Magnesium in PDB 8qpt: Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha

The structure of Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha, PDB code: 8qpt was solved by I.O.Matyuta, E.V.Rodina, N.N.Vorobyeva, S.A.Kurilova, E.Y.Bezpalaya, K.M.Boyko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.724, 83.035, 64.975, 90, 96.89, 90
R / Rfree (%)	17 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha (pdb code 8qpt). 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 Pyrophosphatase From Ogataea Parapolymorpha, PDB code: 8qpt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha


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 Pyrophosphatase From Ogataea Parapolymorpha within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:17.8 occ:1.00 OD2 A:ASP124 2.0 17.8 1.0 OD1 A:ASP161 2.0 19.3 1.0 O A:HOH442 2.0 16.0 1.0 O A:HOH508 2.1 20.6 1.0 OD2 A:ASP129 2.1 16.9 1.0 O A:HOH436 2.1 15.2 1.0 CG A:ASP129 3.0 20.4 1.0 CG A:ASP124 3.0 16.1 1.0 CG A:ASP161 3.1 20.5 1.0 OD1 A:ASP124 3.6 17.1 1.0 OD1 A:ASP129 3.8 20.9 1.0 OD2 A:ASP161 3.9 21.1 1.0 O A:HOH560 3.9 29.5 1.0 CB A:ASP129 4.0 16.1 1.0 CA A:ASP161 4.0 18.2 1.0 OE2 A:GLU108 4.0 20.8 1.0 CB A:ASP161 4.1 19.3 1.0 NZ A:LYS163 4.1 17.0 1.0 O A:TRP162 4.1 13.5 1.0 O A:HOH460 4.2 28.5 1.0 CB A:ASP124 4.3 18.7 1.0 C A:ASP161 4.3 17.0 1.0 O A:HOH532 4.3 34.6 1.0 O A:PRO127 4.4 17.2 1.0 N A:ASP129 4.4 13.9 1.0 N A:TRP162 4.5 14.7 1.0 CD A:GLU108 4.6 22.8 1.0 MG A:MG303 4.8 18.1 0.6 O A:HOH478 4.8 29.8 1.0 CE A:LYS163 4.8 15.2 1.0 CA A:ASP129 4.9 13.0 1.0 O A:ASP161 4.9 16.4 1.0 O A:HOH465 4.9 25.5 1.0 CB A:ASP126 4.9 18.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha


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 Pyrophosphatase From Ogataea Parapolymorpha within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:18.1 occ:0.60 OD1 A:ASP129 2.0 20.9 1.0 O A:HOH465 2.0 25.5 1.0 O A:HOH560 2.0 29.5 1.0 O A:HOH478 2.0 29.8 1.0 O A:HOH572 2.0 24.7 1.0 O A:HOH405 2.1 13.9 1.0 CG A:ASP129 3.1 20.4 1.0 OD2 A:ASP129 3.6 16.9 1.0 O A:HOH504 3.8 16.8 1.0 O A:HOH493 4.1 41.4 1.0 OE1 A:GLU55 4.1 17.6 1.0 O A:PRO127 4.2 17.2 1.0 O A:HOH508 4.3 20.6 1.0 CB A:ASP129 4.3 16.1 1.0 O A:HOH436 4.4 15.2 1.0 OE2 A:GLU55 4.4 16.0 1.0 O A:GLY101 4.6 12.1 1.0 CA A:ASP129 4.6 13.0 1.0 O A:HOH439 4.6 25.8 1.0 CD A:GLU55 4.7 17.3 1.0 O A:HOH438 4.7 31.2 1.0 CB A:ASP126 4.8 18.5 1.0 MG A:MG302 4.8 17.8 1.0 OD2 A:ASP126 4.8 30.5 1.0 O A:HOH564 4.9 29.8 1.0 N A:ASP129 4.9 13.9 1.0 O A:HOH532 4.9 34.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha


