Magnesium in PDB 3gnz: Toxin Fold For Microbial Attack and Plant Defense

The structure of Toxin Fold For Microbial Attack and Plant Defense, PDB code: 3gnz was solved by C.Ottmann, B.Luberacki, I.Kuefner, W.Koch, F.Brunner, M.Weyand, L.Mattinen, M.Pirhonen, G.Anderluh, H.U.Seitz, T.Nuernberger, C.Oecking, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.40 / 1.35
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	69.630, 140.900, 49.620, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.4

The binding sites of Magnesium atom in the Toxin Fold For Microbial Attack and Plant Defense (pdb code 3gnz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Toxin Fold For Microbial Attack and Plant Defense, PDB code: 3gnz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Toxin Fold For Microbial Attack and Plant Defense


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Toxin Fold For Microbial Attack and Plant Defense within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg214 b:12.3 occ:0.60 O P:HOH417 1.9 43.1 0.6 O P:HOH422 1.9 19.8 1.0 O P:HOH353 1.9 7.3 1.0 O P:HOH331 2.0 12.0 1.0 OD1 P:ASP104 2.2 10.5 0.6 OD2 P:ASP93 2.2 11.7 1.0 OD1 P:ASP104 2.7 6.5 0.4 OD2 P:ASP104 2.8 5.5 0.4 CG P:ASP104 3.0 5.9 0.4 O P:HOH432 3.1 24.4 1.0 CG P:ASP104 3.1 9.0 0.6 CG P:ASP93 3.3 9.9 1.0 OD2 P:ASP104 3.3 9.8 0.6 OE2 P:GLU106 3.6 11.4 0.6 CE1 P:HIS101 3.6 11.3 0.3 CB P:ASP93 3.7 10.3 1.0 OD2 P:ASP158 3.8 18.0 0.5 O P:HOH414 3.8 21.5 1.0 O P:HIS159 3.9 8.9 1.0 NE2 P:HIS101 4.1 10.5 0.3 O P:HOH623 4.1 29.5 1.0 NE2 P:HIS101 4.1 11.2 0.3 O P:HOH418 4.2 39.7 0.4 CE1 P:HIS101 4.2 10.7 0.3 N P:HIS159 4.2 8.4 1.0 CG P:ASP158 4.2 14.1 0.5 CB P:HIS159 4.3 8.4 1.0 CB P:ASP104 4.3 6.0 0.4 O P:HOH398 4.3 23.2 1.0 OD1 P:ASP93 4.4 10.8 1.0 CB P:ASP158 4.5 9.3 0.5 CB P:ASP104 4.5 7.2 0.6 CB P:ASP158 4.5 11.4 0.5 C P:HIS159 4.5 8.3 1.0 CA P:HIS159 4.5 8.6 1.0 O P:HOH463 4.6 11.7 1.0 ND1 P:HIS101 4.7 11.1 0.3 CD P:GLU106 4.7 11.1 0.6 OD1 P:ASP158 4.9 17.9 0.5 CA P:ASP93 5.0 11.0 1.0

Magnesium binding site 2 out of 2 in the Toxin Fold For Microbial Attack and Plant Defense


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Toxin Fold For Microbial Attack and Plant Defense within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg215 b:7.1 occ:0.50 O P:HOH424 2.1 12.1 1.0 O P:HOH409 2.1 9.5 1.0 OD2 P:ASP6 2.1 7.6 1.0 CG P:ASP6 3.1 7.3 1.0 OD1 P:ASP6 3.4 8.1 1.0 OH P:TYR40 4.2 7.1 1.0 O P:HOH473 4.2 8.6 1.0 OD2 P:ASP65 4.2 9.7 1.0 NE2 P:HIS5 4.2 9.4 1.0 O P:ALA62 4.5 10.4 1.0 CB P:ASP6 4.5 7.5 1.0 CB P:ASP65 4.6 8.1 1.0 CE1 P:HIS5 4.9 8.7 1.0 CG P:ASP65 4.9 8.2 1.0

C.Ottmann, B.Luberacki, I.Kufner, W.Koch, F.Brunner, M.Weyand, L.Mattinen, M.Pirhonen, G.Anderluh, H.U.Seitz, T.Nurnberger, C.Oecking. A Common Toxin Fold Mediates Microbial Attack and Plant Defense Proc.Natl.Acad.Sci.Usa V. 106 10359 2009.
ISSN: ISSN 0027-8424
PubMed: 19520828
DOI: 10.1073/PNAS.0902362106