Calcium in PDB 3q3l: The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens

The binding sites of Calcium atom in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens (pdb code 3q3l). 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 Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens, PDB code: 3q3l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca436 b:32.5 occ:1.00 OD2 A:ASP71 2.0 39.1 1.0 O A:DOD280 2.1 47.0 1.0 O A:DOD215 2.2 36.8 1.0 OD1 A:ASP103 2.2 35.8 1.0 D1 A:DOD215 2.3 41.7 1.0 OD2 A:ASP66 2.4 35.8 1.0 O A:DOD230 2.6 36.1 1.0 D2 A:DOD280 2.7 46.1 1.0 D2 A:DOD230 2.8 36.7 1.0 D1 A:DOD280 2.8 41.0 1.0 CG A:ASP71 3.0 32.4 1.0 D2 A:DOD215 3.1 34.4 1.0 D1 A:DOD230 3.2 27.9 1.0 OD1 A:ASP71 3.4 41.1 1.0 CG A:ASP103 3.5 36.4 1.0 HA A:ASP103 3.5 24.1 1.0 CG A:ASP66 3.5 37.6 1.0 DZ1 A:LYS105 3.6 34.1 1.0 HZ1 A:LYS105 3.6 34.1 0.0 D1 A:DOD227 3.7 36.5 0.9 HZ3 A:LYS105 3.7 35.9 0.1 DZ2 A:LYS105 3.8 30.5 0.0 H A:ASP71 3.8 24.2 0.0 D A:ASP71 3.8 24.2 1.0 D2 A:DOD227 4.1 28.3 0.9 OD1 A:ASP66 4.1 37.9 1.0 NZ A:LYS105 4.1 37.1 1.0 HZ2 A:LYS105 4.2 30.5 1.0 DZ3 A:LYS105 4.2 35.9 0.9 HB2 A:ASP71 4.2 36.1 1.0 CB A:ASP71 4.2 29.2 1.0 OD2 A:ASP103 4.2 35.4 1.0 O A:PRO69 4.3 34.6 1.0 CA A:ASP103 4.3 38.2 1.0 O A:DOD227 4.3 41.4 0.9 CB A:ASP103 4.4 27.2 1.0 HB2 A:ASP68 4.4 46.0 0.5 HG2 A:LYS105 4.5 33.3 1.0 C A:ASP103 4.6 34.5 1.0 O A:TRP104 4.6 26.4 1.0 N A:ASP71 4.6 25.3 1.0 HB3 A:ASP68 4.7 38.5 0.5 CB A:ASP66 4.7 34.2 1.0 HA A:PHE70 4.7 33.8 1.0 O A:ASP103 4.8 35.8 1.0 HB2 A:ASP66 4.8 35.9 1.0 O A:HOH421 4.8 22.9 1.0 HD2 A:TYR64 4.8 32.2 1.0 HB2 A:ASP103 4.8 35.4 1.0 HB3 A:ASP66 4.9 30.8 1.0 HB3 A:TYR64 4.9 32.5 1.0 HD1 A:PHE70 4.9 36.4 1.0 HB3 A:ASP71 5.0 25.8 1.0

