39.5 1.0
PB B:ANP700 3.7 68.4 1.0
OE2 B:GLU277 3.8 33.7 1.0
NE1 B:TRP600 3.9 30.5 1.0
N3B B:ANP700 4.0 71.7 1.0
OD2 B:ASP70 4.1 31.2 1.0
NH2 B:ARG77 4.2 62.2 1.0
O1G B:ANP700 4.2 79.1 1.0
OG1 B:THR188 4.3 36.9 1.0
CD1 B:TRP600 4.3 31.5 1.0
O3G B:ANP700 4.4 75.2 1.0
OD1 B:ASP70 4.5 31.7 1.0
O3A B:ANP700 4.6 79.7 1.0
PA B:ANP700 4.7 92.0 1.0
CG B:ASP70 4.8 30.9 1.0
CD B:GLU236 4.9 38.6 1.0
O1B B:ANP700 4.9 60.2 1.0
CA B:GLY279 5.0 29.3 1.0

Magnesium binding site 3 out of 4 in 4a5a

Go back to Magnesium Binding Sites List in 4a5a
Magnesium binding site 3 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp


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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:25.0
occ:1.00
 O2G C:ANP700 2.0 36.0 1.0
O2B C:ANP700 2.3 34.4 1.0
PG C:ANP700 3.5 33.0 1.0
O2A C:ANP700 3.6 38.8 1.0
PB C:ANP700 3.7 32.6 1.0
OE2 C:GLU236 3.8 13.4 1.0
OE2 C:GLU277 3.8 16.8 1.0
NE1 C:TRP600 3.9 13.5 1.0
OD2 C:ASP70 4.0 18.0 1.0
N3B C:ANP700 4.1 31.9 1.0
NH2 C:ARG77 4.1 19.9 1.0
O1G C:ANP700 4.3 33.4 1.0
OD1 C:ASP70 4.3 17.8 1.0
CD1 C:TRP600 4.3 13.6 1.0
OG1 C:THR188 4.4 15.4 1.0
O3G C:ANP700 4.5 32.0 1.0
O3A C:ANP700 4.5 35.7 1.0
CG C:ASP70 4.6 17.6 1.0
PA C:ANP700 4.6 36.3 1.0
O1B C:ANP700 4.8 33.2 1.0

Magnesium binding site 4 out of 4 in 4a5a

Go back to Magnesium Binding Sites List in 4a5a
Magnesium binding site 4 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp


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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:25.8
occ:1.00
 O2G D:ANP700 2.1 42.5 1.0
O2B D:ANP700 2.4 45.0 1.0
O2A D:ANP700 3.4 46.0 1.0
PG D:ANP700 3.6 41.6 1.0
OE2 D:GLU277 3.6 21.2 1.0
PB D:ANP700 3.8 41.2 1.0
OE2 D:GLU236 3.8 19.1 1.0
NE1 D:TRP600 3.9 12.6 1.0
N3B D:ANP700 4.1 40.5 1.0
NH2 D:ARG77 4.1 20.2 1.0
OD2 D:ASP70 4.2 17.2 1.0
CD1 D:TRP600 4.3 12.7 1.0
O1G D:ANP700 4.3 45.2 1.0
OG1 D:THR188 4.5 19.0 1.0
O3A D:ANP700 4.6 42.0 1.0
PA D:ANP700 4.6 42.0 1.0
O3G D:ANP700 4.6 36.7 1.0
OD1 D:ASP70 4.6 16.8 1.0
CD D:GLU277 4.8 21.2 1.0
CG D:ASP70 4.8 16.8 1.0
O1B D:ANP700 4.9 37.1 1.0
CA D:GLY279 5.0 22.1 1.0
CD D:GLU236 5.0 18.2 1.0

Reference:

U.Krug, M.Zebisch, M.Krauss, N.Straeter. Structural Insight Into the Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases By Disulfide Reduction. J.Biol.Chem. V. 287 3051 2012.
ISSN: ISSN 0021-9258
PubMed: 22130673
DOI: 10.1074/JBC.M111.294348
Page generated: Thu Aug 15 14:21:02 2024

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