Magnesium in PDB 4b0h: B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg B (P212121)

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

The structure of B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg B (P212121), PDB code: 4b0h 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)	35.04 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.030, 71.310, 91.880, 90.00, 90.00, 90.00
R / Rfree (%)	11.712 / 16.006

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

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg B (P212121) (pdb code 4b0h). 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 B (P212121), PDB code: 4b0h:
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 B (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 B (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1147 b:6.0 occ:1.00 O5 B:POP1146 2.0 5.7 1.0 O3 B:POP1146 2.1 6.7 1.0 O A:HOH2124 2.1 7.1 1.0 O A:HOH2125 2.1 7.2 1.0 O A:HOH2276 2.1 10.2 1.0 O B:HOH2285 2.1 7.6 1.0 P2 B:POP1146 3.2 6.0 1.0 P1 B:POP1146 3.2 6.1 1.0 O B:POP1146 3.5 5.6 1.0 O6 B:POP1146 3.8 6.0 1.0 O2 B:POP1146 3.8 7.3 1.0 NH2 B:ARG135 4.0 6.7 1.0 O A:HOH2120 4.1 9.5 1.0 NE A:ARG63 4.1 7.6 1.0 OD1 A:ASP27 4.2 9.2 1.0 O A:HOH2115 4.2 7.9 1.0 OE1 A:GLN112 4.3 7.0 1.0 OG1 B:THR141 4.4 8.4 1.0 NH2 A:ARG63 4.4 6.6 1.0 OD2 A:ASP27 4.5 8.0 1.0 O4 B:POP1146 4.5 6.3 1.0 O1 B:POP1146 4.5 6.7 1.0 O5' C:DUR1148 4.6 7.5 1.0 C5' C:DUR1148 4.7 5.6 1.0 OD2 C:ASP82 4.7 7.3 1.0 CZ A:ARG63 4.7 6.8 1.0 CG A:ASP27 4.7 7.2 1.0 O A:HOH2277 4.8 11.1 1.0 CG A:ARG63 4.8 6.8 1.0 CD A:ARG63 5.0 8.4 1.0 CZ B:ARG135 5.0 6.3 1.0 CD A:GLN112 5.0 6.2 1.0

Magnesium binding site 2 out of 2 in the B. Subtilis Dutpase Yncf in Complex with Du, Ppi and Mg B (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 B (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1150 b:7.1 occ:1.00 O5 C:POP1149 2.0 6.8 1.0 O3 C:POP1149 2.1 7.9 1.0 O B:HOH2104 2.1 8.8 1.0 O B:HOH2103 2.1 9.0 1.0 O C:HOH2286 2.1 8.6 1.0 O A:HOH2242 2.2 9.9 1.0 P2 C:POP1149 3.2 7.3 1.0 P1 C:POP1149 3.3 7.3 1.0 O C:POP1149 3.5 7.5 1.0 O6 C:POP1149 3.8 8.5 1.0 O2 C:POP1149 3.9 8.7 1.0 NH2 C:ARG135 4.0 8.2 1.0 O B:HOH2098 4.1 10.4 1.0 NE B:ARG63 4.1 8.7 1.0 O A:HOH2241 4.1 9.4 1.0 OD1 B:ASP27 4.2 9.5 1.0 OE1 B:GLN112 4.3 8.7 1.0 OG1 C:THR141 4.4 9.6 1.0 O5' A:DUR1132 4.5 8.9 1.0 OD2 B:ASP27 4.5 10.3 1.0 NH2 B:ARG63 4.5 8.8 1.0 O4 C:POP1149 4.5 7.6 1.0 O1 C:POP1149 4.5 8.2 1.0 C5' A:DUR1132 4.7 7.4 1.0 CZ B:ARG63 4.7 7.8 1.0 OD2 A:ASP82 4.7 9.7 1.0 O A:HOH2239 4.8 15.1 1.0 CG B:ASP27 4.8 9.2 1.0 CG B:ARG63 4.9 7.9 1.0 CD B:ARG63 4.9 8.7 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