Calcium binding site 2 out of 6 in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca437 b:36.0 occ:1.00 OD1 B:ASP103 2.0 36.1 1.0 O B:DOD243 2.1 43.8 1.0 OD2 B:ASP66 2.2 34.1 1.0 OD2 B:ASP71 2.3 34.1 1.0 O B:DOD250 2.3 28.5 0.8 D2 B:DOD250 2.7 30.6 0.8 D2 B:DOD243 2.8 64.4 1.0 D1 B:DOD243 2.8 41.0 1.0 D1 B:DOD250 2.9 29.2 0.8 HA B:ASP103 3.2 27.3 1.0 CG B:ASP103 3.2 41.4 1.0 CG B:ASP66 3.3 37.6 1.0 HZ1 B:LYS105 3.3 31.5 0.4 DZ1 B:LYS105 3.3 31.5 0.6 CG B:ASP71 3.4 32.3 1.0 DZ3 B:LYS105 3.4 28.7 0.6 HZ3 B:LYS105 3.4 28.7 0.4 HZ2 B:LYS105 3.4 32.1 1.0 DZ2 B:LYS105 3.5 32.1 0.0 NZ B:LYS105 3.6 23.2 1.0 OD1 B:ASP71 3.9 30.8 1.0 O B:DOD242 3.9 48.0 1.0 OD1 B:ASP66 3.9 31.3 1.0 HB2 B:ASP68 3.9 25.9 1.0 CA B:ASP103 4.0 36.4 1.0 OD2 B:ASP103 4.1 31.8 1.0 CB B:ASP103 4.1 29.2 1.0 D2 B:DOD242 4.2 47.3 1.0 D B:ASP71 4.3 28.3 1.0 H B:ASP71 4.3 28.3 0.0 HB2 B:ASP66 4.3 33.9 1.0 CB B:ASP66 4.3 32.5 1.0 C B:ASP103 4.5 31.8 1.0 HB2 B:ASP103 4.5 34.1 1.0 HB3 B:ASP66 4.5 40.5 1.0 O B:PRO69 4.6 39.4 1.0 HB2 B:ASP71 4.6 31.5 1.0 HB3 B:ASP68 4.6 36.5 1.0 CB B:ASP71 4.6 26.8 1.0 O B:TRP104 4.7 30.2 1.0 O B:ASP103 4.8 30.7 1.0 D1 B:DOD242 4.8 42.8 1.0 CB B:ASP68 4.8 36.6 1.0 HB3 B:TYR64 4.9 28.1 1.0 HD2 B:TYR64 4.9 36.1 1.0 D2 B:DOD252 4.9 36.7 1.0 HA B:PHE70 5.0 32.0 1.0 O B:LYS102 5.0 31.3 1.0 HG2 B:LYS105 5.0 28.6 1.0

Calcium binding site 3 out of 6 in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca438 b:44.6 occ:1.00 O C:DOD256 2.1 39.4 1.0 OD1 C:ASP103 2.2 45.2 1.0 O C:DOD255 2.2 50.0 1.0 OD2 C:ASP71 2.2 36.3 1.0 O C:DOD257 2.3 45.7 1.0 D2 C:DOD256 2.5 35.5 1.0 D2 C:DOD257 2.6 45.6 1.0 D2 C:DOD255 2.6 50.1 1.0 OD2 C:ASP66 2.8 40.4 1.0 D1 C:DOD256 2.9 38.1 1.0 D1 C:DOD255 3.1 53.1 1.0 CG C:ASP71 3.1 39.5 1.0 D1 C:DOD257 3.3 47.6 1.0 CG C:ASP103 3.4 52.3 1.0 HZ2 C:LYS105 3.4 32.6 0.1 DZ3 C:LYS105 3.5 38.5 0.2 OD1 C:ASP71 3.6 40.4 1.0 HA C:ASP103 3.7 34.7 1.0 CG C:ASP66 3.7 46.6 1.0 HZ1 C:LYS105 3.9 35.6 0.0 DZ2 C:LYS105 3.9 32.6 0.9 D C:ASP71 3.9 27.1 1.0 H C:ASP71 3.9 27.1 0.0 OD1 C:ASP66 4.0 43.2 1.0 NZ C:LYS105 4.0 37.6 1.0 HB2 C:ASP68 4.0 42.5 1.0 OD2 C:ASP103 4.1 34.0 1.0 HZ3 C:LYS105 4.1 38.5 0.8 DZ1 C:LYS105 4.1 35.6 1.0 HB2 C:ASP71 4.2 38.0 1.0 O C:DOD258 4.2 40.7 1.0 O C:PRO69 4.3 42.3 1.0 CB C:ASP71 4.3 27.4 1.0 HG2 C:LYS105 4.4 36.8 1.0 CA C:ASP103 4.4 41.6 1.0 CB C:ASP103 4.5 45.5 1.0 HB3 C:ASP68 4.5 38.6 1.0 D1 C:DOD258 4.6 42.0 1.0 O C:TRP104 4.6 50.9 1.0 DH C:TYR56 4.6 24.7 1.0 HH C:TYR56 4.6 24.7 0.0 N C:ASP71 4.6 28.0 1.0 HA C:PHE70 4.7 36.3 1.0 C C:ASP103 4.7 44.4 1.0 D2 C:DOD258 4.8 41.1 1.0 CB C:ASP68 4.8 45.3 1.0 D1 C:DOD218 4.8 37.6 1.0 HD1 C:PHE70 4.9 37.5 1.0 HB2 C:ASP103 4.9 37.8 1.0 O C:ASP103 4.9 31.7 1.0 O C:DOD218 4.9 41.3 1.0 HD2 C:TYR64 4.9 43.0 1.0

