Calcium in PDB 6ll8: Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form

The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form, PDB code: 6ll8 was solved by M.Horitani, K.Kusubayashi, K.Oshima, A.Yato, H.Sugimoto, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.57 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.490, 78.980, 75.300, 90.00, 98.59, 90.00
R / Rfree (%)	9.7 / 12.2

The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	10 atoms

The binding sites of Calcium atom in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form (pdb code 6ll8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form, PDB code: 6ll8:

Calcium binding site 1 out of 1 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:7.0 occ:0.50 O B:GLY98 2.7 10.0 1.0 O A:GLY98 2.7 10.3 1.0 O A:LEU100 2.7 9.3 1.0 O B:LEU100 2.7 9.6 1.0 O B:HOH854 2.9 15.1 1.0 C B:GLY98 3.9 9.3 1.0 C A:GLY98 3.9 8.8 1.0 C A:LEU100 3.9 8.8 1.0 C B:LEU100 3.9 8.8 1.0 CA B:ASP99 4.0 9.7 1.0 CA A:ASP99 4.0 9.3 1.0 C B:ASP99 4.1 9.7 1.0 C A:ASP99 4.1 9.4 1.0 CG2 A:THR101 4.2 11.0 1.0 CG2 B:THR101 4.3 11.3 1.0 CG B:LEU97 4.3 10.8 1.0 CG A:LEU97 4.3 10.9 1.0 N B:LEU100 4.3 8.9 1.0 N A:LEU100 4.3 9.0 1.0 N B:ASP99 4.4 9.3 1.0 N A:ASP99 4.4 9.0 1.0 O B:ASP99 4.5 10.9 1.0 O A:ASP99 4.5 11.0 1.0 CD1 B:LEU97 4.5 14.5 1.0 CD2 B:LEU97 4.5 11.7 1.0 CD1 A:LEU97 4.5 14.0 1.0 CD2 A:LEU97 4.6 12.0 1.0 CA A:LEU100 4.8 9.3 1.0 CA B:LEU100 4.8 9.0 1.0 N A:THR101 4.9 9.2 1.0 N B:THR101 4.9 9.2 1.0

M.Horitani, K.Kusubayashi, K.Oshima, A.Yato, H.Sugimoto, K.Watanabe. X-Ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase. Sci Rep V. 10 4368 2020.
ISSN: ESSN 2045-2322
PubMed: 32152422
DOI: 10.1038/S41598-020-61217-6