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Magnesium in PDB 6dmf: Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose

Protein crystallography data

The structure of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose, PDB code: 6dmf was solved by N.M.Koropatkin, C.M.Bahr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.60 / 2.40
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 228.845, 228.845, 246.517, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose (pdb code 6dmf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose, PDB code: 6dmf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6dmf

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Magnesium binding site 1 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


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 with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:45.9
occ:1.00
 O A:HOH785 1.9 49.1 1.0
O A:GLU557 2.0 39.9 1.0
O A:ARG492 2.2 22.1 1.0
O A:HOH740 2.3 49.5 1.0
O A:HOH738 2.3 51.2 1.0
OD1 A:ASP555 2.3 28.6 1.0
C A:GLU557 3.2 43.2 1.0
CG A:ASP555 3.2 27.8 1.0
C A:ARG492 3.3 22.4 1.0
OD2 A:ASP555 3.5 30.9 1.0
C A:ASN558 3.7 42.8 1.0
CA A:ARG492 3.8 21.5 1.0
N A:ASN558 4.0 44.2 1.0
CA A:ASN558 4.0 43.0 1.0
CA A:GLU557 4.2 45.1 1.0
O A:HOH794 4.3 56.7 1.0
N A:GLU557 4.3 41.5 1.0
CB A:ARG492 4.4 22.6 1.0
N A:ARG493 4.5 22.0 1.0
CB A:GLU557 4.6 50.0 1.0
CB A:ASP555 4.7 27.9 1.0
O A:ASN558 4.8 51.2 1.0
O A:VAL491 4.8 21.7 1.0
O A:ARG493 4.9 22.4 1.0
CA A:ARG493 4.9 21.5 1.0
CA A:GLY495 5.0 22.5 1.0

Magnesium binding site 2 out of 10 in 6dmf

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Magnesium binding site 2 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


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 with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:48.5
occ:1.00
 O B:HOH779 1.9 34.7 1.0
O B:HOH711 2.0 38.3 1.0
O B:ARG492 2.1 18.8 1.0
O B:GLU557 2.1 36.9 1.0
O B:HOH726 2.2 36.9 1.0
OD1 B:ASP555 2.3 22.3 1.0
C B:ARG492 3.2 17.8 1.0
CG B:ASP555 3.2 21.9 1.0
C B:GLU557 3.3 37.5 1.0
OD2 B:ASP555 3.4 22.4 1.0
CA B:ARG492 3.8 16.8 1.0
O B:HOH795 4.0 41.7 1.0
C B:ASN558 4.0 38.1 1.0
N B:ASN558 4.1 39.7 1.0
CA B:GLU557 4.3 39.3 1.0
CA B:ASN558 4.3 41.5 1.0
N B:GLU557 4.3 34.7 1.0
N B:ARG493 4.3 17.6 1.0
CB B:ARG492 4.4 16.5 1.0
O B:HOH829 4.5 46.6 1.0
CB B:GLU557 4.6 43.4 1.0
CB B:ASP555 4.6 22.6 1.0
O B:VAL491 4.7 18.1 1.0
O B:ASN558 4.7 39.7 1.0
O B:ARG493 4.7 18.1 1.0
CA B:ARG493 4.7 17.4 1.0
C B:ARG493 4.8 17.5 1.0
CA B:GLY495 4.8 18.7 1.0
N B:GLY495 4.9 18.5 1.0

Magnesium binding site 3 out of 10 in 6dmf

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Magnesium binding site 3 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg607

