Calcium in PDB 3r5v: The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K

The structure of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K, PDB code: 3r5v was solved by R.C.Hughes, E.J.Meehan, L.Coates, J.D.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.24 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.092, 95.564, 113.769, 90.00, 98.10, 90.00
R / Rfree (%)	12.2 / 16.3

The binding sites of Calcium atom in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K (pdb code 3r5v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K, PDB code: 3r5v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:23.6 occ:0.89 OD1 A:ASP103 2.3 25.8 1.0 O A:HOH312 2.3 21.5 1.0 OD2 A:ASP66 2.4 26.8 1.0 O A:HOH337 2.4 35.8 1.0 OD1 A:ASP71 2.4 30.1 0.6 OD1 A:ASP71 2.4 34.3 0.4 O A:HOH323 2.4 26.7 0.9 OD2 A:ASP71 2.7 36.2 0.4 CG A:ASP71 2.9 29.6 0.4 CG A:ASP71 3.3 28.1 0.6 CG A:ASP66 3.4 31.0 1.0 CG A:ASP103 3.5 24.9 1.0 OD1 A:ASP66 3.7 31.4 1.0 OD2 A:ASP71 3.8 27.7 0.6 NZ A:LYS105 4.0 23.8 1.0 O A:HOH360 4.1 45.0 1.0 CA A:ASP103 4.2 19.3 1.0 O A:HOH391 4.2 54.7 1.0 OD2 A:ASP103 4.2 27.1 1.0 O A:HOH311 4.3 31.3 0.9 CB A:ASP103 4.3 21.6 1.0 CB A:ASP71 4.4 20.4 0.6 CB A:ASP71 4.4 20.6 0.4 O A:PRO69 4.4 19.1 1.0 O A:TRP104 4.5 18.4 1.0 C A:ASP103 4.5 16.3 1.0 CB A:ASP66 4.7 32.2 1.0 N A:ASP71 4.7 13.1 0.4 N A:ASP71 4.7 13.3 0.6 O A:ASP103 4.8 18.4 1.0 O A:HOH383 4.9 48.7 1.0

Calcium binding site 2 out of 6 in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:21.0 occ:1.00 OD2 B:ASP66 2.3 23.6 1.0 O B:HOH309 2.4 22.2 1.0 O B:HOH371 2.4 29.1 1.0 OD1 B:ASP103 2.4 20.6 1.0 O B:HOH333 2.4 22.8 1.0 OD2 B:ASP71 2.4 24.1 0.5 OD1 B:ASP71 2.5 23.2 0.5 CG B:ASP71 2.8 17.4 0.5 OD2 B:ASP71 2.9 26.4 0.5 CG B:ASP66 3.3 24.8 1.0 CG B:ASP71 3.5 22.0 0.5 CG B:ASP103 3.5 21.0 1.0 OD1 B:ASP66 3.7 26.5 1.0 OD1 B:ASP71 3.9 23.7 0.5 CA B:ASP103 4.1 18.7 1.0 O B:HOH346 4.2 32.1 0.8 O B:HOH373 4.3 45.7 1.0 O B:HOH326 4.3 26.2 1.0 NZ B:LYS105 4.3 22.4 1.0 CB B:ASP71 4.4 16.2 0.5 OD2 B:ASP103 4.4 23.7 1.0 CB B:ASP71 4.4 17.2 0.5 CB B:ASP103 4.4 19.5 1.0 O B:PRO69 4.4 18.5 1.0 C B:ASP103 4.5 16.5 1.0 O B:TRP104 4.5 17.6 1.0 CB B:ASP66 4.7 25.5 1.0 N B:ASP71 4.7 14.3 1.0 O B:ASP103 4.8 16.8 1.0 O B:HOH381 4.9 49.5 1.0 CB B:ASP68 4.9 28.3 1.0

Calcium binding site 3 out of 6 in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:23.7 occ:0.80 O C:HOH318 2.3 29.9 1.0 OD2 C:ASP71 2.4 33.3 1.0 O C:HOH345 2.4 22.1 1.0 OD2 C:ASP66 2.4 29.5 1.0 OD1 C:ASP103 2.4 27.1 1.0 O C:HOH378 2.4 35.5 1.0 CG C:ASP71 3.4 31.9 1.0 CG C:ASP66 3.4 32.6 1.0 CG C:ASP103 3.6 27.0 1.0 OD1 C:ASP66 3.7 31.1 1.0 OD1 C:ASP71 3.9 35.2 1.0 O C:HOH393 4.1 42.1 0.8 NZ C:LYS105 4.1 25.9 1.0 O C:HOH382 4.2 38.7 0.6 CA C:ASP103 4.2 23.4 1.0 O C:PRO69 4.4 18.7 1.0 OD2 C:ASP103 4.4 30.1 1.0 O C:HOH333 4.4 31.9 1.0 CB C:ASP103 4.4 26.1 1.0 CB C:ASP71 4.5 20.8 1.0 C C:ASP103 4.6 22.8 1.0 O C:TRP104 4.6 16.5 1.0 CB C:ASP66 4.7 34.6 1.0 CB C:ASP68 4.7 31.8 1.0 N C:ASP71 4.8 12.9 1.0 O C:ASP103 4.8 21.9 1.0 O C:HOH361 4.9 53.2 1.0

