Magnesium in PDB 3q5v: The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate

The structure of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate, PDB code: 3q5v 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)	47.03 / 1.29
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	114.490, 114.490, 148.600, 90.00, 90.00, 120.00
R / Rfree (%)	12 / 15.5

The binding sites of Magnesium atom in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate (pdb code 3q5v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate, PDB code: 3q5v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg598 b:11.7 occ:0.72 OD2 A:ASP71 2.0 17.3 0.8 OD1 A:ASP103 2.1 16.4 0.9 O A:HOH269 2.1 17.7 1.0 OD1 A:ASP66 2.1 15.9 1.0 O A:HOH221 2.1 15.6 1.0 O A:HOH228 2.1 10.9 0.7 CG A:ASP71 3.0 17.9 0.8 CG A:ASP66 3.1 14.9 1.0 CG A:ASP103 3.2 19.6 0.9 OD1 A:ASP71 3.4 14.9 0.2 CG A:ASP71 3.4 14.5 0.2 OD2 A:ASP71 3.4 13.5 0.2 OD1 A:ASP71 3.4 25.9 0.8 OD2 A:ASP66 3.5 16.1 1.0 O A:HOH389 3.5 18.9 0.4 OD2 A:ASP103 3.9 26.8 0.9 CA A:ASP103 4.0 17.2 0.9 CB A:ASP103 4.1 19.4 0.9 O A:HOH230 4.1 28.9 0.7 O A:TRP104 4.2 13.5 1.0 O A:PRO69 4.2 13.3 1.0 CB A:ASP71 4.2 10.4 0.2 O A:HOH271 4.3 23.4 1.0 CB A:ASP71 4.3 16.0 0.8 OD2 A:ASP68 4.3 24.4 1.0 C A:ASP103 4.4 13.9 0.9 O A:HOH389 4.4 30.8 0.6 NZ A:LYS105 4.4 26.2 0.8 CB A:ASP66 4.4 16.6 1.0 CB A:ASP68 4.5 16.9 1.0 N A:ASP71 4.6 11.9 1.0 O A:ASP103 4.7 14.9 0.9 N A:TRP104 4.8 13.7 1.0 CD2 A:TYR64 4.9 17.0 1.0 NZ A:LYS105 4.9 17.9 0.2 CG A:ASP68 5.0 21.9 1.0

Magnesium binding site 2 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:39.7 occ:0.55 O A:HOH230 2.2 28.9 0.7 OD2 A:ASP103 2.2 26.8 0.9 OD1 A:ASP98 2.4 26.9 0.8 O A:HOH389 2.5 30.8 0.6 O A:HOH416 2.5 43.8 1.0 O3 A:SO4646 2.6 34.1 0.5 CG A:ASP103 3.2 19.6 0.9 CG A:ASP98 3.3 25.4 0.8 O A:HOH389 3.5 18.9 0.4 O A:HOH215 3.6 32.6 1.0 O A:HOH498 3.7 58.7 1.0 CB A:ASP98 3.7 19.1 0.8 S A:SO4646 3.8 30.6 0.5 O2 A:SO4646 3.9 31.9 0.5 O A:HOH367 3.9 45.2 1.0 NZ A:LYS141 3.9 23.1 0.8 CB A:ASP103 4.0 19.4 0.9 OD1 A:ASP103 4.1 16.4 0.9 OD2 A:ASP98 4.3 30.0 0.8 O A:HOH497 4.5 46.3 0.8 O A:HOH269 4.5 17.7 1.0 O4 A:SO4646 4.6 32.6 0.5 O2 A:SO4645 4.6 26.8 0.6 OD2 A:ASP68 4.8 24.4 1.0 OD1 A:ASP66 4.8 15.9 1.0 O1 A:SO4646 4.8 30.2 0.5 NZ A:LYS105 4.8 26.2 0.8 O A:HOH494 4.9 49.6 1.0 O A:HOH499 5.0 52.9 1.0

Magnesium binding site 3 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg599 b:16.0 occ:1.00 OD1 B:ASP71 1.9 17.0 0.7 OD2 B:ASP66 2.0 17.4 1.0 OD1 B:ASP103 2.1 21.0 1.0 O B:HOH203 2.1 18.1 1.0 O B:HOH224 2.1 17.7 1.0 O B:HOH251 2.1 20.6 1.0 CG B:ASP71 3.0 16.7 0.7 CG B:ASP66 3.1 16.1 1.0 CG B:ASP103 3.2 20.8 1.0 OD2 B:ASP71 3.2 15.2 0.3 CG B:ASP71 3.5 17.9 0.3 OD1 B:ASP66 3.5 16.6 1.0 OD2 B:ASP71 3.5 22.6 0.7 OD1 B:ASP71 3.6 22.5 0.3 OD2 B:ASP103 3.9 27.5 1.0 CA B:ASP103 4.1 15.7 1.0 O B:HOH216 4.1 33.1 0.8 CB B:ASP103 4.1 18.2 1.0 NZ B:LYS105 4.1 21.0 0.7 O B:HOH248 4.2 35.3 0.8 O B:TRP104 4.2 14.3 1.0 O B:PRO69 4.3 15.0 1.0 CB B:ASP71 4.3 15.3 0.7 C B:ASP103 4.4 13.2 1.0 CB B:ASP71 4.4 12.8 0.3 OD2 B:ASP68 4.4 20.7 0.7 CB B:ASP66 4.4 15.6 1.0 N B:ASP71 4.5 13.2 0.7 NZ B:LYS105 4.5 25.3 0.3 N B:ASP71 4.6 10.2 0.3 CB B:ASP68 4.6 18.2 0.7 O B:ASP103 4.6 15.3 1.0 CD2 B:TYR64 4.6 17.0 1.0 O B:HOH294 4.7 27.4 1.0 N B:TRP104 4.9 13.9 1.0