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 Pyrophosphatase From Ogataea Parapolymorpha within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:15.2 occ:0.70 O B:HOH574 2.0 22.2 1.0 OD1 B:ASP129 2.0 19.7 1.0 O B:HOH534 2.0 24.3 1.0 O B:HOH507 2.0 22.6 1.0 O B:HOH403 2.1 13.8 1.0 O B:HOH498 2.1 24.2 1.0 CG B:ASP129 3.2 18.9 1.0 OD2 B:ASP129 3.7 18.0 1.0 O B:HOH447 3.8 14.2 1.0 OE1 B:GLU55 4.1 15.9 1.0 O B:PRO127 4.3 16.0 1.0 O B:HOH463 4.3 19.1 1.0 CB B:ASP129 4.3 16.4 1.0 O B:HOH567 4.4 29.3 1.0 O B:HOH446 4.6 18.6 1.0 OE2 B:GLU55 4.6 16.6 1.0 O B:HOH483 4.6 24.9 1.0 O B:GLY101 4.6 12.8 1.0 OD2 B:ASP126 4.7 27.3 1.0 CA B:ASP129 4.7 14.7 1.0 O B:HOH462 4.7 27.7 1.0 CB B:ASP126 4.8 16.6 1.0 CD B:GLU55 4.8 14.4 1.0 O B:HOH562 4.8 26.8 1.0 O B:HOH546 4.9 20.3 1.0 MG B:MG303 4.9 22.0 1.0 CG B:ASP126 5.0 23.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Pyrophosphatase From Ogataea Parapolymorpha


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 Pyrophosphatase From Ogataea Parapolymorpha within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:22.0 occ:1.00 O B:HOH407 2.0 18.7 1.0 O B:HOH463 2.0 19.1 1.0 OD1 B:ASP161 2.0 20.8 1.0 O B:HOH446 2.0 18.6 1.0 OD2 B:ASP129 2.1 18.0 1.0 OD2 B:ASP124 2.1 25.7 1.0 CG B:ASP129 3.1 18.9 1.0 CG B:ASP124 3.1 22.8 1.0 CG B:ASP161 3.1 23.4 1.0 OD1 B:ASP124 3.6 19.9 1.0 OD1 B:ASP129 3.8 19.7 1.0 O B:HOH534 3.9 24.3 1.0 OD2 B:ASP161 3.9 22.0 1.0 NZ B:LYS163 4.0 18.2 1.0 O B:TRP162 4.0 20.2 1.0 CA B:ASP161 4.0 23.8 1.0 CB B:ASP129 4.0 16.4 1.0 CB B:ASP161 4.1 22.7 1.0 OE2 B:GLU108 4.1 20.1 1.0 O B:HOH467 4.2 29.0 1.0 C B:ASP161 4.3 23.0 1.0 CB B:ASP124 4.3 23.5 1.0 O B:PRO127 4.4 16.0 1.0 N B:ASP129 4.4 15.3 1.0 CD B:GLU108 4.4 27.9 1.0 N B:TRP162 4.4 22.0 1.0 O B:HOH567 4.5 29.3 1.0 CE B:LYS163 4.8 15.7 1.0 OE1 B:GLU108 4.8 23.1 1.0 CA B:ASP129 4.9 14.7 1.0 MG B:MG302 4.9 15.2 0.7 O B:ASP161 4.9 19.9 1.0 CB B:ASP126 5.0 16.6 1.0

E.Y.Bezpalaya, I.O.Matyuta, N.N.Vorobyeva, S.A.Kurilova, S.D.Oreshkov, M.E.Minyaev, K.M.Boyko, E.V.Rodina. The Crystal Structure of Yeast Mitochondrial Type Pyrophosphatase Provides A Model to Study Pathological Mutations in Its Human Ortholog. Biochem.Biophys.Res.Commun. V. 738 50563 2024.
ISSN: ESSN 1090-2104
PubMed: 39178581
DOI: 10.1016/J.BBRC.2024.150563