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Magnesium in PDB 4kh4: Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp

Enzymatic activity of Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp

All present enzymatic activity of Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp:
3.6.1.15;

Protein crystallography data

The structure of Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp, PDB code: 4kh4 was solved by U.Krug, R.Totzauer, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.94 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.156, 148.267, 242.176, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp (pdb code 4kh4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp, PDB code: 4kh4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4kh4

Go back to Magnesium Binding Sites List in 4kh4
Magnesium binding site 1 out of 2 in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:38.1
occ:1.00
O2G A:ANP700 2.0 74.2 0.8
O1B A:ANP700 2.9 72.6 0.8
PG A:ANP700 3.4 73.7 0.8
OE1 A:GLU236 3.4 57.7 1.0
NE1 A:TRP600 3.7 37.0 1.0
O1A A:ANP700 3.7 74.0 0.8
OE1 A:GLU277 3.8 59.0 1.0
PB A:ANP700 4.0 72.5 0.8
O1G A:ANP700 4.0 73.3 0.8
N3B A:ANP700 4.1 73.2 0.8
CD1 A:TRP600 4.2 37.8 1.0
OD2 A:ASP70 4.3 54.9 1.0
O3G A:ANP700 4.4 73.4 0.8
OG1 A:THR188 4.4 41.0 1.0
OD1 A:ASP70 4.5 46.4 1.0
NH2 A:ARG77 4.5 70.8 1.0
CD A:GLU236 4.5 62.7 1.0
O3A A:ANP700 4.6 73.5 0.8
PA A:ANP700 4.7 74.5 0.8
CG A:ASP70 4.8 47.1 1.0
CG2 A:THR188 4.9 37.5 1.0
CE2 A:TRP600 5.0 37.5 1.0

Magnesium binding site 2 out of 2 in 4kh4

Go back to Magnesium Binding Sites List in 4kh4
Magnesium binding site 2 out of 2 in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:43.7
occ:1.00
O1B B:ANP700 2.1 71.5 0.0
O1B B:ANP700 2.4 69.1 0.8
O1G B:ANP700 2.4 69.9 0.8
O1G B:ANP700 2.6 71.5 0.0
PB B:ANP700 3.0 71.5 0.0
O3A B:ANP700 3.0 71.5 0.0
PB B:ANP700 3.3 68.7 0.8
OD2 B:ASP70 3.4 57.4 1.0
O3A B:ANP700 3.5 69.2 0.8
OD1 B:ASP70 3.5 54.5 1.0
NE1 B:TRP600 3.6 49.0 1.0
N3B B:ANP700 3.6 71.5 0.0
PG B:ANP700 3.6 69.6 0.8
PG B:ANP700 3.7 71.5 0.0
N3B B:ANP700 3.7 69.2 0.8
OE1 B:GLU236 3.8 73.6 1.0
CG B:ASP70 3.9 52.7 1.0
PA B:ANP700 4.0 71.5 0.0
OG1 B:THR188 4.1 49.7 1.0
O1A B:ANP700 4.1 71.5 0.0
CD1 B:TRP600 4.2 49.6 1.0
O1A B:ANP700 4.2 71.2 0.8
O2A B:ANP700 4.4 71.5 0.0
O2B B:ANP700 4.4 71.5 0.0
PA B:ANP700 4.4 70.6 0.8
OE1 B:GLU277 4.5 55.8 1.0
O2G B:ANP700 4.5 69.6 0.8
O2G B:ANP700 4.5 71.5 0.0
NH1 B:ARG77 4.5 68.7 1.0
NH2 B:ARG77 4.6 66.0 1.0
O3G B:ANP700 4.7 69.7 0.8
O2B B:ANP700 4.7 68.0 0.8
O3G B:ANP700 4.8 71.5 0.0
CE2 B:TRP600 4.8 49.5 1.0
CD B:GLU236 4.8 69.4 1.0
O2A B:ANP700 4.8 71.2 0.8
CG2 B:THR188 4.8 45.5 1.0
CB B:THR188 4.9 48.1 1.0
CA B:GLY72 4.9 41.3 1.0
CZ B:ARG77 4.9 81.1 1.0

Reference:

U.Krug, R.Totzauer, M.Zebisch, N.Strater. The Atp/Adp Substrate Specificity Switch Between Toxoplasma Gondii NTPDASE1 and NTPDASE3 Is Caused By An Altered Mode of Binding of the Substrate Base. Chembiochem V. 14 2292 2013.
ISSN: ISSN 1439-4227
PubMed: 24115522
DOI: 10.1002/CBIC.201300441
Page generated: Mon Dec 14 19:02:55 2020

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