Magnesium in PDB 5wrt: Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii.

The structure of Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii., PDB code: 5wrt was solved by A.Jamwal, M.Yogavel, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.60 / 2.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.957, 88.957, 158.665, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.2

The binding sites of Magnesium atom in the Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii. (pdb code 5wrt). 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 Type I Inorganic Pyrophosphatase From Toxoplasma Gondii., PDB code: 5wrt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii.


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 Type I Inorganic Pyrophosphatase From Toxoplasma Gondii. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:24.4 occ:1.00 OD1 A:ASP227 2.0 25.0 1.0 OD2 A:ASP195 2.0 22.9 1.0 O A:HOH523 2.1 21.8 1.0 OD1 A:ASP190 2.1 26.7 1.0 O A:HOH502 2.2 25.6 1.0 O A:HOH545 2.3 21.5 1.0 CG A:ASP195 3.0 22.1 1.0 CG A:ASP227 3.1 23.8 1.0 CG A:ASP190 3.2 28.4 1.0 OD1 A:ASP195 3.6 22.1 1.0 OD2 A:ASP227 3.8 22.4 1.0 O A:HOH585 3.8 23.4 1.0 NZ A:LYS229 3.9 22.4 1.0 CB A:ASP190 4.0 30.2 1.0 O A:HOH507 4.0 23.7 1.0 CB A:ASP195 4.1 21.9 1.0 CB A:ASP227 4.1 25.3 1.0 OD2 A:ASP190 4.1 30.7 1.0 CA A:ASP227 4.1 25.1 1.0 O A:TRP228 4.2 21.4 1.0 O A:HOH622 4.3 24.4 1.0 O A:PRO193 4.4 23.7 1.0 N A:ASP195 4.4 20.6 1.0 C A:ASP227 4.5 22.8 1.0 N A:TRP228 4.7 22.8 1.0 CB A:ASP192 4.9 28.4 1.0 O A:HOH530 4.9 24.2 1.0 CA A:ASP195 4.9 21.2 1.0 MG A:MG402 4.9 23.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii.


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 Type I Inorganic Pyrophosphatase From Toxoplasma Gondii. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.4 occ:1.00 O A:HOH578 2.0 25.7 1.0 O A:HOH585 2.0 23.4 1.0 O A:HOH605 2.1 27.2 1.0 O A:HOH549 2.1 23.5 1.0 OD1 A:ASP195 2.1 22.1 1.0 O A:HOH530 2.2 24.2 1.0 CG A:ASP195 3.2 22.1 1.0 OD2 A:ASP195 3.8 22.9 1.0 O A:HOH528 3.8 27.4 1.0 OE1 A:GLU125 3.9 25.5 1.0 OH A:TYR166 4.1 22.6 1.0 O A:HOH622 4.1 24.4 1.0 O A:PRO193 4.2 23.7 1.0 O A:HOH502 4.2 25.6 1.0 O A:HOH539 4.3 31.5 1.0 O A:HOH531 4.3 28.9 1.0 CB A:ASP195 4.4 21.9 1.0 O A:HOH523 4.4 21.8 1.0 O A:HOH557 4.5 25.6 1.0 CE2 A:TYR166 4.5 23.1 1.0 O A:GLY167 4.5 22.4 1.0 OD2 A:ASP192 4.6 29.8 1.0 CZ A:TYR166 4.6 23.2 1.0 CB A:ALA168 4.8 23.4 1.0 CA A:ASP195 4.8 21.2 1.0 CD A:GLU125 4.9 26.1 1.0 OE2 A:GLU135 4.9 34.4 1.0 MG A:MG401 4.9 24.4 1.0 CB A:ASP192 5.0 28.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii.


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 Type I Inorganic Pyrophosphatase From Toxoplasma Gondii. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:29.8 occ:1.00 O B:HOH534 2.0 29.8 1.0 O B:HOH565 2.0 34.7 1.0 OD1 B:ASP195 2.1 33.0 1.0 O B:HOH521 2.1 31.6 1.0 O B:HOH568 2.1 31.5 1.0 O B:HOH541 2.3 30.9 1.0 CG B:ASP195 3.1 29.8 1.0 OD2 B:ASP195 3.6 30.6 1.0 OH B:TYR166 3.7 27.4 1.0 O B:HOH514 3.7 36.0 1.0 O B:HOH587 3.9 40.5 1.0 O B:HOH509 3.9 31.5 1.0 OE1 B:GLU125 4.1 31.5 1.0 O B:HOH585 4.2 31.1 1.0 CB B:ASP195 4.3 30.0 1.0 CE2 B:TYR166 4.3 28.1 1.0 CZ B:TYR166 4.3 28.5 1.0 O B:PRO193 4.4 33.2 1.0 O B:HOH547 4.5 28.6 1.0 O B:HOH515 4.5 35.9 1.0 O B:GLY167 4.6 30.6 1.0 OD1 B:ASP192 4.7 39.8 1.0 MG B:MG402 4.7 37.0 1.0 CA B:ASP195 4.8 30.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Type I Inorganic Pyrophosphatase From Toxoplasma Gondii.


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 Type I Inorganic Pyrophosphatase From Toxoplasma Gondii. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:37.0 occ:1.00 OD2 B:ASP190 1.9 43.3 1.0 OD1 B:ASP227 2.0 38.0 1.0 OD2 B:ASP195 2.0 30.6 1.0 O B:HOH514 2.0 36.0 1.0 O B:HOH515 2.2 35.9 1.0 O B:HOH546 2.4 36.5 1.0 CG B:ASP195 3.0 29.8 1.0 CG B:ASP227 3.1 36.8 1.0 CG B:ASP190 3.1 46.1 1.0 OD1 B:ASP195 3.6 33.0 1.0 OD2 B:ASP227 3.7 34.6 1.0 O B:HOH565 3.7 34.7 1.0 OD1 B:ASP190 3.7 45.4 1.0 NZ B:LYS229 3.8 33.9 1.0 CB B:ASP195 4.0 30.0 1.0 CB B:ASP227 4.1 38.7 1.0 CB B:ASP190 4.2 46.9 1.0 CA B:ASP227 4.2 39.0 1.0 O B:TRP228 4.3 34.2 1.0 O B:PRO193 4.4 33.2 1.0 N B:ASP195 4.5 31.2 1.0 O B:HOH585 4.5 31.1 1.0 C B:ASP227 4.6 37.7 1.0 MG B:MG401 4.7 29.8 1.0 N B:TRP228 4.8 36.3 1.0 CB B:ASP192 4.8 39.9 1.0 O B:HOH541 4.9 30.9 1.0 CA B:ASP195 4.9 30.9 1.0 CE B:LYS229 4.9 31.7 1.0 O B:HOH516 5.0 36.0 1.0

A.Jamwal, M.Yogavel, M.Z.Abdin, S.K.Jain, A.Sharma. Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases Sci Rep V. 7 5255 2017.
ISSN: ESSN 2045-2322
PubMed: 28701714
DOI: 10.1038/S41598-017-05234-Y