Magnesium in PDB 4aoz: B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121)

All present enzymatic activity of B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121):
3.6.1.23;

The structure of B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121), PDB code: 4aoz was solved by J.Timm, J.Garcia-Nafria, 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)	56.54 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.270, 71.534, 92.299, 90.00, 90.00, 90.00
R / Rfree (%)	15.898 / 21.288

The structure of B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121) (pdb code 4aoz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121), PDB code: 4aoz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121)


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 (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1147 b:9.8 occ:1.00 O A:HOH2076 2.0 4.6 1.0 O A:HOH2183 2.0 11.6 1.0 O2 B:POP1146 2.0 9.1 1.0 O A:HOH2075 2.1 10.5 1.0 O B:HOH2172 2.1 5.7 1.0 O5 B:POP1146 2.1 9.0 1.0 P1 B:POP1146 3.2 11.1 1.0 P2 B:POP1146 3.2 11.1 1.0 O B:POP1146 3.5 9.5 1.0 O4 B:POP1146 3.8 9.2 1.0 O3 B:POP1146 3.8 8.8 1.0 NH2 B:ARG135 3.9 8.8 1.0 O A:HOH2073 4.0 8.5 1.0 NE A:ARG63 4.0 12.1 1.0 OD1 A:ASP27 4.1 14.1 1.0 O A:HOH2070 4.1 7.6 1.0 OE1 A:GLN112 4.2 11.3 1.0 OD2 A:ASP27 4.4 12.0 1.0 OG1 B:THR141 4.4 12.6 1.0 NH2 A:ARG63 4.5 12.1 1.0 O1 B:POP1146 4.5 11.0 1.0 O6 B:POP1146 4.5 8.4 1.0 O5' C:DUR1148 4.6 10.3 1.0 C5' C:DUR1148 4.6 8.6 1.0 OD2 C:ASP82 4.7 12.8 1.0 CZ A:ARG63 4.7 11.5 1.0 CG A:ASP27 4.7 10.9 1.0 O A:HOH2184 4.9 19.9 1.0 CD A:ARG63 4.9 11.2 1.0 CG A:ARG63 4.9 9.2 1.0 CZ B:ARG135 5.0 10.2 1.0

Magnesium binding site 2 out of 2 in the B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg (P212121)


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 (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1150 b:20.3 occ:1.00 O2 C:POP1149 2.0 17.6 1.0 O5 C:POP1149 2.0 17.8 1.0 O A:HOH2156 2.1 16.2 1.0 O B:HOH2053 2.1 12.4 1.0 O B:HOH2052 2.2 14.4 1.0 O C:HOH2160 2.2 12.8 1.0 P1 C:POP1149 3.2 18.7 1.0 P2 C:POP1149 3.3 18.9 1.0 O C:POP1149 3.5 18.4 1.0 O3 C:POP1149 3.8 17.1 1.0 O4 C:POP1149 3.9 21.4 1.0 NH2 C:ARG135 4.0 17.9 1.0 O A:HOH2155 4.1 9.1 1.0 NE B:ARG63 4.1 16.3 1.0 O B:HOH2050 4.2 12.7 1.0 OD1 B:ASP27 4.2 17.7 1.0 OE1 B:GLN112 4.3 14.3 1.0 OG1 C:THR141 4.3 19.1 1.0 NH2 B:ARG63 4.4 16.9 1.0 O5' A:DUR1132 4.4 20.6 1.0 O1 C:POP1149 4.5 17.2 1.0 OD2 B:ASP27 4.5 15.3 1.0 O6 C:POP1149 4.5 20.2 1.0 C5' A:DUR1132 4.7 19.8 1.0 CZ B:ARG63 4.7 16.9 1.0 CG B:ASP27 4.8 14.5 1.0 O A:HOH2154 4.8 26.6 1.0 OD2 A:ASP82 4.9 14.8 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