Calcium in PDB 6ll7: Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form

The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form, PDB code: 6ll7 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)	47.51 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.530, 75.570, 85.670, 107.40, 90.06, 92.17
R / Rfree (%)	25.6 / 29.7

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

Manganese

(Mn)

8 atoms

The binding sites of Calcium atom in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form (pdb code 6ll7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form, PDB code: 6ll7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated 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, Mn-Activated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:33.9 occ:1.00 O B:LEU100 2.6 31.7 1.0 O B:HOH561 2.6 24.8 1.0 O B:GLY98 2.8 32.5 1.0 O A:LEU100 2.8 32.0 1.0 O A:GLY98 2.8 35.9 1.0 C B:LEU100 3.9 32.5 1.0 C B:GLY98 3.9 32.6 1.0 C A:GLY98 4.0 35.5 1.0 C B:ASP99 4.0 34.4 1.0 C A:LEU100 4.0 32.0 1.0 CA B:ASP99 4.1 34.2 1.0 CG2 A:THR101 4.1 32.6 1.0 N B:LEU100 4.2 33.6 1.0 CA A:ASP99 4.2 35.1 1.0 C A:ASP99 4.2 33.7 1.0 CG2 B:THR101 4.3 33.4 1.0 CG A:LEU97 4.3 31.4 1.0 CG B:LEU97 4.3 32.8 1.0 N A:LEU100 4.4 32.5 1.0 CD2 A:LEU97 4.4 31.5 1.0 N B:ASP99 4.4 33.0 1.0 O B:ASP99 4.4 34.8 1.0 N A:ASP99 4.5 35.5 1.0 CD1 B:LEU97 4.5 32.6 1.0 O A:ASP99 4.6 34.2 1.0 CD2 B:LEU97 4.6 33.0 1.0 CD1 A:LEU97 4.6 31.2 1.0 CA B:LEU100 4.7 33.0 1.0 N B:THR101 4.8 32.0 1.0 CA A:LEU100 4.9 31.6 1.0 N A:THR101 5.0 31.9 1.0

Calcium binding site 2 out of 2 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:30.7 occ:1.00 O C:LEU100 2.5 28.5 1.0 O C:HOH561 2.5 24.7 1.0 O D:GLY98 2.8 34.0 1.0 O C:GLY98 2.8 32.6 1.0 O D:LEU100 3.0 29.3 1.0 C C:LEU100 3.7 29.2 1.0 C D:GLY98 3.9 33.9 1.0 C C:GLY98 3.9 32.3 1.0 C C:ASP99 4.0 30.6 1.0 CA C:ASP99 4.1 31.4 1.0 CG D:LEU97 4.1 37.1 1.0 CG2 C:THR101 4.1 29.5 1.0 N C:LEU100 4.1 29.7 1.0 C D:LEU100 4.2 30.1 1.0 CA D:ASP99 4.3 34.1 1.0 O C:ASP99 4.4 30.7 1.0 C D:ASP99 4.4 32.5 1.0 CG C:LEU97 4.4 32.6 1.0 CD1 D:LEU97 4.4 37.7 1.0 N C:ASP99 4.4 31.4 1.0 CD2 D:LEU97 4.5 36.9 1.0 N D:LEU100 4.5 31.8 1.0 CD2 C:LEU97 4.5 33.0 1.0 N D:ASP99 4.5 33.7 1.0 CA C:LEU100 4.6 29.2 1.0 CG2 D:THR101 4.6 29.0 1.0 N C:THR101 4.6 28.4 1.0 CD1 C:LEU97 4.7 32.5 1.0 O D:ASP99 4.8 30.7 1.0 CA C:THR101 4.9 28.8 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