Magnesium in PDB 2pza: Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+

All present enzymatic activity of Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+:
6.3.1.5;

The structure of Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+, PDB code: 2pza was solved by H.M.Mcdonald, P.S.Pruett, C.Deivanayagam, I.I.Protasevich, W.M.Carson, L.J.Delucas, W.J.Brouillette, C.G.Brouillette, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.77 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.046, 96.375, 68.612, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.9

The binding sites of Magnesium atom in the Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+ (pdb code 2pza). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+, PDB code: 2pza:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg6242 b:15.1 occ:1.00 O5 A:POP6000 2.1 15.3 1.0 O1P A:AMP4000 2.1 14.5 1.0 O A:HOH6362 2.1 11.6 1.0 OE2 A:GLU163 2.1 21.9 1.0 O1 A:POP6000 2.2 19.0 1.0 OD2 A:ASP51 2.4 16.1 1.0 CD A:GLU163 3.2 20.5 1.0 P1 A:POP6000 3.3 18.0 1.0 CG A:ASP51 3.4 17.8 1.0 P2 A:POP6000 3.4 18.2 1.0 P A:AMP4000 3.4 16.1 1.0 O A:POP6000 3.5 18.3 1.0 CB A:ASP51 3.6 16.1 1.0 OE1 A:GLU163 3.6 21.0 1.0 C5' A:AMP4000 3.8 13.9 1.0 O5' A:AMP4000 3.8 14.0 1.0 O3P A:AMP4000 4.0 16.5 1.0 O3 A:POP6000 4.1 17.1 1.0 O A:HOH6247 4.1 20.5 1.0 O3' A:AMP4000 4.1 16.5 1.0 O A:HOH6252 4.2 16.9 1.0 OG1 A:THR158 4.2 9.5 1.0 O6 A:POP6000 4.2 16.0 1.0 CE1 A:HIS160 4.3 10.0 1.0 O A:HOH6279 4.3 20.8 1.0 O2 A:POP6000 4.5 17.7 1.0 CG A:GLU163 4.5 20.8 1.0 O4 A:POP6000 4.5 18.1 1.0 OD1 A:ASP51 4.5 16.1 1.0 O2P A:AMP4000 4.6 15.8 1.0 C3' A:AMP4000 4.8 14.0 1.0 C4' A:AMP4000 4.8 14.5 1.0 NZ A:LYS187 4.9 14.9 1.0 MG A:MG6243 4.9 9.7 1.0 CA A:ASP51 4.9 15.6 1.0

Magnesium binding site 2 out of 4 in the Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg6243 b:9.7 occ:1.00 O3P A:AMP4000 2.0 16.5 1.0 O A:HOH6361 2.0 16.4 1.0 O6 A:POP6000 2.1 16.0 1.0 O A:THR209 2.1 18.8 1.0 O A:HOH6360 2.1 11.2 1.0 O3 A:POP6000 2.2 17.1 1.0 C A:THR209 3.2 18.4 1.0 P2 A:POP6000 3.4 18.2 1.0 P1 A:POP6000 3.4 18.0 1.0 P A:AMP4000 3.5 16.1 1.0 O A:POP6000 3.5 18.3 1.0 OG A:SER47 3.8 10.5 1.0 O5' A:AMP4000 3.9 14.0 1.0 CA A:ALA210 4.0 16.5 0.0 N A:ALA210 4.0 17.1 1.0 O5 A:POP6000 4.0 15.3 1.0 O A:HOH6252 4.1 16.9 1.0 O1 A:POP6000 4.1 19.0 1.0 N A:THR209 4.1 18.4 0.0 O1P A:AMP4000 4.2 14.5 1.0 O A:HOH6266 4.2 16.6 1.0 CA A:THR209 4.3 17.9 1.0 O A:HOH6309 4.4 23.1 1.0 O A:HOH6323 4.4 37.6 1.0 CB A:SER47 4.5 12.9 1.0 O2P A:AMP4000 4.5 15.8 1.0 O4 A:POP6000 4.5 18.1 1.0 C A:ALA210 4.6 16.1 0.0 O2 A:POP6000 4.6 17.7 1.0 CG2 A:THR209 4.6 18.8 1.0 CA A:GLY49 4.7 15.2 1.0 O A:ALA210 4.9 16.9 1.0 MG A:MG6242 4.9 15.1 1.0