Calcium binding site 4 out of 6 in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:28.5 occ:0.75 O D:HOH360 2.3 40.9 0.9 OD2 D:ASP71 2.3 37.1 1.0 O D:HOH325 2.4 27.1 1.0 OD1 D:ASP103 2.4 26.1 1.0 O D:HOH380 2.4 21.1 1.0 OD2 D:ASP66 2.4 36.0 1.0 CG D:ASP71 3.4 33.5 1.0 CG D:ASP66 3.4 40.1 1.0 CG D:ASP103 3.6 28.1 1.0 OD1 D:ASP66 3.8 42.3 1.0 OD1 D:ASP71 4.0 34.8 1.0 O D:HOH378 4.0 63.1 1.0 NZ D:LYS105 4.2 29.9 1.0 O D:HOH317 4.2 30.0 0.8 CA D:ASP103 4.2 24.3 1.0 O D:HOH385 4.3 35.8 0.6 O D:PRO69 4.3 23.6 1.0 OD2 D:ASP103 4.4 30.7 1.0 CB D:ASP103 4.4 24.4 1.0 CB D:ASP71 4.4 23.2 1.0 C D:ASP103 4.5 19.8 1.0 O D:TRP104 4.5 19.8 1.0 O D:ASP103 4.7 22.0 1.0 CB D:ASP66 4.7 40.9 1.0 N D:ASP71 4.8 14.2 1.0 CB D:ASP68 4.8 41.5 1.0 O D:HOH390 4.8 57.2 1.0 N D:TRP104 5.0 16.0 1.0

Calcium binding site 5 out of 6 in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:28.4 occ:0.89 OD1 E:ASP103 2.3 30.5 1.0 OD2 E:ASP71 2.3 34.7 1.0 O E:HOH373 2.3 40.6 1.0 O E:HOH321 2.4 26.7 1.0 OD2 E:ASP66 2.4 32.5 1.0 O E:HOH344 2.4 33.9 0.9 CG E:ASP71 3.2 31.8 1.0 CG E:ASP66 3.4 38.7 1.0 CG E:ASP103 3.5 30.9 1.0 OD1 E:ASP71 3.6 37.1 1.0 OD1 E:ASP66 3.7 38.4 1.0 NZ E:LYS105 4.1 30.1 1.0 CA E:ASP103 4.3 22.4 1.0 O E:HOH335 4.3 34.4 1.0 OD2 E:ASP103 4.4 31.5 1.0 O E:PRO69 4.4 23.4 1.0 CB E:ASP71 4.4 21.4 1.0 CB E:ASP103 4.5 26.2 1.0 C E:ASP103 4.6 19.6 1.0 O E:TRP104 4.6 19.1 1.0 CB E:ASP68 4.7 44.5 1.0 CB E:ASP66 4.7 40.6 1.0 O E:ASP103 4.7 21.6 1.0 N E:ASP71 4.8 16.0 1.0 O E:HOH362 4.9 47.2 1.0

Calcium binding site 6 out of 6 in the The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca201 b:25.2 occ:0.82 OD1 F:ASP103 2.3 27.2 1.0 OD2 F:ASP66 2.3 30.9 1.0 O F:HOH353 2.3 32.5 1.0 O F:HOH340 2.4 30.0 1.0 O F:HOH327 2.4 26.5 1.0 OD2 F:ASP71 2.4 33.6 1.0 CG F:ASP71 3.3 32.7 1.0 CG F:ASP66 3.3 37.2 1.0 CG F:ASP103 3.5 29.1 1.0 OD1 F:ASP71 3.7 37.7 1.0 OD1 F:ASP66 3.7 35.5 1.0 NZ F:LYS105 4.2 28.6 1.0 CA F:ASP103 4.2 23.9 1.0 O F:HOH355 4.2 28.9 1.0 OD2 F:ASP103 4.3 28.6 1.0 CB F:ASP103 4.4 27.4 1.0 O F:PRO69 4.4 23.3 1.0 CB F:ASP71 4.5 22.3 1.0 C F:ASP103 4.5 22.1 1.0 O F:TRP104 4.6 22.6 1.0 CB F:ASP66 4.6 40.7 1.0 O F:ASP103 4.7 22.8 1.0 O F:HOH356 4.7 26.6 0.7 CB F:ASP68 4.8 41.3 1.0 N F:ASP71 4.8 15.7 1.0 O F:HOH394 4.9 43.0 0.8

R.C.Hughes, E.J.Meehan, L.Coates, J.D.Ng. The Structure of Calcium Bound Thermococcus Thioreducens Inorganic Pyrophosphatase at 298K To Be Published.