Magnesium in PDB 4kh5: Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Ampnp

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

The structure of Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Ampnp, PDB code: 4kh5 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)	38.93 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.537, 150.250, 240.967, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.3

The binding sites of Magnesium atom in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Ampnp (pdb code 4kh5). 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 Ampnp, PDB code: 4kh5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Ampnp


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 Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:10.0 occ:1.00 O3B A:AU1700 2.2 55.4 0.8 O5' A:AU1700 2.5 53.7 0.8 PB A:AU1700 3.3 54.8 0.8 NE1 A:TRP600 3.6 20.9 1.0 PA A:AU1700 3.6 53.6 0.8 N3A A:AU1700 3.6 54.1 0.8 O2B A:AU1700 3.7 54.4 0.8 OG1 A:THR188 3.8 29.3 1.0 OD1 A:ASP70 3.9 22.8 1.0 OE2 A:GLU236 4.0 38.4 1.0 OD2 A:ASP70 4.2 28.2 1.0 CD1 A:TRP600 4.2 21.6 1.0 O2A A:AU1700 4.3 53.2 0.8 NH2 A:ARG77 4.3 52.6 1.0 CG2 A:THR188 4.4 26.8 1.0 CB A:THR188 4.4 28.9 1.0 CG A:ASP70 4.5 22.7 1.0 O1B A:AU1700 4.7 54.3 0.8 CD A:GLU236 4.8 42.6 1.0 CE2 A:TRP600 4.8 21.8 1.0 NH1 A:ARG77 4.9 52.4 1.0 O1A A:AU1700 4.9 53.8 0.8

Magnesium binding site 2 out of 2 in the Toxoplasma Gondii NTPDASE1 C258S/C268S in Complex with Mg and Ampnp


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 Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:10.4 occ:1.00 O2A B:AU1700 2.2 59.9 0.0 O2A B:AU1700 2.2 47.7 0.8 O2B B:AU1700 2.5 50.2 0.8 O2B B:AU1700 2.5 59.9 0.0 OG1 B:THR188 3.2 34.9 1.0 OD1 B:ASP70 3.3 34.3 1.0 NE1 B:TRP600 3.3 24.1 1.0 PA B:AU1700 3.5 59.9 0.0 PA B:AU1700 3.6 47.4 0.8 PB B:AU1700 3.6 59.9 0.0 NH2 B:ARG77 3.7 53.3 1.0 PB B:AU1700 3.7 49.4 0.8 OE2 B:GLU236 3.8 57.0 1.0 O1B B:AU1700 3.9 59.9 0.0 CG2 B:THR188 4.0 30.8 1.0 OD2 B:ASP70 4.0 40.9 1.0 CB B:THR188 4.0 33.2 1.0 N3A B:AU1700 4.0 59.9 0.0 CG B:ASP70 4.0 33.5 1.0 N3A B:AU1700 4.1 48.4 0.8 O1B B:AU1700 4.1 49.2 0.8 CD1 B:TRP600 4.2 24.7 1.0 O5' B:AU1700 4.2 59.9 0.0 CA B:GLY72 4.2 18.7 1.0 CE2 B:TRP600 4.4 24.9 1.0 O5' B:AU1700 4.5 47.7 0.8 O1A B:AU1700 4.6 46.9 0.8 CD B:GLU236 4.7 57.5 1.0 O1A B:AU1700 4.7 59.9 0.0 CZ2 B:TRP600 4.8 24.1 1.0 CZ B:ARG77 4.8 68.2 1.0 O3B B:AU1700 4.9 59.9 0.0 N B:GLY72 4.9 18.5 1.0 O3B B:AU1700 5.0 49.4 0.8

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