Magnesium in PDB 4pu5: Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg

The structure of Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg, PDB code: 4pu5 was solved by Y.Wen, E.Behiels, J.Felix, J.Elegheert, B.Vergauwen, B.Devreese, S.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.61 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.700, 75.830, 110.320, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.5

The structure of Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg (pdb code 4pu5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg, PDB code: 4pu5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:15.7 occ:1.00 O A:HOH858 2.0 12.5 1.0 O3G A:ANP503 2.0 11.8 1.0 O2B A:ANP503 2.1 12.3 1.0 O A:HOH857 2.1 11.0 1.0 OD1 A:ASP328 2.2 11.0 1.0 OD2 A:ASP328 2.2 11.3 1.0 CG A:ASP328 2.5 10.4 1.0 PG A:ANP503 3.0 13.1 1.0 PB A:ANP503 3.2 12.0 1.0 HZ1 A:LYS178 3.4 18.7 1.0 N3B A:ANP503 3.4 8.2 0.9 O2G A:ANP503 3.4 13.7 0.9 HD21 A:ASN311 3.7 13.7 1.0 MG A:MG502 3.7 11.7 1.0 O A:HOH859 3.9 28.5 1.0 O A:HOH1057 3.9 34.4 1.0 HG2 A:GLN152 4.0 24.7 1.0 CB A:ASP328 4.0 9.5 1.0 O A:HOH804 4.1 17.4 1.0 O1B A:ANP503 4.2 12.5 1.0 NZ A:LYS178 4.2 15.6 1.0 HNB1 A:ANP503 4.3 9.8 0.9 O3A A:ANP503 4.3 12.4 1.0 OD2 A:ASP306 4.3 15.5 1.0 O A:HOH843 4.3 11.2 1.0 HG3 A:GLN152 4.3 24.7 1.0 HZ2 A:LYS178 4.4 18.7 1.0 HG21 A:VAL330 4.4 17.5 1.0 HB2 A:ASP328 4.4 11.4 1.0 O1G A:ANP503 4.5 11.6 1.0 HB3 A:ASP328 4.5 11.4 1.0 ND2 A:ASN311 4.5 11.4 1.0 O2A A:ANP503 4.5 9.7 1.0 O A:HOH1074 4.5 43.1 1.0 HA A:ASP328 4.6 11.6 1.0 HZ3 A:LYS178 4.6 18.7 1.0 CG A:GLN152 4.6 20.6 1.0 O A:HOH1055 4.7 36.7 1.0 O A:ASP328 4.8 11.4 1.0 PA A:ANP503 4.8 10.7 1.0 HG23 A:VAL330 4.8 17.5 1.0 HE21 A:GLN152 4.8 35.0 1.0 CA A:ASP328 4.8 9.7 1.0 HE2 A:HIS308 4.9 14.1 1.0 OD1 A:ASN311 4.9 10.7 1.0 HG22 A:VAL151 4.9 27.1 1.0 O1A A:ANP503 5.0 10.0 0.9 HD22 A:ASN311 5.0 13.7 1.0

Magnesium binding site 2 out of 2 in the Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Shewanella Oneidensis Toxin Antitoxin System Toxin Protein Hipa Bound with Amppnp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:11.7 occ:1.00 O2A A:ANP503 2.0 9.7 1.0 OD1 A:ASN311 2.0 10.7 1.0 OD2 A:ASP328 2.1 11.3 1.0 O A:HOH907 2.2 9.2 1.0 O2G A:ANP503 2.2 13.7 0.9 N3B A:ANP503 2.3 8.2 0.9 HNB1 A:ANP503 2.7 9.8 0.9 PG A:ANP503 2.8 13.1 1.0 CG A:ASN311 3.0 10.7 1.0 HD21 A:ASN311 3.0 13.7 1.0 CG A:ASP328 3.1 10.4 1.0 PA A:ANP503 3.3 10.7 1.0 ND2 A:ASN311 3.4 11.4 1.0 HB2 A:ASP328 3.4 11.4 1.0 PB A:ANP503 3.4 12.0 1.0 HE1 A:HIS308 3.6 14.0 1.0 CB A:ASP328 3.6 9.5 1.0 HB3 A:ASP328 3.7 11.4 1.0 O3A A:ANP503 3.7 12.4 1.0 MG A:MG501 3.7 15.7 1.0 H5'2 A:ANP503 3.7 13.5 1.0 HE2 A:HIS308 3.8 14.1 1.0 O3G A:ANP503 3.8 11.8 1.0 HE1 A:TYR327 3.8 10.6 1.0 O2B A:ANP503 3.9 12.3 1.0 O A:HOH890 4.0 12.8 1.0 O1G A:ANP503 4.0 11.6 1.0 HA A:ASN311 4.1 11.9 1.0 CE1 A:HIS308 4.1 11.7 1.0 H3' A:ANP503 4.1 13.2 1.0 OD1 A:ASP328 4.2 11.0 1.0 NE2 A:HIS308 4.2 11.8 1.0 HO3' A:ANP503 4.2 13.8 0.9 O1A A:ANP503 4.2 10.0 0.9 HD22 A:ASN311 4.2 13.7 1.0 O3' A:ANP503 4.3 11.5 0.9 O5' A:ANP503 4.3 11.2 1.0 CB A:ASN311 4.4 9.8 1.0 HA2 A:GLY150 4.4 15.3 1.0 HD1 A:TYR327 4.4 10.4 1.0 C5' A:ANP503 4.5 11.3 1.0 HA3 A:GLY150 4.5 15.3 1.0 O A:LYS310 4.5 11.6 1.0 CE1 A:TYR327 4.6 8.8 1.0 O A:HOH857 4.6 11.0 1.0 C3' A:ANP503 4.6 11.0 1.0 CA A:ASN311 4.7 9.9 1.0 O1B A:ANP503 4.7 12.5 1.0 HB3 A:ASN311 4.8 11.8 1.0 CD1 A:TYR327 4.9 8.7 1.0 C A:LYS310 4.9 11.6 1.0 CA A:GLY150 4.9 12.8 1.0 HB2 A:ASN311 4.9 11.8 1.0 N A:ASN311 5.0 10.8 1.0

Y.Wen, E.Behiels, J.Felix, J.Elegheert, B.Vergauwen, B.Devreese, S.N.Savvides. The Bacterial Antitoxin Hipb Establishes A Ternary Complex with Operator Dna and Phosphorylated Toxin Hipa to Regulate Bacterial Persistence. Nucleic Acids Res. V. 42 10134 2014.
ISSN: ISSN 0305-1048
PubMed: 25056321
DOI: 10.1093/NAR/GKU665