Magnesium in PDB 7bxo: Crystal Structure of the Toxin-Antitoxin with Amp-Pnp

The structure of Crystal Structure of the Toxin-Antitoxin with Amp-Pnp, PDB code: 7bxo was solved by S.Y.Ouyang, X.K.Zhen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.14 / 2.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.510, 100.680, 132.510, 90.00, 96.44, 90.00
R / Rfree (%)	21.5 / 24.9

The binding sites of Magnesium atom in the Crystal Structure of the Toxin-Antitoxin with Amp-Pnp (pdb code 7bxo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Toxin-Antitoxin with Amp-Pnp, PDB code: 7bxo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Toxin-Antitoxin with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Toxin-Antitoxin with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:66.7 occ:1.00 O2B A:ANP201 2.1 98.4 1.0 O2G A:ANP201 2.2 99.1 1.0 O A:ASP39 2.3 83.3 1.0 OD2 A:ASP41 2.3 70.5 1.0 O2A A:ANP201 2.5 0.5 1.0 OD2 A:ASP39 3.2 0.4 1.0 CG A:ASP41 3.2 66.8 1.0 OD1 A:ASP41 3.3 65.9 1.0 PB A:ANP201 3.3 98.8 1.0 C A:ASP39 3.4 82.6 1.0 PG A:ANP201 3.5 99.1 1.0 PA A:ANP201 3.7 0.5 1.0 OG A:SER28 3.7 88.7 1.0 N3B A:ANP201 3.7 99.9 1.0 O3A A:ANP201 3.7 0.6 1.0 CB A:ASP39 3.8 85.0 1.0 CG A:ASP39 3.9 96.2 1.0 CA A:ASP39 4.0 83.3 1.0 C5' A:ANP201 4.0 0.1 1.0 N A:ASP39 4.1 85.7 1.0 O1G A:ANP201 4.2 99.1 1.0 MG A:MG203 4.2 86.3 1.0 O5' A:ANP201 4.3 0.7 1.0 N A:SER28 4.3 76.0 1.0 N A:ILE40 4.5 74.1 1.0 O1B A:ANP201 4.5 96.9 1.0 CB A:ASP41 4.6 63.6 1.0 CB A:SER28 4.6 80.3 1.0 O3G A:ANP201 4.7 99.3 1.0 N A:ASP41 4.7 64.0 1.0 CA A:GLY27 4.7 70.4 1.0 C A:ILE40 4.8 70.3 1.0 O1A A:ANP201 4.9 0.6 1.0 CA A:ILE40 4.9 71.6 1.0 OD1 A:ASP39 5.0 97.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Toxin-Antitoxin with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Toxin-Antitoxin with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:86.3 occ:1.00 OD2 A:ASP39 1.9 0.4 1.0 OD2 A:ASP71 2.7 0.3 1.0 OD1 A:ASP41 2.7 65.9 1.0 O2A A:ANP201 2.9 0.5 1.0 CG A:ASP39 3.0 96.2 1.0 CG A:ASP71 3.5 90.8 1.0 OD1 A:ASP39 3.5 97.2 1.0 O5' A:ANP201 3.6 0.7 1.0 CB A:ASP71 3.6 69.8 1.0 PA A:ANP201 3.7 0.5 1.0 CG A:ASP41 3.9 66.8 1.0 C5' A:ANP201 4.2 0.1 1.0 MG A:MG202 4.2 66.7 1.0 O1A A:ANP201 4.2 0.6 1.0 CB A:ASP39 4.2 85.0 1.0 OD2 A:ASP41 4.5 70.5 1.0 OD1 A:ASP71 4.6 92.8 1.0 ND2 D:ASN98 4.7 0.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Toxin-Antitoxin with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Toxin-Antitoxin with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:58.3 occ:1.00 OD2 E:ASP41 2.1 71.8 1.0 O2G E:ANP201 2.1 86.0 1.0 O2B E:ANP201 2.2 81.0 1.0 O E:ASP39 2.6 69.7 1.0 O2A E:ANP201 2.8 81.8 1.0 CB E:ASP39 3.0 72.7 1.0 CG E:ASP41 3.2 67.3 1.0 C E:ASP39 3.2 70.3 1.0 PB E:ANP201 3.5 81.2 1.0 PG E:ANP201 3.5 85.2 1.0 CA E:ASP39 3.6 70.8 1.0 N E:ASP39 3.7 72.8 1.0 OD1 E:ASP41 3.7 69.6 1.0 OD2 E:ASP39 3.8 86.3 1.0 N3B E:ANP201 3.8 82.7 1.0 CG E:ASP39 3.9 83.6 1.0 PA E:ANP201 3.9 80.5 1.0 O3A E:ANP201 4.0 81.3 1.0 OG E:SER28 4.1 78.0 1.0 N E:SER28 4.2 65.6 1.0 N E:ILE40 4.3 63.0 1.0 O1G E:ANP201 4.3 84.3 1.0 MG E:MG203 4.3 72.0 1.0 C5' E:ANP201 4.3 76.3 1.0 CA E:GLY27 4.3 62.4 1.0 CB E:ASP41 4.4 57.7 1.0 N E:ASP41 4.5 57.5 1.0 O3G E:ANP201 4.6 87.5 1.0 O5' E:ANP201 4.6 77.7 1.0 O1B E:ANP201 4.7 81.0 1.0 CA E:ILE40 4.8 61.2 1.0 C E:ILE40 4.8 62.7 1.0 C E:GLY27 4.8 67.3 1.0 CB E:SER28 4.8 69.2 1.0 C E:SER38 5.0 79.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Toxin-Antitoxin with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Toxin-Antitoxin with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:72.0 occ:1.00 OD2 E:ASP39 1.9 86.3 1.0 O2A E:ANP201 2.5 81.8 1.0 OD1 E:ASP41 2.6 69.6 1.0 CG E:ASP39 3.1 83.6 1.0 PA E:ANP201 3.4 80.5 1.0 OD2 E:ASP71 3.6 90.7 1.0 O5' E:ANP201 3.6 77.7 1.0 CG E:ASP41 3.6 67.3 1.0 O1A E:ANP201 3.7 82.4 1.0 CG E:ASP71 3.7 82.8 1.0 CB E:ASP71 3.8 60.7 1.0 CB E:ASP39 3.9 72.7 1.0 OD2 E:ASP41 4.0 71.8 1.0 OD1 E:ASP39 4.0 86.0 1.0 CB H:ALA104 4.3 0.7 1.0 C5' E:ANP201 4.3 76.3 1.0 MG E:MG202 4.3 58.3 1.0 OD1 E:ASP71 4.4 85.7 1.0 OD1 H:ASN98 4.4 97.7 1.0 O3A E:ANP201 4.9 81.3 1.0 CB E:ASP41 4.9 57.7 1.0

J.Yao, X.Zhen, K.Tang, T.Liu, X.Xu, Z.Chen, Y.Guo, X.Liu, T.K.Wood, S.Ouyang, X.Wang. Novel Polyadenylylation-Dependent Neutralization Mechanism of the Hepn/Mnt Toxin/Antitoxin System. Nucleic Acids Res. V. 48 11054 2020.
ISSN: ESSN 1362-4962
PubMed: 33045733
DOI: 10.1093/NAR/GKAA855