Magnesium in PDB 3q46: Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution

The structure of Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution, PDB code: 3q46 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)	18.76 / 0.99
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	99.253, 99.253, 98.557, 90.00, 90.00, 120.00
R / Rfree (%)	11 / 12.3

The structure of Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution (pdb code 3q46). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution, PDB code: 3q46:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:5.0 occ:1.00 OD2 A:ASP71 2.0 5.0 1.0 O A:HOH465 2.0 5.5 1.0 O A:HOH184 2.1 5.8 1.0 O A:HOH185 2.1 5.8 1.0 O4 A:PO4301 2.1 5.4 1.0 O1 A:PO4301 2.2 5.3 1.0 P A:PO4301 2.7 5.3 1.0 CG A:ASP71 3.0 4.6 1.0 OD1 A:ASP71 3.5 4.9 1.0 MG A:MG306 3.6 5.0 1.0 O A:HOH216 3.7 6.2 0.9 O3 A:PO4301 3.7 5.9 1.0 O2 A:PO4301 3.9 5.3 1.0 O A:HOH458 3.9 12.7 1.0 OH A:TYR56 4.0 5.7 1.0 O A:HOH454 4.0 5.6 1.0 O A:PRO69 4.1 5.7 1.0 CE2 A:TYR56 4.2 5.4 1.0 NZ A:LYS30 4.2 7.4 0.7 NZ A:LYS30 4.2 7.8 0.3 CB A:ASP71 4.3 5.0 1.0 OE1 A:GLU22 4.3 5.7 1.0 CG2 A:ILE58 4.4 6.7 1.0 CZ A:TYR56 4.5 5.1 1.0 O A:HOH193 4.5 6.0 0.9 OE1 A:GLU32 4.6 9.9 1.0 O A:GLY57 4.7 4.9 1.0 CA A:ASP71 4.8 4.2 0.9 MG A:MG308 4.9 7.2 1.0

Magnesium binding site 2 out of 4 in the Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:5.0 occ:1.00 O A:HOH454 2.1 5.6 1.0 OD1 A:ASP103 2.1 5.3 1.0 OD1 A:ASP71 2.1 4.9 1.0 OD2 A:ASP66 2.1 5.8 1.0 O2 A:PO4301 2.2 5.3 1.0 O4 A:PO4301 2.2 5.4 1.0 P A:PO4301 2.7 5.3 1.0 CG A:ASP103 3.0 5.0 1.0 CG A:ASP71 3.0 4.6 1.0 CG A:ASP66 3.1 6.0 1.0 OD2 A:ASP71 3.3 5.0 1.0 OD2 A:ASP103 3.3 5.7 1.0 OD1 A:ASP66 3.4 7.2 1.0 O1 A:PO4301 3.6 5.3 1.0 MG A:MG305 3.6 5.0 1.0 MG A:MG307 3.7 5.5 1.0 O A:HOH213 3.7 6.8 1.0 O A:HOH191 3.9 6.0 1.0 NZ A:LYS105 3.9 5.3 1.0 O3 A:PO4301 4.0 5.9 1.0 CB A:ASP66 4.4 8.0 1.0 O A:HOH184 4.4 5.8 1.0 CB A:ASP71 4.4 5.0 1.0 CB A:ASP103 4.4 5.2 1.0 O A:HOH458 4.5 12.7 1.0 O A:PRO69 4.5 5.7 1.0 OH A:TYR56 4.6 5.7 1.0 O A:HOH211 4.6 7.1 1.0 CA A:ASP103 4.9 4.9 1.0 O A:HOH218 4.9 7.6 1.0

Magnesium binding site 3 out of 4 in the Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:5.5 occ:1.00 OD2 A:ASP98 2.0 6.3 1.0 OD2 A:ASP103 2.0 5.7 1.0 O2 A:PO4301 2.1 5.3 1.0 O A:HOH218 2.1 7.6 1.0 O A:HOH211 2.1 7.1 1.0 O A:HOH213 2.1 6.8 1.0 CG A:ASP98 3.1 6.8 1.0 CG A:ASP103 3.1 5.0 1.0 P A:PO4301 3.3 5.3 1.0 O3 A:PO4301 3.6 5.9 1.0 OD1 A:ASP103 3.7 5.3 1.0 MG A:MG306 3.7 5.0 1.0 CB A:ASP98 3.7 6.4 1.0 OD2 A:ASP66 3.8 5.8 1.0 NZ A:LYS105 3.9 5.3 1.0 O3S A:EPE309 4.1 9.5 0.4 OD1 A:ASP98 4.2 12.9 1.0 NZ A:LYS141 4.2 12.0 0.7 O A:HOH457 4.2 10.5 1.0 O A:HOH254 4.3 9.0 0.8 O4 A:PO4301 4.3 5.4 1.0 CB A:ASP103 4.3 5.2 1.0 O1 A:PO4301 4.4 5.3 1.0 OH A:TYR140 4.5 7.8 1.0 O A:HOH386 4.5 9.8 0.7 CL A:CL310 4.5 8.8 0.9 OD1 A:ASP71 4.6 4.9 1.0 CE A:LYS105 4.9 5.5 1.0 CG A:ASP66 4.9 6.0 1.0 CE A:LYS141 4.9 12.8 0.7 MG A:MG308 5.0 7.2 1.0

Magnesium binding site 4 out of 4 in the Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound to Hydrolyzed Product at 0.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:7.2 occ:1.00 O3 A:PO4301 2.0 5.9 1.0 O A:HOH455 2.0 10.3 1.0 O A:HOH232 2.1 9.3 1.0 O A:HOH458 2.1 12.7 1.0 OE1 A:GLU32 2.1 9.9 1.0 O A:HOH457 2.1 10.5 1.0 CD A:GLU32 3.1 7.6 1.0 P A:PO4301 3.3 5.3 1.0 OE2 A:GLU32 3.5 9.2 1.0 O4 A:PO4301 3.7 5.4 1.0 O A:HOH218 3.7 7.6 1.0 O A:HOH185 3.9 5.8 1.0 O A:HOH266 4.0 9.4 0.6 NZ A:LYS30 4.1 7.4 0.7 CE A:LYS30 4.1 10.8 0.7 OD2 A:ASP68 4.2 11.2 1.0 O A:HOH236 4.2 14.1 0.4 NZ A:LYS30 4.2 7.8 0.3 O2S A:EPE309 4.2 9.9 0.4 OD2 A:ASP43 4.2 13.5 0.9 O1 A:PO4301 4.3 5.3 1.0 O A:HOH386 4.3 12.4 0.3 O A:HOH470 4.3 21.5 0.4 O2 A:PO4301 4.3 5.3 1.0 O A:HOH213 4.4 6.8 1.0 CG A:GLU32 4.4 7.4 1.0 O3S A:EPE309 4.7 9.5 0.4 MG A:MG305 4.9 5.0 1.0 CG A:ASP43 4.9 13.2 0.9 O A:HOH313 4.9 10.4 0.5 CE A:LYS30 4.9 9.7 0.3 S A:EPE309 5.0 8.0 0.3 MG A:MG307 5.0 5.5 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: ISSN 1744-3091
PubMed: 23192028
DOI: 10.1107/S1744309112032447