Calcium binding site 4 out of 6 in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca439 b:39.3 occ:1.00 O D:DOD221 1.9 44.5 1.0 OD1 D:ASP103 2.2 57.1 1.0 O D:DOD220 2.3 50.4 1.0 D2 D:DOD220 2.6 50.7 1.0 D2 D:DOD221 2.6 42.9 1.0 OD2 D:ASP66 2.6 59.2 1.0 D1 D:DOD221 2.7 40.5 1.0 OD2 D:ASP71 2.7 36.1 1.0 D1 D:DOD220 3.2 51.7 1.0 HA D:ASP103 3.3 36.9 1.0 CG D:ASP103 3.4 43.2 1.0 CG D:ASP71 3.5 41.3 1.0 DZ3 D:LYS105 3.6 33.7 1.0 HZ3 D:LYS105 3.6 33.7 0.0 CG D:ASP66 3.6 54.1 1.0 OD1 D:ASP66 3.9 55.1 1.0 H D:ASP71 4.0 30.4 0.0 D D:ASP71 4.0 30.4 1.0 HB2 D:ASP68 4.0 45.8 1.0 DZ2 D:LYS105 4.0 34.1 0.5 HZ2 D:LYS105 4.0 34.1 0.6 CA D:ASP103 4.1 41.6 1.0 OD1 D:ASP71 4.1 34.3 1.0 NZ D:LYS105 4.2 28.9 1.0 HB2 D:ASP71 4.2 31.1 1.0 HZ1 D:LYS105 4.3 36.2 0.5 DZ1 D:LYS105 4.3 36.2 0.5 CB D:ASP103 4.3 40.2 1.0 OD2 D:ASP103 4.3 40.8 1.0 C D:ASP103 4.3 30.8 1.0 O D:TRP104 4.4 27.4 1.0 HG2 D:LYS105 4.4 30.0 1.0 O D:PRO69 4.4 37.7 1.0 O D:ASP103 4.5 34.4 1.0 CB D:ASP71 4.5 30.7 1.0 HB2 D:ASP103 4.7 45.5 1.0 HD2 D:TYR64 4.7 37.0 1.0 N D:ASP71 4.8 29.8 1.0 HA D:PHE70 4.8 36.7 1.0 HD1 D:PHE70 4.8 36.3 1.0 HB3 D:ASP68 4.9 39.8 1.0 HB3 D:TYR64 4.9 42.5 1.0 CB D:ASP66 4.9 36.4 1.0 CB D:ASP68 5.0 43.6 1.0 N D:TRP104 5.0 25.8 1.0

Calcium binding site 5 out of 6 in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca440 b:41.0 occ:1.00 O E:DOD264 1.8 49.9 1.0 O E:DOD260 2.0 45.3 1.0 OD1 E:ASP103 2.3 33.5 1.0 D2 E:DOD264 2.4 37.6 1.0 OD2 E:ASP71 2.5 37.1 1.0 OD2 E:ASP66 2.5 46.4 1.0 D2 E:DOD260 2.5 49.6 1.0 D1 E:DOD260 2.6 36.5 1.0 D1 E:DOD264 2.6 42.2 1.0 CG E:ASP66 3.4 55.4 1.0 CG E:ASP71 3.4 40.6 1.0 D2 E:DOD222 3.4 43.7 1.0 HA E:ASP103 3.5 45.1 1.0 CG E:ASP103 3.5 57.9 1.0 OD1 E:ASP66 3.7 52.4 1.0 O E:DOD263 3.7 41.0 1.0 HZ2 E:LYS105 3.8 43.3 0.0 DZ2 E:LYS105 3.8 43.3 1.0 HZ3 E:LYS105 3.8 41.5 0.3 DZ3 E:LYS105 3.8 41.5 0.7 HB2 E:ASP68 3.8 47.7 1.0 D2 E:DOD263 3.8 52.2 1.0 OD1 E:ASP71 3.9 39.1 1.0 D1 E:DOD263 4.0 49.1 1.0 O E:DOD222 4.1 43.5 1.0 D E:ASP71 4.1 33.5 1.0 H E:ASP71 4.1 33.5 0.0 NZ E:LYS105 4.2 44.6 1.0 DZ1 E:LYS105 4.2 41.5 0.7 HZ1 E:LYS105 4.2 41.5 0.3 OD2 E:ASP103 4.3 50.5 1.0 CA E:ASP103 4.3 40.0 1.0 O E:PRO69 4.4 37.7 1.0 D1 E:DOD222 4.4 31.4 1.0 HB2 E:ASP71 4.4 35.1 1.0 CB E:ASP103 4.5 49.4 1.0 HB3 E:ASP68 4.5 45.3 1.0 CB E:ASP71 4.6 32.5 1.0 HD2 E:TYR64 4.6 38.3 1.0 HG2 E:LYS105 4.6 37.8 1.0 C E:ASP103 4.7 31.0 1.0 CB E:ASP68 4.7 52.3 1.0 O E:TRP104 4.7 34.5 1.0 HB3 E:TYR64 4.7 42.6 1.0 CB E:ASP66 4.8 31.3 1.0 O E:DOD262 4.8 48.3 1.0 O E:ASP103 4.8 35.1 1.0 HA E:PHE70 4.8 42.9 1.0 N E:ASP71 4.9 33.5 1.0 HD1 E:PHE70 4.9 40.3 1.0 HB2 E:ASP103 4.9 42.6 1.0 HB3 E:ASP66 5.0 36.0 1.0