b:50.7
occ:1.00
 O C:HOH720 1.9 62.9 1.0
O C:GLU557 1.9 40.4 1.0
O C:ARG492 2.1 27.7 1.0
O C:HOH703 2.2 34.0 1.0
OD1 C:ASP555 2.5 31.2 1.0
O C:HOH755 2.5 32.7 1.0
C C:GLU557 3.1 45.3 1.0
C C:ARG492 3.3 26.3 1.0
CG C:ASP555 3.5 30.8 1.0
O C:HOH790 3.5 74.2 1.0
OD2 C:ASP555 3.7 30.6 1.0
CA C:ASN558 3.9 45.8 1.0
N C:ASN558 3.9 45.6 1.0
C C:ASN558 3.9 52.6 1.0
CA C:ARG492 4.0 24.2 1.0
N C:GLU557 4.2 39.8 1.0
CA C:GLU557 4.3 43.3 1.0
N C:ARG493 4.4 26.5 1.0
CA C:GLY495 4.6 25.7 1.0
CG C:GLU557 4.6 51.1 1.0
O C:ARG493 4.6 27.9 1.0
N C:GLY495 4.6 26.0 1.0
O C:VAL491 4.7 26.5 1.0
CA C:ARG493 4.7 27.0 1.0
C C:ARG493 4.7 26.5 1.0
CB C:ARG492 4.7 24.0 1.0
CB C:ASP555 4.9 32.0 1.0
O C:ASN558 5.0 55.5 1.0

Magnesium binding site 4 out of 10 in 6dmf

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Magnesium binding site 4 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg607

b:44.9
occ:1.00
 O D:HOH740 1.8 53.8 1.0
O D:GLU557 2.1 38.8 1.0
O D:ARG492 2.1 25.6 1.0
O D:HOH737 2.2 50.9 1.0
OD1 D:ASP555 2.3 33.1 1.0
O D:HOH706 2.5 59.7 1.0
C D:GLU557 3.3 45.3 1.0
C D:ARG492 3.3 24.4 1.0
CG D:ASP555 3.3 31.4 1.0
OD2 D:ASP555 3.7 32.9 1.0
CA D:ARG492 4.0 23.7 1.0
N D:GLU557 4.1 41.6 1.0
N D:ASN558 4.2 51.3 1.0
CA D:GLU557 4.2 45.0 1.0
C D:ASN558 4.2 53.5 1.0
CA D:ASN558 4.3 52.1 1.0
N D:ARG493 4.3 25.8 1.0
O D:ARG493 4.6 23.9 1.0
CB D:ASP555 4.6 31.3 1.0
CA D:ARG493 4.7 24.5 1.0
CB D:GLU557 4.7 50.4 1.0
O D:ASN558 4.7 54.4 1.0
CA D:GLY495 4.7 24.2 1.0
CB D:ARG492 4.7 24.5 1.0
N D:GLY495 4.7 24.1 1.0
C D:ARG493 4.7 24.0 1.0
O D:VAL491 4.8 24.9 1.0
N D:THR556 4.8 31.1 1.0
CA D:ASP555 4.9 30.9 1.0

Magnesium binding site 5 out of 10 in 6dmf

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Magnesium binding site 5 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg607

b:54.3
occ:1.00
 O E:HOH779 1.9 56.4 1.0
O E:ARG492 2.1 24.0 1.0
OD1 E:ASP555 2.3 28.8 1.0
O E:HOH702 2.4 36.4 1.0
O E:GLU557 2.6 59.7 1.0
C E:GLU557 3.2 55.2 1.0
C E:ARG492 3.3 22.1 1.0
CG E:ASP555 3.4 29.3 1.0
OE1 E:GLU557 3.6 64.4 1.0
OD2 E:ASP555 3.8 30.5 1.0
N E:ASN558 3.9 57.7 1.0
CA E:GLU557 3.9 54.9 1.0
N E:GLU557 4.0 50.4 1.0
CB E:GLU557 4.1 60.2 1.0
CA E:ARG492 4.1 20.8 1.0
C E:ASN558 4.1 53.2 1.0
O E:ARG493 4.3 22.6 1.0
CA E:ASN558 4.3 53.7 1.0
N E:ARG493 4.3 21.7 1.0
CD E:GLU557 4.4 67.3 1.0
C E:ARG493 4.5 21.4 1.0
CA E:ARG493 4.6 21.4 1.0
N E:GLY495 4.6 23.3 1.0
CB E:ASP555 4.7 30.3 1.0
CA E:GLY495 4.7 24.1 1.0
N E:THR556 4.7 33.1 1.0
CG E:GLU557 4.8 66.3 1.0
CB E:ARG492 4.8 20.5 1.0
CA E:ASP555 4.9 29.9 1.0
O E:VAL491 4.9 23.9 1.0
C E:ASP555 5.0 33.3 1.0

