Fluorine 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:

Magnesium	(Mg)	10 atoms
Calcium	(Ca)	1 atom

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form, PDB code: 6ll8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 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 Fluorine with other atoms in the F 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:F411 b:7.4 occ:1.00 MG A:MG401 2.0 6.6 1.0 MG A:MG402 2.0 7.3 1.0 MG A:MG404 2.2 10.4 1.0 O1 A:2PN407 2.7 8.0 1.0 O3 A:2PN407 2.8 8.0 1.0 OD2 A:ASP72 2.8 7.3 1.0 OD2 A:ASP12 2.8 7.9 1.0 P1 A:2PN407 2.9 7.6 1.0 CB A:ASP14 2.9 7.3 1.0 OD2 A:ASP146 3.0 8.7 1.0 OD1 A:ASP72 3.0 8.1 1.0 OD1 A:ASP146 3.1 11.5 1.0 O2 A:2PN407 3.1 7.9 1.0 OD2 A:ASP14 3.1 8.3 1.0 OD1 A:ASP12 3.2 7.8 1.0 CG A:ASP72 3.2 7.5 1.0 CG A:ASP12 3.3 7.5 1.0 CG A:ASP146 3.4 9.8 1.0 CG A:ASP14 3.5 8.9 1.0 O A:HOH574 3.6 11.3 1.0 CA A:ASP14 4.2 7.7 1.0 NE2 A:HIS8 4.2 7.1 1.0 NE2 A:HIS94 4.2 7.1 1.0 N A:ASP14 4.4 7.7 1.0 N1 A:2PN407 4.5 7.3 1.0 O A:HOH735 4.5 10.8 1.0 N A:SER15 4.6 7.6 1.0 O A:HOH800 4.6 10.4 1.0 CB A:ASP72 4.7 7.5 1.0 CB A:ASP12 4.7 7.7 1.0 O A:HOH596 4.7 9.1 1.0 OD1 A:ASP14 4.7 10.4 1.0 C A:ASP14 4.7 7.5 1.0 MG A:MG403 4.8 8.2 1.0 CB A:ASP146 4.9 9.4 1.0 CE1 A:HIS94 4.9 6.8 1.0

Fluorine binding site 2 out of 2 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 Fluorine with other atoms in the F binding site number 2 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 B:F410 b:8.1 occ:1.00 MG B:MG401 2.0 7.1 1.0 MG B:MG402 2.0 7.9 1.0 MG B:MG404 2.2 10.7 1.0 O2 B:2PN406 2.7 8.4 1.0 O3 B:2PN406 2.8 8.7 1.0 OD2 B:ASP72 2.8 8.1 1.0 OD2 B:ASP12 2.8 8.6 1.0 P1 B:2PN406 2.9 8.1 1.0 CB B:ASP14 2.9 8.7 1.0 OD2 B:ASP146 3.0 9.3 1.0 OD1 B:ASP72 3.0 8.5 1.0 OD1 B:ASP146 3.1 12.3 1.0 O1 B:2PN406 3.1 8.3 1.0 OD2 B:ASP14 3.1 8.6 1.0 OD1 B:ASP12 3.1 8.2 1.0 CG B:ASP72 3.2 7.8 1.0 CG B:ASP12 3.3 8.0 1.0 CG B:ASP146 3.4 9.7 1.0 CG B:ASP14 3.5 8.9 1.0 O B:HOH561 3.6 11.8 1.0 CA B:ASP14 4.2 8.5 1.0 NE2 B:HIS8 4.2 8.1 1.0 NE2 B:HIS94 4.2 7.2 1.0 N B:ASP14 4.4 8.3 1.0 O B:HOH714 4.5 11.2 1.0 N1 B:2PN406 4.5 7.6 1.0 N B:SER15 4.6 8.2 1.0 O B:HOH790 4.6 11.2 1.0 CB B:ASP72 4.7 7.9 1.0 CB B:ASP12 4.7 8.0 1.0 O B:HOH584 4.7 9.5 1.0 OD1 B:ASP14 4.7 10.6 1.0 C B:ASP14 4.8 8.2 1.0 MG B:MG403 4.8 8.8 1.0 CB B:ASP146 4.9 9.5 1.0 CE1 B:HIS94 4.9 7.4 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