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Sodium in PDB 6d50: Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone

Protein crystallography data

The structure of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone, PDB code: 6d50 was solved by W.G.Walton, S.J.Pellock, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.489, 141.880, 180.803, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 23.1

Other elements in 6d50:

The structure of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone (pdb code 6d50). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone, PDB code: 6d50:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6d50

Go back to Sodium Binding Sites List in 6d50
Sodium binding site 1 out of 2 in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:25.7
occ:1.00
O A:VAL725 2.4 36.1 1.0
O A:ASN878 2.5 36.3 1.0
OD1 A:ASN724 2.5 32.1 1.0
O A:THR776 2.6 38.6 1.0
O A:LEU773 2.7 33.4 1.0
OG1 A:THR776 2.8 36.8 1.0
C A:THR776 3.3 38.4 1.0
C A:VAL725 3.4 40.4 1.0
N A:VAL725 3.4 34.1 1.0
C A:ASN878 3.6 36.1 1.0
C A:ASN724 3.6 32.4 1.0
CG A:ASN724 3.7 32.0 1.0
C A:LEU773 3.8 33.4 1.0
CB A:THR776 3.9 39.4 1.0
CA A:VAL725 3.9 38.5 1.0
O A:ASN724 4.0 38.5 1.0
CA A:THR776 4.0 32.7 1.0
N A:LEU777 4.1 35.4 1.0
CA A:ASN724 4.1 32.6 1.0
CA A:ASN878 4.2 33.1 1.0
N A:THR776 4.2 36.7 1.0
CD1 A:LEU773 4.4 33.2 1.0
CA A:LEU777 4.4 34.8 1.0
N A:GLY726 4.5 39.4 1.0
CB A:ASN724 4.5 32.2 1.0
ND2 A:ASN724 4.5 35.3 1.0
CB A:ASN878 4.6 32.0 1.0
CB A:VAL725 4.6 34.5 1.0
CA A:LEU773 4.6 31.7 1.0
CB A:SER727 4.7 38.0 1.0
N A:GLY879 4.7 36.1 1.0
O A:PRO772 4.8 34.9 1.0
CA A:GLY726 4.8 40.2 1.0
N A:PHE774 4.8 32.3 1.0
O A:HOH1168 4.9 33.6 1.0
CA A:GLY879 4.9 30.7 1.0

Sodium binding site 2 out of 2 in 6d50

Go back to Sodium Binding Sites List in 6d50
Sodium binding site 2 out of 2 in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na902

b:26.8
occ:1.00
OD1 B:ASN724 2.4 39.9 1.0
O B:THR776 2.5 37.5 1.0
O B:ASN878 2.6 41.5 1.0
O B:VAL725 2.6 38.9 1.0
O B:LEU773 2.6 37.9 1.0
OG1 B:THR776 2.6 34.8 1.0
C B:THR776 3.3 40.8 1.0
CG B:ASN724 3.5 35.6 1.0
C B:VAL725 3.6 35.9 1.0
CB B:THR776 3.6 42.0 1.0
N B:VAL725 3.6 41.8 1.0
C B:ASN878 3.7 41.4 1.0
C B:LEU773 3.7 36.2 1.0
C B:ASN724 3.7 39.0 1.0
CA B:THR776 3.9 35.9 1.0
O B:ASN724 4.0 36.6 1.0
N B:THR776 4.1 26.4 1.0
CA B:ASN724 4.1 35.5 1.0
CA B:VAL725 4.2 38.4 1.0
CA B:ASN878 4.2 35.3 1.0
N B:LEU777 4.3 43.0 1.0
CA B:LEU773 4.3 33.5 1.0
CD1 B:LEU773 4.4 32.9 1.0
ND2 B:ASN724 4.4 32.6 1.0
CB B:ASN878 4.4 34.6 1.0
CB B:ASN724 4.5 34.5 1.0
CB B:SER727 4.6 34.6 1.0
CA B:LEU777 4.7 46.0 1.0
N B:GLY726 4.7 37.7 1.0
O B:PRO772 4.7 38.0 1.0
O B:HOH1186 4.8 27.2 1.0
N B:PHE774 4.8 37.7 1.0
CB B:VAL725 4.8 35.6 1.0
N B:GLY879 4.8 38.4 1.0
N B:SER727 4.9 40.5 1.0
CG B:LEU773 5.0 32.2 1.0

Reference:

S.J.Pellock, W.G.Walton, K.A.Biernat, D.Torres-Rivera, B.C.Creekmore, Y.Xu, J.Liu, A.Tripathy, L.J.Stewart, M.R.Redinbo. Three Structurally and Functionally Distinct Beta-Glucuronidases From the Human Gut Microbebacteroides Uniformis. J. Biol. Chem. V. 293 18559 2018.
ISSN: ESSN 1083-351X
PubMed: 30301767
DOI: 10.1074/JBC.RA118.005414
Page generated: Tue Dec 15 12:07:23 2020

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