Calcium in PDB 3i98: X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens

The structure of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens, PDB code: 3i98 was solved by R.C.Hughes, L.Coates, E.J.Meehan, J.D.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.21 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.112, 95.464, 113.677, 90.00, 98.12, 90.00
R / Rfree (%)	14.8 / 18.4

The binding sites of Calcium atom in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens (pdb code 3i98). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens, PDB code: 3i98:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca627 b:26.3 occ:1.00 OD1 A:ASP103 2.2 27.8 1.0 O A:HOH193 2.3 23.8 1.0 O A:HOH274 2.3 34.0 1.0 OD2 A:ASP71 2.4 16.9 0.3 O A:HOH207 2.4 27.8 1.0 OD1 A:ASP71 2.4 21.9 0.7 OD2 A:ASP66 2.5 28.1 1.0 CG A:ASP71 3.2 23.5 0.7 CG A:ASP103 3.4 29.4 1.0 CG A:ASP66 3.5 38.7 1.0 OD1 A:ASP71 3.5 23.9 0.3 OD2 A:ASP71 3.6 23.4 0.7 OD1 A:ASP66 3.7 26.4 1.0 CA A:ASP103 4.2 22.0 1.0 NZ A:LYS105 4.2 18.0 1.0 OD2 A:ASP103 4.3 32.5 1.0 O A:HOH191 4.3 27.9 1.0 CB A:ASP103 4.3 21.1 1.0 O A:PRO69 4.4 19.2 1.0 CB A:ASP71 4.4 13.8 0.7 C A:ASP103 4.5 15.2 1.0 CB A:ASP71 4.5 14.2 0.3 O A:TRP104 4.6 14.3 1.0 O A:ASP103 4.7 18.4 1.0 N A:ASP71 4.7 11.9 0.3 N A:ASP71 4.8 11.8 0.7 CB A:ASP66 4.8 28.0 1.0 O A:HOH435 4.9 44.5 1.0 CB A:ASP68 4.9 25.6 1.0

Calcium binding site 2 out of 6 in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca622 b:23.4 occ:1.00 OD1 B:ASP103 2.2 22.1 1.0 O B:HOH629 2.3 27.6 1.0 O B:HOH187 2.3 19.7 1.0 OD2 B:ASP66 2.4 25.5 1.0 O B:HOH216 2.5 27.2 1.0 OD2 B:ASP71 2.5 20.6 0.6 OD1 B:ASP71 2.6 26.6 0.6 CG B:ASP71 2.9 12.0 0.6 OD2 B:ASP71 2.9 22.6 0.4 CG B:ASP66 3.4 32.7 1.0 CG B:ASP103 3.4 25.7 1.0 CG B:ASP71 3.6 20.1 0.4 OD1 B:ASP66 3.7 21.7 1.0 OD1 B:ASP71 4.1 14.5 0.4 CA B:ASP103 4.2 15.8 1.0 O B:HOH259 4.2 38.5 1.0 O B:HOH209 4.2 24.0 1.0 NZ B:LYS105 4.3 21.5 1.0 OD2 B:ASP103 4.3 24.8 1.0 CB B:ASP103 4.3 19.1 1.0 O B:PRO69 4.4 19.7 1.0 CB B:ASP71 4.4 14.0 0.6 CB B:ASP71 4.4 14.0 0.4 O B:TRP104 4.5 14.9 1.0 C B:ASP103 4.5 13.2 1.0 N B:ASP71 4.7 12.5 1.0 CB B:ASP66 4.8 22.0 1.0 CB B:ASP68 4.8 22.5 1.0 O B:ASP103 4.8 19.4 1.0

Calcium binding site 3 out of 6 in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca623 b:32.1 occ:1.00 O C:HOH400 2.2 33.4 1.0 OD1 C:ASP103 2.3 32.7 1.0 O C:HOH243 2.3 33.5 1.0 O C:HOH196 2.4 22.9 1.0 OD2 C:ASP66 2.5 27.8 1.0 OD2 C:ASP71 2.5 38.1 1.0 CG C:ASP71 3.4 37.3 1.0 CG C:ASP66 3.4 39.8 1.0 CG C:ASP103 3.5 36.3 1.0 OD1 C:ASP66 3.7 31.9 1.0 OD1 C:ASP71 3.9 32.4 1.0 O C:HOH587 4.1 45.2 1.0 NZ C:LYS105 4.2 27.3 1.0 CA C:ASP103 4.2 26.4 1.0 OD2 C:ASP103 4.3 32.2 1.0 O C:HOH184 4.3 32.9 1.0 O C:PRO69 4.4 21.2 1.0 CB C:ASP103 4.4 22.5 1.0 C C:ASP103 4.5 26.0 1.0 CB C:ASP71 4.5 20.2 1.0 O C:TRP104 4.5 16.4 1.0 O C:ASP103 4.7 23.4 1.0 N C:ASP71 4.8 9.8 1.0 CB C:ASP66 4.8 39.7 1.0 CB C:ASP68 4.8 33.1 1.0

