Magnesium in PDB 2xy3: Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp

All present enzymatic activity of Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp:
3.6.1.23;

The structure of Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp, PDB code: 2xy3 was solved by J.Garcia-Nafria, M.Harkiolaki, R.Persson, M.J.Fogg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.474, 98.400, 97.993, 90.00, 90.00, 90.00
R / Rfree (%)	19.409 / 25.1

The binding sites of Magnesium atom in the Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp (pdb code 2xy3). 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 Bacillus Subtilis Prophage Dutpase with Dupnhpp, PDB code: 2xy3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp


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 Bacillus Subtilis Prophage Dutpase with Dupnhpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1130 b:38.7 occ:1.00 O1B C:DUP1129 2.0 40.7 1.0 O2G C:DUP1129 2.2 42.3 1.0 O1A C:DUP1129 2.3 41.7 1.0 PB C:DUP1129 3.4 41.1 1.0 PG C:DUP1129 3.4 41.6 1.0 PA C:DUP1129 3.7 40.9 1.0 O3B C:DUP1129 3.7 42.6 1.0 OD1 B:ASP25 3.9 42.0 1.0 N3A C:DUP1129 4.0 39.5 1.0 O1G C:DUP1129 4.0 38.4 1.0 OD2 B:ASP25 4.1 42.3 1.0 NE B:ARG61 4.1 41.9 1.0 NE2 B:GLN110 4.4 34.9 1.0 CG B:ASP25 4.5 42.1 1.0 O2A C:DUP1129 4.5 42.9 1.0 CG B:ARG61 4.6 42.0 1.0 O3G C:DUP1129 4.6 42.9 1.0 O2B C:DUP1129 4.7 39.5 1.0 O5' C:DUP1129 4.7 44.1 1.0 CD B:ARG61 4.8 42.9 1.0 O C:HOH2010 4.8 56.3 1.0 NZ F:LYS103 4.8 60.5 1.0 NH2 B:ARG61 4.9 42.9 1.0 CZ B:ARG61 5.0 44.1 1.0

Magnesium binding site 2 out of 3 in the Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp


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 Bacillus Subtilis Prophage Dutpase with Dupnhpp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1131 b:50.7 occ:1.00 O1A E:DUP1130 2.1 40.0 1.0 O2G E:DUP1130 2.1 45.2 1.0 O1B E:DUP1130 2.3 40.0 1.0 PA E:DUP1130 3.4 42.6 1.0 PG E:DUP1130 3.4 43.8 1.0 PB E:DUP1130 3.5 41.6 1.0 O3B E:DUP1130 3.9 41.2 1.0 N3A E:DUP1130 4.0 42.5 1.0 OD1 D:ASP25 4.0 38.1 1.0 O1G E:DUP1130 4.1 40.9 1.0 O E:HOH2018 4.1 75.1 1.0 OE1 D:GLN110 4.1 34.2 1.0 OD2 D:ASP25 4.2 39.1 1.0 NE D:ARG61 4.3 40.5 1.0 O2A E:DUP1130 4.3 39.5 1.0 O5' E:DUP1130 4.6 41.0 1.0 CG D:ASP25 4.6 37.3 1.0 O3G E:DUP1130 4.6 46.1 1.0 CG D:ARG61 4.8 38.2 1.0 C5' E:DUP1130 4.9 38.1 1.0 O E:HOH2020 4.9 40.8 1.0 CD D:GLN110 4.9 34.7 1.0 O2B E:DUP1130 4.9 40.3 1.0 NH2 D:ARG61 4.9 39.5 1.0

Magnesium binding site 3 out of 3 in the Structure of the Bacillus Subtilis Prophage Dutpase with Dupnhpp


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 Bacillus Subtilis Prophage Dutpase with Dupnhpp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1130 b:50.3 occ:1.00 O1A F:DUP1129 2.2 48.9 1.0 O1B F:DUP1129 2.2 46.6 1.0 O2G F:DUP1129 2.4 46.6 1.0 PB F:DUP1129 3.4 43.8 1.0 PG F:DUP1129 3.5 50.6 1.0 PA F:DUP1129 3.6 48.1 1.0 O E:HOH2003 3.6 42.2 1.0 O F:HOH2015 3.7 45.4 1.0 O F:HOH2016 3.7 39.6 1.0 O3B F:DUP1129 3.7 46.6 1.0 OD1 E:ASP25 3.9 40.6 1.0 O1G F:DUP1129 4.0 48.1 1.0 N3A F:DUP1129 4.0 44.5 1.0 NE E:ARG61 4.1 36.4 1.0 OD2 E:ASP25 4.1 42.6 1.0 O F:HOH2009 4.5 53.4 1.0 OE1 E:GLN110 4.5 32.3 1.0 CG E:ASP25 4.5 39.1 1.0 O2A F:DUP1129 4.5 46.7 1.0 NH2 E:ARG61 4.6 40.4 1.0 O5' F:DUP1129 4.6 51.2 1.0 O2B F:DUP1129 4.7 42.6 1.0 CG E:ARG61 4.8 35.2 1.0 O3G F:DUP1129 4.8 53.2 1.0 CZ E:ARG61 4.8 38.1 1.0 CD E:ARG61 4.9 35.5 1.0 C5' F:DUP1129 4.9 49.2 1.0

J.Garcia-Nafria, M.Harkiolaki, R.Persson, M.J.Fogg, K.S.Wilson. The Structure of Bacillus Subtilis Sp Beta Prophage Dutpase and Its Complexes with Two Nucleotides Acta Crystallogr.,Sect.D V. 67 167 2011.
ISSN: ISSN 0907-4449
PubMed: 21358047
DOI: 10.1107/S0907444911003234