Magnesium binding site 6 out of 10 in 6dmf

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Magnesium binding site 6 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg607

b:52.3
occ:1.00
 O F:HOH718 1.8 72.3 1.0
O F:HOH715 2.0 47.9 1.0
OD1 F:ASP555 2.1 38.4 1.0
O F:GLU557 2.2 54.5 1.0
O F:ARG492 2.3 30.1 1.0
O F:HOH721 2.3 54.7 1.0
CG F:ASP555 3.1 37.8 1.0
C F:GLU557 3.3 57.0 1.0
C F:ARG492 3.4 29.2 1.0
OD2 F:ASP555 3.5 42.9 1.0
C F:ASN558 3.7 79.6 1.0
O F:HOH757 3.9 91.5 1.0
CA F:ARG492 3.9 28.7 1.0
N F:ASN558 4.1 65.2 1.0
CA F:ASN558 4.1 68.6 1.0
N F:GLU557 4.4 51.2 1.0
CA F:GLU557 4.4 55.3 1.0
OE1 F:GLU557 4.4 68.9 1.0
N F:ARG493 4.5 27.7 1.0
CB F:ASP555 4.5 36.7 1.0
CB F:ARG492 4.5 30.8 1.0
CD F:GLU557 4.5 63.0 1.0
O F:ASN558 4.6 84.9 1.0
O F:ARG493 4.8 28.7 1.0
CD2 F:LEU551 4.8 41.7 1.0
OE2 F:GLU557 4.8 58.0 1.0
CA F:ARG493 4.8 27.2 1.0
CA F:ASP555 4.8 35.1 1.0
C F:ARG493 4.9 27.3 1.0
C F:ASP555 4.9 37.0 1.0
CG F:GLU557 5.0 61.0 1.0
O F:VAL491 5.0 33.1 1.0
N F:THR556 5.0 38.4 1.0

Magnesium binding site 7 out of 10 in 6dmf

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Magnesium binding site 7 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg607

b:53.2
occ:1.00
 O G:HOH743 1.9 49.8 1.0
O G:GLU557 2.1 54.8 1.0
O G:HOH774 2.1 43.9 1.0
O G:ARG492 2.1 27.7 1.0
OD1 G:ASP555 2.2 40.2 1.0
O G:HOH710 2.3 54.3 1.0
C G:ARG492 3.2 26.4 1.0
C G:GLU557 3.2 54.0 1.0
CG G:ASP555 3.3 37.4 1.0
OD2 G:ASP555 3.7 42.3 1.0
CA G:ARG492 3.9 24.8 1.0
N G:GLU557 4.0 48.8 1.0
C G:ASN558 4.1 52.9 1.0
CA G:GLU557 4.1 51.3 1.0
N G:ASN558 4.2 57.6 1.0
O G:HOH783 4.2 45.4 1.0
N G:ARG493 4.3 26.5 1.0
CA G:ASN558 4.4 53.1 1.0
CB G:GLU557 4.5 55.3 1.0
CB G:ARG492 4.5 24.1 1.0
O G:ARG493 4.6 27.9 1.0
CB G:ASP555 4.6 37.7 1.0
CA G:ARG493 4.6 26.8 1.0
O G:ASN558 4.7 55.2 1.0
C G:ARG493 4.7 26.1 1.0
N G:THR556 4.7 38.9 1.0
CA G:ASP555 4.8 36.0 1.0
C G:ASP555 4.9 37.5 1.0
O G:VAL491 4.9 27.1 1.0
N G:GLY495 4.9 25.8 1.0
CA G:GLY495 4.9 27.1 1.0

Magnesium binding site 8 out of 10 in 6dmf

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Magnesium binding site 8 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg607

b:51.1
occ:1.00
 O H:HOH771 2.1 69.7 1.0
O H:ARG492 2.1 27.5 1.0
O H:HOH722 2.1 47.5 1.0
O H:HOH706 2.3 33.5 1.0
O H:GLU557 2.3 50.2 1.0
OD1 H:ASP555 2.4 34.3 1.0
C H:ARG492 3.3 26.5 1.0
CG H:ASP555 3.4 34.7 1.0
C H:GLU557 3.4 52.0 1.0
OD2 H:ASP555 3.6 36.1 1.0
CA H:ARG492 4.0 24.9 1.0
C H:ASN558 4.1 55.5 1.0
N H:GLU557 4.3 46.2 1.0
O H:ASN558 4.3 60.7 1.0
N H:ASN558 4.3 59.2 1.0
CA H:GLU557 4.3 49.2 1.0
N H:ARG493 4.4 24.7 1.0
O H:ARG493 4.4 26.7 1.0
CA H:ASN558 4.5 57.4 1.0
C H:ARG493 4.6 24.9 1.0
CB H:GLU557 4.6 51.7 1.0
CA H:ARG493 4.7 24.8 1.0
N H:GLY495 4.7 27.2 1.0
CA H:GLY495 4.7 27.4 1.0
CB H:ASP555 4.7 36.3 1.0
CB H:ARG492 4.8 25.5 1.0
O H:VAL491 4.8 26.2 1.0
O H:HOH783 4.9 49.1 1.0

Magnesium binding site 9 out of 10 in 6dmf

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Magnesium binding site 9 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg607

b:55.6
occ:1.00
 O I:HOH721 2.0 48.1 1.0
O I:HOH761 2.0 55.4 1.0
O I:ARG492 2.2 31.8 1.0
O I:HOH712 2.2 41.0 1.0
O I:GLU557 2.3 53.5 1.0
OD1 I:ASP555 2.4 31.8 1.0
C I:GLU557 3.2 54.5 1.0
C I:ARG492 3.3 30.4 1.0
CG I:ASP555 3.4 32.2 1.0
C I:ASN558 3.7 59.0 1.0
OD2 I:ASP555 3.7 32.9 1.0
CA I:ARG492 4.0 28.5 1.0
N I:ASN558 4.0 60.4 1.0
O I:HOH745 4.1 44.0 1.0
CA I:ASN558 4.1 58.0 1.0
CA I:GLU557 4.1 58.5 1.0
CB I:GLU557 4.2 62.2 1.0
N I:GLU557 4.3 56.7 1.0
N I:ARG493 4.4 30.1 1.0
OE1 I:GLU557 4.5 62.7 1.0
O I:ARG493 4.5 27.5 1.0
CA I:GLY495 4.7 32.8 1.0
CB I:ARG492 4.7 28.4 1.0
O I:ASN558 4.7 55.6 1.0
CA I:ARG493 4.8 29.0 1.0
C I:ARG493 4.8 29.1 1.0
O I:VAL491 4.8 30.9 1.0
CB I:ASP555 4.8 33.3 1.0
N I:GLY495 4.8 33.1 1.0

Magnesium binding site 10 out of 10 in 6dmf

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Magnesium binding site 10 out of 10 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-A with Cellohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg607

b:43.9
occ:1.00
 O J:HOH792 1.9 70.6 1.0
O J:ARG492 2.2 25.0 1.0
O J:HOH742 2.3 61.6 1.0
O J:HOH751 2.4 53.5 1.0
OD1 J:ASP555 2.4 28.6 1.0
O J:GLU557 2.9 49.1 1.0
C J:ARG492 3.3 25.2 1.0
CG J:ASP555 3.4 30.6 1.0
C J:GLU557 3.5 52.5 1.0
OD2 J:ASP555 3.6 30.5 1.0
CA J:ARG492 3.9 23.1 1.0
O J:HOH771 3.9 43.0 1.0
N J:ASN558 4.0 60.5 1.0
CA J:ASN558 4.1 59.6 1.0
CA J:GLU557 4.3 53.0 1.0
N J:GLU557 4.4 49.4 1.0
CB J:GLU557 4.4 56.7 1.0
N J:ARG493 4.5 25.3 1.0
CB J:ARG492 4.5 23.3 1.0
C J:ASN558 4.6 55.0 1.0
OE1 J:GLU557 4.6 56.6 1.0
O J:VAL491 4.8 23.5 1.0
CB J:ASP555 4.8 31.2 1.0
O J:ARG493 4.8 24.2 1.0
CA J:GLY495 4.8 24.0 1.0
CA J:ARG493 4.9 23.4 1.0
C J:ARG493 4.9 24.0 1.0
N J:GLY495 4.9 24.7 1.0
O J:ASN558 5.0 50.3 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 Sep 30 23:12:53 2024

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