Calcium binding site 4 out of 6 in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca624 b:44.0 occ:1.00 O D:HOH562 2.2 44.8 1.0 OD1 D:ASP103 2.3 30.9 1.0 O D:HOH205 2.5 28.1 1.0 OD2 D:ASP66 2.6 31.2 1.0 O D:HOH226 2.6 33.4 1.0 OD2 D:ASP71 2.7 45.4 1.0 CG D:ASP103 3.5 39.2 1.0 CG D:ASP71 3.5 35.3 1.0 CG D:ASP66 3.6 42.5 1.0 OD1 D:ASP66 3.9 41.1 1.0 OD1 D:ASP71 4.0 28.6 1.0 O D:HOH195 4.1 33.2 1.0 NZ D:LYS105 4.2 25.4 1.0 CA D:ASP103 4.2 28.4 1.0 O D:HOH479 4.3 50.4 1.0 OD2 D:ASP103 4.3 38.9 1.0 O D:PRO69 4.4 22.0 1.0 CB D:ASP103 4.4 25.2 1.0 C D:ASP103 4.5 22.3 1.0 CB D:ASP71 4.5 19.6 1.0 O D:TRP104 4.6 17.2 1.0 CB D:ASP68 4.6 37.0 1.0 O D:ASP103 4.7 27.0 1.0 N D:ASP71 4.9 12.6 1.0 CB D:ASP66 4.9 37.3 1.0

Calcium binding site 5 out of 6 in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca625 b:35.1 occ:1.00 OD1 E:ASP103 2.3 29.6 1.0 O E:HOH388 2.4 44.0 1.0 O E:HOH196 2.4 23.0 1.0 OD2 E:ASP66 2.5 39.5 1.0 OD2 E:ASP71 2.5 34.0 1.0 O E:HOH312 2.5 35.9 1.0 CG E:ASP66 3.4 50.2 1.0 CG E:ASP71 3.4 36.9 1.0 CG E:ASP103 3.5 40.0 1.0 OD1 E:ASP66 3.7 37.1 1.0 OD1 E:ASP71 3.9 33.7 1.0 NZ E:LYS105 4.2 26.7 1.0 O E:HOH224 4.2 29.1 1.0 OD2 E:ASP103 4.3 37.2 1.0 CA E:ASP103 4.3 29.2 1.0 O E:PRO69 4.4 23.4 1.0 CB E:ASP103 4.5 26.3 1.0 CB E:ASP71 4.6 22.8 1.0 C E:ASP103 4.7 19.6 1.0 CB E:ASP68 4.7 35.9 1.0 O E:TRP104 4.7 16.4 1.0 CB E:ASP66 4.8 46.6 1.0 O E:ASP103 4.8 23.8 1.0 O E:HOH638 4.8 43.1 1.0 N E:ASP71 4.9 16.4 1.0

Calcium binding site 6 out of 6 in the X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca626 b:32.9 occ:1.00 O F:HOH304 2.2 34.4 1.0 OD1 F:ASP103 2.2 31.1 1.0 OD2 F:ASP66 2.4 35.1 1.0 O F:HOH229 2.5 33.5 1.0 O F:HOH199 2.5 30.7 1.0 OD2 F:ASP71 2.5 35.8 1.0 CG F:ASP71 3.3 31.2 1.0 CG F:ASP66 3.4 42.0 1.0 CG F:ASP103 3.5 43.0 1.0 OD1 F:ASP71 3.7 38.2 1.0 OD1 F:ASP66 3.7 38.4 1.0 NZ F:LYS105 4.2 24.4 1.0 CA F:ASP103 4.2 24.7 1.0 O F:HOH323 4.2 33.2 1.0 OD2 F:ASP103 4.3 39.9 1.0 CB F:ASP103 4.4 30.6 1.0 O F:PRO69 4.4 24.3 1.0 CB F:ASP71 4.5 15.7 1.0 C F:ASP103 4.6 21.1 1.0 O F:TRP104 4.7 19.7 1.0 CB F:ASP66 4.7 35.3 1.0 CB F:ASP68 4.8 38.8 1.0 O F:ASP103 4.8 25.2 1.0 O F:HOH332 4.9 37.6 1.0 N F:ASP71 4.9 16.4 1.0

R.C.Hughes, L.Coates, E.J.Meehan, J.D.Ng. X-Ray Crystallographic Structure of Inorganic Pyrophosphatase at 298K From Archaeon Thermococcus Thioreducens To Be Published.