Calcium binding site 6 out of 6 in the The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Neutron Crystallographic Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca441 b:47.1 occ:1.00 O F:DOD182 2.1 47.4 1.0 OD1 F:ASP103 2.2 34.4 1.0 O F:DOD226 2.3 59.7 1.0 OD2 F:ASP66 2.4 41.2 1.0 OD2 F:ASP71 2.5 33.0 1.0 D1 F:DOD226 2.5 49.5 1.0 D2 F:DOD182 2.6 46.8 1.0 D1 F:DOD182 2.7 48.3 1.0 D2 F:DOD226 3.1 55.8 1.0 D1 F:DOD224 3.1 46.0 1.0 CG F:ASP71 3.3 29.7 1.0 CG F:ASP66 3.4 55.7 1.0 D2 F:DOD224 3.4 48.1 1.0 HA F:ASP103 3.4 46.7 1.0 CG F:ASP103 3.5 45.9 1.0 O F:DOD224 3.5 45.8 1.0 OD1 F:ASP71 3.7 33.6 1.0 OD1 F:ASP66 3.7 68.2 1.0 HZ1 F:LYS105 3.8 40.9 0.0 DZ3 F:LYS105 3.8 41.9 1.0 DZ2 F:LYS105 3.8 32.3 0.9 HB2 F:ASP68 3.8 45.7 1.0 D F:ASP71 4.1 33.5 1.0 H F:ASP71 4.1 33.5 0.0 NZ F:LYS105 4.2 31.1 1.0 CA F:ASP103 4.2 35.4 1.0 HZ2 F:LYS105 4.3 32.3 0.1 OD2 F:ASP103 4.3 43.9 1.0 DZ1 F:LYS105 4.3 40.9 1.0 CB F:ASP103 4.4 48.4 1.0 O F:PRO69 4.4 46.5 1.0 HB2 F:ASP71 4.4 38.6 1.0 O F:HOH357 4.5 15.6 1.0 HD2 F:TYR64 4.5 52.4 1.0 CB F:ASP71 4.5 34.3 1.0 HG2 F:LYS105 4.6 37.1 1.0 C F:ASP103 4.6 41.5 1.0 O F:TRP104 4.7 35.0 1.0 HB3 F:ASP68 4.7 52.5 1.0 CB F:ASP66 4.7 40.4 1.0 HB2 F:ASP103 4.7 49.0 1.0 CB F:ASP68 4.8 53.7 1.0 HB3 F:TYR64 4.8 46.0 1.0 O F:ASP103 4.8 38.8 1.0 HA F:PHE70 4.9 42.3 1.0 N F:ASP71 4.9 32.0 1.0 HB3 F:ASP66 4.9 43.2 1.0 HD1 F:PHE70 4.9 38.5 1.0 HB2 F:ASP66 4.9 47.6 1.0

R.C.Hughes, L.Coates, M.P.Blakeley, S.J.Tomanicek, P.Langan, A.Y.Kovalevsky, J.M.Garcia-Ruiz, J.D.Ng. Inorganic Pyrophosphatase Crystals From Thermococcus Thioreducens For X-Ray and Neutron Diffraction. Acta Crystallogr.,Sect.F V. 68 1482 2012.
ISSN: ESSN 1744-3091
PubMed: 23192028
DOI: 10.1107/S1744309112032447