Magnesium in PDB 2xcd: Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis

All present enzymatic activity of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis:
3.6.1.23;

The structure of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis, PDB code: 2xcd was solved by J.Garcia, L.Burchell, M.Takezawa, N.J.Rzechorzek, M.Fogg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.810, 98.840, 99.110, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.4

The structure of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	6 atoms

The binding sites of Magnesium atom in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis (pdb code 2xcd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis, PDB code: 2xcd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg146 b:38.6 occ:1.00 O A:HOH2042 2.9 37.1 1.0 O B:HOH2050 3.3 41.8 1.0 O C:HOH2056 3.4 45.2 1.0 O B:HOH2051 3.4 62.5 1.0 OD1 B:ASP39 3.7 34.2 1.0 O A:HOH2041 3.7 42.5 1.0 OD1 A:ASP39 3.9 35.4 1.0 OD1 C:ASP39 4.1 35.1 1.0 OD2 B:ASP39 4.2 33.9 1.0 CG B:ASP39 4.3 33.3 1.0 OD2 A:ASP39 4.3 30.7 1.0 O C:HOH2095 4.4 48.4 1.0 CG A:ASP39 4.4 31.1 1.0 OD2 C:ASP39 4.5 33.5 1.0 NZ A:LYS38 4.5 37.6 1.0 CG C:ASP39 4.6 32.7 1.0 O A:HOH2039 4.7 44.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1131 b:43.8 occ:1.00 O E:HOH2047 3.1 43.3 1.0 O F:HOH2055 3.2 39.0 1.0 O D:HOH2056 3.5 39.0 1.0 O E:HOH2046 3.6 36.2 1.0 OD1 E:ASP39 3.6 36.8 1.0 OD2 E:ASP39 3.8 34.1 1.0 OD1 F:ASP39 4.0 29.9 1.0 CG E:ASP39 4.0 33.5 1.0 OD2 F:ASP39 4.1 31.3 1.0 CG F:ASP39 4.3 31.1 1.0 OD1 D:ASP39 4.4 34.4 1.0 O D:HOH2099 4.5 41.6 1.0 O F:HOH2106 4.5 35.8 1.0 OD2 D:ASP39 4.6 30.2 1.0 CG D:ASP39 4.9 30.8 1.0

J.Garcia-Nafria, L.Burchell, M.Takezawa, N.J.Rzechorzek, M.Fogg, K.S.Wilson. The Structure of the Genomic Bacillus Subtilis Dutpase: Novel Features in the Phe-Lid. Acta Crystallogr.,Sect.D V. 66 953 2010.
ISSN: ISSN 0907-4449
PubMed: 20823546
DOI: 10.1107/S0907444910026272