Magnesium in PDB 6e61: Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide

Protein crystallography data

The structure of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide, PDB code: 6e61 was solved by K.Tamura, B.R.Gardill, H.Brumer, F.Van Petegem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.65 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.826, 92.943, 155.253, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide (pdb code 6e61). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide, PDB code: 6e61:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6e61

Go back to Magnesium Binding Sites List in 6e61
Magnesium binding site 1 out of 2 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:22.6
occ:1.00
OD1 A:ASP555 2.0 27.3 1.0
O A:GLU557 2.0 46.8 1.0
O A:ARG492 2.1 24.1 1.0
O A:HOH859 2.2 36.5 1.0
O A:HOH865 2.2 16.3 1.0
O A:HOH753 2.2 19.1 1.0
CG A:ASP555 3.0 27.4 1.0
C A:ARG492 3.3 23.1 1.0
C A:GLU557 3.3 49.7 1.0
OD2 A:ASP555 3.5 27.9 1.0
CA A:ARG492 3.9 23.4 1.0
N A:GLU557 4.0 47.5 1.0
C A:ASN558 4.0 55.6 1.0
O A:HOH840 4.1 19.1 1.0
CA A:GLU557 4.2 49.3 1.0
N A:ASN558 4.2 53.4 1.0
N A:ARG493 4.3 22.2 1.0
CB A:ASP555 4.3 27.7 1.0
CA A:ASN558 4.4 56.1 1.0
CB A:ARG492 4.6 23.6 1.0
O A:ARG493 4.6 21.9 1.0
CA A:ASP555 4.6 28.5 1.0
CG A:GLU557 4.6 53.4 1.0
N A:THR556 4.6 34.9 1.0
C A:ASP555 4.7 31.3 1.0
CA A:ARG493 4.7 21.7 1.0
C A:ARG493 4.8 21.6 1.0
CD2 A:LEU551 4.8 23.8 1.0
O A:ASN558 4.9 54.0 1.0
N A:GLY495 4.9 23.4 1.0
CA A:GLY495 4.9 23.9 1.0
O A:VAL491 4.9 24.5 1.0
CB A:GLU557 5.0 51.0 1.0

Magnesium binding site 2 out of 2 in 6e61

Go back to Magnesium Binding Sites List in 6e61
Magnesium binding site 2 out of 2 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A in Complex with Mixed-Linkage Heptasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:24.1
occ:1.00
O B:HOH795 2.0 21.0 1.0
O B:GLU557 2.0 50.6 1.0
OD1 B:ASP555 2.0 27.8 1.0
O B:HOH723 2.0 20.1 1.0
O B:ARG492 2.2 23.9 1.0
O B:HOH754 2.3 20.6 1.0
CG B:ASP555 3.0 27.8 1.0
C B:GLU557 3.2 54.1 1.0
C B:ARG492 3.3 22.5 1.0
OD2 B:ASP555 3.4 26.1 1.0
N B:GLU557 4.0 46.8 1.0
CA B:ARG492 4.0 21.9 1.0
N B:ASN558 4.1 59.2 1.0
CA B:GLU557 4.2 50.6 1.0
CA B:ASN558 4.3 59.6 1.0
CB B:ASP555 4.4 28.2 1.0
N B:ARG493 4.4 22.2 1.0
O B:ARG493 4.6 22.1 1.0
N B:THR556 4.6 35.5 1.0
CB B:ARG492 4.6 22.0 1.0
CA B:ASP555 4.7 28.9 1.0
CA B:ARG493 4.7 21.9 1.0
O B:HOH899 4.7 24.5 1.0
CD2 B:LEU551 4.8 29.5 1.0
C B:ARG493 4.8 21.1 1.0
C B:ASP555 4.9 32.1 1.0
CB B:GLU557 4.9 48.7 1.0

Reference:

K.Tamura, M.H.Foley, B.R.Gardill, G.Dejean, M.Schnizlein, C.M.E.Bahr, A.Louise Creagh, F.Van Petegem, N.M.Koropatkin, H.Brumer. Surface Glycan-Binding Proteins Are Essential For Cereal Beta-Glucan Utilization By the Human Gut Symbiont Bacteroides Ovatus. Cell.Mol.Life Sci. V. 76 4319 2019.
ISSN: ESSN 1420-9071
PubMed: 31062073
DOI: 10.1007/S00018-019-03115-3
Page generated: Mon Dec 14 22:38:00 2020

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