Magnesium in PDB 3p48: Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp

All present enzymatic activity of Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp:
3.6.1.23;

The structure of Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp, PDB code: 3p48 was solved by P.Petit, A.U.Singer, E.Evdokimova, M.Kudritska, A.M.Edwards, A.F.Yakunin, A.Savchenko, Ontario Centre For Structural Proteomics (Ocsp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.47 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.784, 58.868, 112.381, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.3

The binding sites of Magnesium atom in the Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp (pdb code 3p48). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp, PDB code: 3p48:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg149 b:20.7 occ:1.00 O2G A:DUP148 2.0 23.4 1.0 O1A A:DUP148 2.0 20.7 1.0 O A:HOH247 2.1 23.9 1.0 O2B A:DUP148 2.1 21.8 1.0 O A:HOH246 2.1 20.1 1.0 O A:HOH168 2.1 19.8 1.0 PB A:DUP148 3.1 23.8 1.0 PG A:DUP148 3.2 33.8 1.0 PA A:DUP148 3.3 21.8 1.0 O A:HOH406 3.5 34.2 1.0 O3B A:DUP148 3.6 30.8 1.0 N3A A:DUP148 3.7 18.9 1.0 O A:HOH260 4.0 45.0 1.0 O A:HOH173 4.0 18.3 1.0 O1G A:DUP148 4.1 35.4 1.0 OD1 A:ASP32 4.2 19.9 1.0 O3G A:DUP148 4.3 36.8 1.0 O2A A:DUP148 4.4 24.6 1.0 NE A:ARG68 4.4 25.6 1.0 O5' A:DUP148 4.5 24.4 1.0 OE1 A:GLN114 4.5 19.7 1.0 O1B A:DUP148 4.5 22.8 1.0 OD2 A:ASP32 4.5 26.0 1.0 NH1 A:ARG68 4.5 21.8 1.0 C5' A:DUP148 4.6 19.8 1.0 O A:HOH191 4.7 20.6 1.0 CG A:ASP32 4.8 17.1 1.0 O C:HOH160 5.0 29.6 1.0 CZ A:ARG68 5.0 27.9 1.0 NE2 A:GLN114 5.0 14.7 1.0

Magnesium binding site 2 out of 3 in the Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg150 b:19.2 occ:1.00 O1A B:DUP148 2.0 15.0 1.0 O2B B:DUP148 2.0 18.8 1.0 O2G B:DUP148 2.1 18.9 1.0 O B:HOH249 2.1 17.1 1.0 O B:HOH248 2.1 20.4 1.0 O B:HOH250 2.2 20.3 1.0 PB B:DUP148 3.1 19.6 1.0 PA B:DUP148 3.2 16.9 1.0 PG B:DUP148 3.3 23.0 1.0 O3B B:DUP148 3.6 19.3 1.0 N3A B:DUP148 3.7 16.1 1.0 O B:HOH219 4.1 29.6 1.0 O1G B:DUP148 4.1 26.8 1.0 O B:HOH226 4.2 19.9 1.0 NE B:ARG68 4.2 16.7 0.9 OD1 B:ASP32 4.3 24.2 1.0 OE1 B:GLN114 4.3 20.7 1.0 O2A B:DUP148 4.3 17.3 1.0 NH1 B:ARG68 4.4 15.1 0.9 O3G B:DUP148 4.4 26.2 1.0 O5' B:DUP148 4.4 16.3 1.0 OD2 B:ASP32 4.5 26.6 1.0 O B:HOH396 4.5 47.4 1.0 O1B B:DUP148 4.5 16.1 1.0 C5' B:DUP148 4.6 14.1 1.0 O B:HOH261 4.6 23.2 1.0 CZ B:ARG68 4.8 15.8 0.9 CG B:ASP32 4.8 22.8 1.0 CD B:GLN114 4.9 19.9 1.0 NE2 B:GLN114 4.9 14.6 1.0

Magnesium binding site 3 out of 3 in the Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Yeast Dutpase DUT1 in Complex with Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg148 b:64.6 occ:1.00 O B:HOH276 2.1 34.9 1.0 O1A B:DUP149 2.1 58.2 1.0 O2B B:DUP149 2.4 56.3 1.0 O2G B:DUP149 3.2 91.6 1.0 OD1 C:ASP32 3.6 34.8 1.0 PA B:DUP149 3.6 68.0 1.0 PB B:DUP149 3.6 75.2 1.0 O C:HOH392 3.7 45.0 1.0 O C:HOH251 3.9 28.6 1.0 N3A B:DUP149 4.2 72.6 1.0 O B:HOH234 4.3 24.6 1.0 O B:HOH200 4.4 24.8 1.0 PG B:DUP149 4.4 93.5 1.0 O3B B:DUP149 4.5 88.5 1.0 CD C:ARG68 4.6 38.0 1.0 NE2 C:GLN114 4.6 20.3 1.0 CG C:ASP32 4.6 30.8 1.0 O2A B:DUP149 4.8 80.2 1.0 OE1 C:GLN114 4.8 25.4 1.0 O5' B:DUP149 4.8 46.0 1.0 CD C:GLN114 4.8 21.6 1.0 O1G B:DUP149 4.9 90.8 1.0 OD2 C:ASP32 4.9 35.1 1.0

A.Tchigvintsev, A.U.Singer, R.Flick, P.Petit, G.Brown, E.Evdokimova, A.Savchenko, A.F.Yakunin. Structure and Activity of the Saccharomyces Cerevisiae Dutp Pyrophosphatase DUT1, An Essential Housekeeping Enzyme. Biochem.J. V. 437 243 2011.
ISSN: ISSN 0264-6021
PubMed: 21548881
DOI: 10.1042/BJ20110304