Magnesium binding site 3 out of 4 in the Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg6240 b:6.6 occ:1.00 O B:HOH7111 1.8 16.6 1.0 O B:HOH7110 2.0 5.8 1.0 O6 B:POP7000 2.0 14.5 1.0 O B:THR209 2.0 12.7 1.0 O3 B:POP7000 2.1 14.4 1.0 O3P B:AMP5000 2.1 11.1 1.0 C B:THR209 3.1 13.2 1.0 P1 B:POP7000 3.3 15.1 1.0 P2 B:POP7000 3.3 15.4 1.0 O B:POP7000 3.4 15.1 1.0 P B:AMP5000 3.6 16.3 1.0 OG B:SER47 3.9 11.2 1.0 N B:THR209 3.9 14.1 0.0 O1 B:POP7000 3.9 16.0 1.0 N B:ALA210 4.0 11.9 1.0 O5 B:POP7000 4.0 12.7 1.0 CA B:ALA210 4.0 13.1 0.0 O5' B:AMP5000 4.0 13.6 1.0 O B:HOH7007 4.1 13.1 1.0 O B:HOH7035 4.1 19.0 1.0 CA B:THR209 4.1 12.6 1.0 O B:HOH7060 4.2 20.8 1.0 O B:HOH7096 4.2 37.8 1.0 O1P B:AMP5000 4.3 11.1 1.0 O2 B:POP7000 4.4 17.4 1.0 O4 B:POP7000 4.5 16.3 1.0 CB B:SER47 4.5 10.5 1.0 CA B:GLY49 4.5 11.0 1.0 CG2 B:THR209 4.6 11.7 1.0 C B:ALA210 4.7 13.0 0.0 O2P B:AMP5000 4.7 15.1 1.0 MG B:MG6241 4.7 11.6 1.0 CB B:THR209 5.0 13.3 1.0

Magnesium binding site 4 out of 4 in the Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nad+ Synthetase From Bacillus Anthracis with Amp + Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg6241 b:11.6 occ:1.00 O1P B:AMP5000 1.9 11.1 1.0 O1 B:POP7000 2.0 16.0 1.0 O5 B:POP7000 2.0 12.7 1.0 O B:HOH7112 2.2 10.4 1.0 OD2 B:ASP51 2.2 9.9 1.0 OE1 B:GLU163 2.6 15.5 1.0 P1 B:POP7000 3.1 15.1 1.0 P B:AMP5000 3.1 16.3 1.0 CG B:ASP51 3.2 11.1 1.0 P2 B:POP7000 3.3 15.4 1.0 O B:POP7000 3.3 15.1 1.0 CD B:GLU163 3.6 19.1 1.0 CB B:ASP51 3.6 11.5 1.0 O5' B:AMP5000 3.7 13.6 1.0 O3P B:AMP5000 3.7 11.1 1.0 O B:HOH7007 3.9 13.1 1.0 C5' B:AMP5000 3.9 13.7 1.0 OE2 B:GLU163 4.0 21.8 1.0 O3 B:POP7000 4.0 14.4 1.0 O B:HOH7047 4.1 17.3 1.0 O6 B:POP7000 4.1 14.5 1.0 O B:HOH7003 4.1 22.8 1.0 O3' B:AMP5000 4.2 17.2 1.0 O2 B:POP7000 4.3 17.4 1.0 OD1 B:ASP51 4.3 11.9 1.0 O2P B:AMP5000 4.4 15.1 1.0 NZ B:LYS187 4.4 10.0 1.0 CE1 B:HIS160 4.4 8.8 1.0 O4 B:POP7000 4.5 16.3 1.0 OG1 B:THR158 4.7 8.9 1.0 MG B:MG6240 4.7 6.6 1.0 C3' B:AMP5000 4.8 15.8 1.0 C4' B:AMP5000 4.9 15.5 1.0 CG B:GLU163 4.9 19.8 1.0 CA B:ASP51 5.0 11.8 1.0

H.M.Mcdonald, P.S.Pruett, C.Deivanayagam, I.I.Protasevich, W.M.Carson, L.J.Delucas, W.J.Brouillette, C.G.Brouillette. Structural Adaptation of An Interacting Non-Native C-Terminal Helical Extension Revealed in the Crystal Structure of Nad(+) Synthetase From Bacillus Anthracis. Acta Crystallogr.,Sect.D V. 63 891 2007.
ISSN: ISSN 0907-4449
PubMed: 17642516
DOI: 10.1107/S0907444907029769