Magnesium in PDB 6oq7: Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3

The structure of Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3, PDB code: 6oq7 was solved by P.Chen, K.Lam, R.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.14 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.018, 104.096, 113.825, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

The structure of Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3 (pdb code 6oq7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3, PDB code: 6oq7:

Magnesium binding site 1 out of 1 in the Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Gtd Domain of Clostridium Difficile Toxin B in Complex with Vhh E3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:25.7 occ:1.00 O A:HOH783 2.5 38.6 1.0 O A:HOH728 2.6 31.4 1.0 O A:ASN518 2.7 47.8 1.0 OD2 A:ASP288 2.8 39.3 1.0 O A:GLN515 2.9 42.8 1.0 O1A A:UDP601 3.0 38.4 1.0 O2A A:UDP601 3.0 35.7 1.0 PA A:UDP601 3.5 37.6 1.0 C A:ASN518 3.6 46.5 1.0 O A:HOH730 3.6 41.5 1.0 CG A:ASP288 3.7 38.4 1.0 MN A:MN603 3.8 39.6 1.0 C A:GLN515 3.9 45.5 1.0 CB A:ASP288 3.9 37.0 1.0 CD1 A:LEU520 4.0 49.3 1.0 CG A:LEU520 4.2 50.2 1.0 N A:SER519 4.3 45.8 1.0 CA A:SER519 4.4 46.7 1.0 CA A:GLU516 4.5 48.7 1.0 CA A:ASN518 4.5 49.6 1.0 O5' A:UDP601 4.6 39.0 1.0 N A:GLU516 4.6 46.6 1.0 N A:ASN518 4.6 48.5 1.0 O1B A:UDP601 4.6 38.6 1.0 NE2 A:GLN515 4.7 52.4 1.0 N A:LEU520 4.7 46.9 1.0 O3A A:UDP601 4.7 37.2 1.0 C A:GLU516 4.7 49.5 1.0 O A:GLU516 4.7 51.9 1.0 OD1 A:ASP288 4.8 35.9 1.0 CB A:ASN518 4.8 55.5 1.0 CB A:GLN515 4.8 47.2 1.0 OE2 A:GLU516 4.9 44.4 1.0 C A:SER519 4.9 47.5 1.0 CA A:GLN515 4.9 46.2 1.0

P.Chen, K.H.Lam, Z.Liu, F.A.Mindlin, B.Chen, C.B.Gutierrez, L.Huang, Y.Zhang, T.Hamza, H.Feng, T.Matsui, M.E.Bowen, K.Perry, R.Jin. Structure of the Full-Length Clostridium Difficile Toxin B. Nat.Struct.Mol.Biol. V. 26 712 2019.
ISSN: ESSN 1545-9985
PubMed: 31308519
DOI: 10.1038/S41594-019-0268-0