Atomistry » Magnesium » PDB 6oiw-6oqv » 6oq7
Atomistry »
  Magnesium »
    PDB 6oiw-6oqv »
      6oq7 »

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

Protein crystallography data

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

Other elements in 6oq7:

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

Magnesium Binding Sites:

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 6oq7

Go back to Magnesium Binding Sites List in 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

Reference:

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
Page generated: Tue Oct 1 13:31:43 2024

Last articles

Mn in 2GU7
Mn in 2GU6
Mn in 2GU5
Mn in 2GUI
Mn in 2GU4
Mn in 2GLF
Mn in 2G50
Mn in 2GTX
Mn in 2GND
Mn in 2GNM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy