Magnesium in PDB 4xgq: Crystal Structure of Addiction Module From Mycobacterial Species

The structure of Crystal Structure of Addiction Module From Mycobacterial Species, PDB code: 4xgq was solved by B.-J.Lee, I.-G.Lee, S.J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.66 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.381, 96.381, 232.788, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Addiction Module From Mycobacterial Species (pdb code 4xgq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Addiction Module From Mycobacterial Species, PDB code: 4xgq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Addiction Module From Mycobacterial Species


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 Addiction Module From Mycobacterial Species within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:38.8 occ:1.00 OD1 A:ASP99 2.8 54.7 1.0 OD1 A:ASP4 2.9 50.3 1.0 OD2 A:ASP4 3.1 50.2 1.0 CG A:ASP4 3.4 52.0 1.0 OE1 A:GLU40 3.5 67.1 1.0 CA A:ASP99 3.6 49.2 1.0 N A:ASP99 3.7 50.5 1.0 OG1 A:THR5 3.7 54.1 1.0 CB A:THR5 3.8 51.3 1.0 C A:GLY98 3.8 50.0 1.0 CG A:ASP99 3.9 55.0 1.0 O A:GLY98 3.9 56.0 1.0 CB A:ASP99 4.3 50.9 1.0 N A:THR5 4.3 54.3 1.0 CZ A:PHE120 4.3 55.9 1.0 CD A:GLU40 4.5 59.4 1.0 O A:HOH325 4.6 48.2 1.0 CE1 A:PHE120 4.6 54.8 1.0 OG A:SER37 4.6 49.5 1.0 CA A:GLY98 4.7 46.2 1.0 CA A:THR5 4.7 51.6 1.0 C A:ASP99 4.7 49.8 1.0 OE2 A:GLU40 4.7 63.6 1.0 N A:SER6 4.7 48.3 1.0 CB A:ASP4 4.9 51.8 1.0 CG2 A:THR5 4.9 49.5 1.0 O A:ASP99 5.0 52.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Addiction Module From Mycobacterial Species


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 Addiction Module From Mycobacterial Species within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:42.0 occ:1.00 O E:HOH321 2.8 55.8 1.0 OD1 E:ASP99 2.8 57.8 1.0 OE1 E:GLU40 2.8 62.6 1.0 OE2 E:GLU40 2.9 65.7 1.0 CD E:GLU40 3.2 60.5 1.0 CB E:THR5 3.5 47.6 1.0 OD1 E:ASP4 3.7 56.2 1.0 CG E:ASP99 3.8 60.7 1.0 OG1 E:THR5 3.9 47.6 1.0 C E:GLY98 4.0 49.0 1.0 N E:ASP99 4.0 48.0 1.0 CG2 E:THR5 4.0 50.2 1.0 OD2 E:ASP4 4.1 58.7 1.0 O E:GLY98 4.2 52.9 1.0 CA E:ASP99 4.3 52.2 1.0 CG E:ASP4 4.3 56.6 1.0 CA E:GLY98 4.5 54.4 1.0 O E:HOH329 4.5 46.6 1.0 CA E:THR5 4.6 48.0 1.0 OD2 E:ASP99 4.6 58.6 1.0 N E:SER6 4.6 52.0 1.0 OD1 E:ASN96 4.6 58.8 1.0 N E:THR5 4.7 50.0 1.0 CG E:GLU40 4.7 46.2 1.0 CB E:ASP99 4.7 54.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Addiction Module From Mycobacterial Species


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 Addiction Module From Mycobacterial Species within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:39.5 occ:1.00 OD1 C:ASP4 2.8 63.7 1.0 OD1 C:ASP99 2.8 52.6 1.0 OE1 C:GLU40 3.2 51.3 1.0 OD2 C:ASP4 3.2 59.8 1.0 O C:HOH306 3.3 53.0 1.0 CG C:ASP4 3.4 62.0 1.0 OG1 C:THR5 3.4 53.4 1.0 N C:ASP99 3.4 49.8 1.0 C C:GLY98 3.5 51.0 1.0 CA C:ASP99 3.6 49.6 1.0 O C:GLY98 3.8 53.0 1.0 CG C:ASP99 3.9 52.7 1.0 O C:HOH318 3.9 61.8 1.0 CD C:GLU40 4.1 48.9 1.0 OE2 C:GLU40 4.1 51.6 1.0 CA C:GLY98 4.2 49.1 1.0 CG2 C:THR5 4.2 50.3 1.0 CB C:THR5 4.3 51.6 1.0 CB C:ASP99 4.4 49.2 1.0 N C:THR5 4.4 51.0 1.0 OD1 C:ASN96 4.5 60.2 1.0 CZ C:PHE120 4.7 49.3 1.0 OG C:SER102 4.7 60.5 1.0 N C:SER6 4.8 46.3 1.0 CE1 C:PHE120 4.8 52.5 1.0 CB C:ASP4 4.9 50.9 1.0 CA C:THR5 4.9 53.7 1.0 C C:ASP99 4.9 50.1 1.0 OD2 C:ASP99 4.9 45.9 1.0

I.-G.Lee, S.J.Lee, S.Chae, K.Y.Lee, J.H.Kim, B.-J.Lee. Structural and Functional Studies of the Mycobacterium Tuberculosis VAPBC30 Toxin-Antitoxin System: Implications For the Design of Novel Antimicrobial Peptides Nucleic Acids Res. V. 43 7624 2015.
ISSN: ESSN 1362-4962
PubMed: 26150422
DOI: 10.1093/NAR/GKV689