Magnesium binding site 4 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg672 b:34.0 occ:0.46 O A:HOH671 2.2 41.2 1.0 O A:HOH313 2.4 27.0 1.0 O A:HOH441 2.4 30.9 1.0 OE1 A:GLU22 2.5 18.8 1.0 O A:HOH404 2.9 44.0 1.0 O A:HOH207 2.9 31.5 1.0 CD A:GLU22 3.3 17.2 1.0 OE2 A:GLU22 3.4 19.3 1.0 O A:HOH271 3.6 23.4 1.0 O A:HOH332 3.7 32.0 1.0 CE2 A:TYR56 3.9 21.2 1.0 CG2 A:ILE58 4.1 13.5 1.0 O A:HOH499 4.3 52.9 1.0 CG A:GLU32 4.3 28.7 0.5 OD2 A:ASP71 4.4 13.5 0.2 CB A:GLU32 4.5 15.1 0.5 CB A:GLU32 4.5 24.5 0.5 CD2 A:TYR56 4.6 18.3 1.0 CD A:GLU32 4.7 31.1 0.5 NZ A:LYS30 4.7 24.2 0.3 OE2 A:GLU32 4.7 28.6 0.5 CG A:GLU22 4.7 16.1 1.0 CZ A:TYR56 4.8 22.6 1.0 O A:TYR31 4.8 13.5 1.0 OH A:TYR56 4.8 30.4 1.0 OD1 A:ASP71 4.9 25.9 0.8 CA A:GLU32 4.9 12.6 0.5 O A:GLY57 4.9 11.3 1.0 CA A:GLU32 4.9 18.8 0.5

Magnesium binding site 5 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg600 b:23.5 occ:0.41 O B:GLY100 2.0 29.3 1.0 O B:HOH633 2.3 55.2 1.0 O B:HOH282 2.3 41.9 1.0 O B:HOH315 2.5 30.8 1.0 O B:HOH313 2.5 38.4 1.0 C B:GLY100 3.1 24.4 1.0 CA B:GLY100 3.7 26.1 1.0 O B:HOH537 4.0 44.2 1.0 O B:HOH578 4.1 58.9 1.0 N B:ASP101 4.3 21.2 1.0 O B:HOH265 4.3 22.6 1.0 CA B:ASP101 4.6 21.0 1.0 O B:HOH235 4.6 21.7 1.0 OE1 B:GLU97 4.8 36.7 1.0

Magnesium binding site 6 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:29.5 occ:0.29 O B:HOH216 2.1 33.1 0.8 OD2 B:ASP103 2.2 27.5 1.0 O3 B:SO4602 2.2 21.8 0.4 OD1 B:ASP98 2.3 34.0 1.0 O B:HOH359 2.3 33.2 1.0 O B:HOH464 2.7 44.6 0.9 O B:HOH248 2.7 35.3 0.8 CG B:ASP98 3.2 31.7 1.0 CG B:ASP103 3.3 20.8 1.0 S B:SO4602 3.5 19.1 0.4 O1 B:SO4602 3.6 22.3 0.4 CB B:ASP98 3.6 25.1 1.0 NZ B:LYS141 3.8 31.3 1.0 MG B:MG666 3.9 30.4 0.3 O B:HOH280 3.9 34.5 0.7 OD1 B:ASP103 4.0 21.0 1.0 NZ B:LYS105 4.0 21.0 0.7 NZ B:LYS105 4.1 25.3 0.3 O4 B:SO4602 4.1 19.8 0.4 O B:HOH662 4.2 38.8 0.6 OH B:TYR140 4.2 20.1 1.0 OD2 B:ASP98 4.3 34.0 1.0 CB B:ASP103 4.3 18.2 1.0 O B:HOH251 4.3 20.6 1.0 O2 B:SO4602 4.5 21.2 0.4 CE B:LYS141 4.8 28.8 1.0 CE B:LYS105 4.9 18.5 0.7 OD2 B:ASP66 5.0 17.4 1.0

Magnesium binding site 7 out of 7 in the The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg666 b:30.4 occ:0.35 O B:HOH662 2.0 38.8 0.6 O B:HOH280 2.0 34.5 0.7 O B:HOH464 2.0 44.6 0.9 O B:HOH248 2.0 35.3 0.8 O B:HOH667 2.3 37.6 0.6 O B:HOH667 2.9 36.2 0.4 MG B:MG604 3.9 29.5 0.3 CB B:ASP66 4.3 15.6 1.0 O B:ASP66 4.3 19.2 1.0 OD2 B:ASP68 4.3 20.7 0.7 OD2 B:ASP101 4.3 36.4 1.0 O3 B:SO4602 4.4 21.8 0.4 O B:HOH365 4.6 43.1 1.0 OD1 B:ASP98 4.7 34.0 1.0 O B:ASP98 4.7 23.2 1.0 CG B:ASP98 4.7 31.7 1.0 OD2 B:ASP66 4.7 17.4 1.0 OD2 B:ASP103 4.8 27.5 1.0 OD1 B:ASP68 4.8 23.6 0.3 O B:HOH216 4.8 33.1 0.8 CG B:ASP66 4.8 16.1 1.0 CB B:ASP98 4.9 25.1 1.0

R.C.Hughes, L.Coates, E.J.Meehan, J.D.Ng. The Structure of Inorganic Pyrophosphatase From Thermococcus Thioreducens in Complex with Magnesium and Sulfate To Be Published.