Magnesium in PDB 4aoo: B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32

All present enzymatic activity of B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32:
3.6.1.23;

The structure of B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32, PDB code: 4aoo was solved by J.Garcia-Nafria, J.Timm, C.Harrison, J.P.Turkenburg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.47 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	146.628, 146.628, 144.800, 90.00, 90.00, 120.00
R / Rfree (%)	16.265 / 21.861

The binding sites of Magnesium atom in the B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32 (pdb code 4aoo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32, PDB code: 4aoo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1148 b:25.3 occ:1.00 O1 A:POP1146 1.9 28.4 1.0 O5 A:POP1146 2.0 27.7 1.0 O A:HOH2038 2.1 18.1 1.0 O A:HOH2054 2.1 23.5 1.0 O A:HOH2052 2.1 27.1 1.0 O A:HOH2053 2.2 19.9 1.0 P1 A:POP1146 3.1 26.2 1.0 P2 A:POP1146 3.1 29.1 1.0 O A:POP1146 3.3 25.1 1.0 O2 A:POP1146 3.6 27.3 1.0 O6 A:POP1146 3.8 24.1 1.0 O A:HOH2037 4.2 18.8 1.0 O3 A:POP1146 4.3 26.1 1.0 O4 A:POP1146 4.4 32.6 1.0 O5' A:DUR1145 4.7 21.8 1.0 OD2 A:ASP82 4.8 24.0 1.0 C5' A:DUR1145 4.8 22.3 1.0 O A:HOH2036 5.0 25.5 1.0

Magnesium binding site 2 out of 4 in the B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1148 b:26.0 occ:1.00 O5 B:POP1146 1.9 20.4 1.0 O1 B:POP1146 2.0 25.4 1.0 O B:HOH2074 2.1 18.9 1.0 O B:HOH2072 2.1 17.2 1.0 O B:HOH2070 2.1 17.7 1.0 O B:HOH2069 2.2 17.8 1.0 P1 B:POP1146 3.1 24.2 1.0 P2 B:POP1146 3.1 23.9 1.0 O B:POP1146 3.4 21.6 1.0 O2 B:POP1146 3.6 22.3 1.0 NH2 B:ARG135 3.9 18.4 1.0 O6 B:POP1146 4.0 21.4 1.0 NE C:ARG63 4.0 25.9 1.0 O C:HOH2013 4.1 14.2 1.0 OD1 C:ASP27 4.1 24.6 1.0 OG1 B:THR141 4.2 26.6 1.0 NE2 C:GLN112 4.3 17.7 1.0 O C:HOH2015 4.3 27.8 1.0 OD2 C:ASP27 4.3 26.3 1.0 NH2 C:ARG63 4.4 27.2 1.0 O4 B:POP1146 4.4 21.2 1.0 O3 B:POP1146 4.4 23.0 1.0 CG C:ASP27 4.7 26.1 1.0 O5' D:DUR1145 4.7 22.2 1.0 CZ C:ARG63 4.7 26.8 1.0 O B:HOH2075 4.8 29.6 1.0 OD2 D:ASP82 4.8 18.9 1.0 CG C:ARG63 4.8 23.6 1.0 CD C:ARG63 4.9 24.3 1.0 C5' D:DUR1145 4.9 19.9 1.0

Magnesium binding site 3 out of 4 in the B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1148 b:25.1 occ:1.00 O1 C:POP1147 1.9 23.9 1.0 O5 C:POP1147 2.0 22.8 1.0 O C:HOH2054 2.1 19.9 1.0 O B:HOH2049 2.1 18.0 1.0 O C:HOH2053 2.1 17.7 1.0 O C:HOH2051 2.2 20.2 1.0 P2 C:POP1147 3.1 25.8 1.0 P1 C:POP1147 3.1 21.6 1.0 O C:POP1147 3.4 21.2 1.0 O6 C:POP1147 3.7 24.1 1.0 O2 C:POP1147 3.8 24.6 1.0 NH2 C:ARG135 3.9 23.5 1.0 O B:HOH2048 4.0 10.8 1.0 NE D:ARG63 4.1 22.2 1.0 O D:HOH2014 4.2 18.9 1.0 OD1 D:ASP27 4.2 19.4 1.0 NE2 D:GLN112 4.2 13.5 1.0 O3 C:POP1147 4.4 21.7 1.0 NH2 D:ARG63 4.4 23.4 1.0 OG1 C:THR141 4.4 23.8 1.0 O4 C:POP1147 4.5 23.8 1.0 O5' B:DUR1145 4.5 19.2 1.0 OD2 D:ASP27 4.5 18.5 1.0 C5' B:DUR1145 4.6 20.6 1.0 O B:HOH2047 4.7 27.6 1.0 CZ D:ARG63 4.7 23.0 1.0 OD2 B:ASP82 4.8 17.0 1.0 CG D:ARG63 4.8 21.5 1.0 CG D:ASP27 4.8 18.6 1.0 CD D:ARG63 5.0 21.6 1.0

Magnesium binding site 4 out of 4 in the B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of B. Subtilis Dutpase Yncf in Complex with Du Ppi and Mg in H32 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1148 b:19.2 occ:1.00 O1 D:POP1146 2.0 24.3 1.0 O5 D:POP1146 2.1 26.9 1.0 O C:HOH2037 2.1 21.9 1.0 O B:HOH2023 2.1 17.0 1.0 O D:HOH2042 2.2 28.2 1.0 O B:HOH2022 2.2 17.9 1.0 P2 D:POP1146 3.2 26.7 1.0 P1 D:POP1146 3.2 23.5 1.0 O D:POP1146 3.4 25.2 1.0 O6 D:POP1146 3.7 27.3 1.0 O2 D:POP1146 3.8 22.0 1.0 NH2 D:ARG135 3.9 22.2 1.0 O B:HOH2019 3.9 12.8 1.0 OD1 B:ASP27 4.1 22.6 1.0 OE1 B:GLN112 4.1 18.7 1.0 NE B:ARG63 4.2 25.5 1.0 O B:HOH2021 4.2 25.1 1.0 NH2 B:ARG63 4.4 25.8 1.0 O4 D:POP1146 4.4 26.8 1.0 O3 D:POP1146 4.4 23.6 1.0 OD2 B:ASP27 4.5 22.7 1.0 OG1 D:THR141 4.5 26.1 1.0 O5' C:DUR1145 4.5 19.8 1.0 OD2 C:ASP82 4.5 20.5 1.0 O B:HOH2056 4.6 24.1 1.0 C5' C:DUR1145 4.7 20.8 1.0 CG B:ASP27 4.8 22.3 1.0 CZ B:ARG63 4.8 24.0 1.0 CD B:GLN112 4.8 19.2 1.0 CZ D:ARG135 4.9 21.9 1.0 CG2 D:THR141 5.0 28.9 1.0

J.Garcia-Nafria, J.Timm, C.Harrison, J.P.Turkenburg, K.S.Wilson. Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism Acta Crystallogr.,Sect.D V. 69 1367 2013.
ISSN: ISSN 0907-4449
PubMed: 23897460
DOI: 10.1107/S090744491300735X