Sodium in PDB 6ed1: Bacteroides Dorei Beta-Glucuronidase
Protein crystallography data
The structure of Bacteroides Dorei Beta-Glucuronidase, PDB code: 6ed1
was solved by
K.A.Biernat,
M.R.Redinbo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.54 /
2.90
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
242.663,
101.355,
168.600,
90.00,
94.97,
90.00
|
R / Rfree (%)
|
17.8 /
26.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Bacteroides Dorei Beta-Glucuronidase
(pdb code 6ed1). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Bacteroides Dorei Beta-Glucuronidase, PDB code: 6ed1:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6ed1
Go back to
Sodium Binding Sites List in 6ed1
Sodium binding site 1 out
of 4 in the Bacteroides Dorei Beta-Glucuronidase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na901
b:27.3
occ:1.00
|
OG1
|
A:THR770
|
2.3
|
22.5
|
1.0
|
O
|
A:LEU705
|
2.3
|
21.8
|
1.0
|
O
|
A:THR770
|
2.4
|
22.2
|
1.0
|
OD1
|
A:ASN704
|
2.4
|
23.9
|
1.0
|
O
|
A:LEU767
|
2.5
|
17.8
|
1.0
|
O
|
A:SER871
|
2.5
|
26.6
|
1.0
|
C
|
A:THR770
|
3.0
|
22.2
|
1.0
|
C
|
A:SER871
|
3.3
|
23.4
|
1.0
|
C
|
A:LEU705
|
3.4
|
24.6
|
1.0
|
CB
|
A:THR770
|
3.4
|
24.2
|
1.0
|
CA
|
A:SER871
|
3.5
|
21.6
|
1.0
|
N
|
A:LEU705
|
3.6
|
25.1
|
1.0
|
CG
|
A:ASN704
|
3.6
|
23.8
|
1.0
|
C
|
A:LEU767
|
3.7
|
18.9
|
1.0
|
CA
|
A:THR770
|
3.8
|
19.4
|
1.0
|
N
|
A:PHE771
|
3.8
|
18.3
|
1.0
|
CB
|
A:SER871
|
3.8
|
23.4
|
1.0
|
C
|
A:ASN704
|
4.0
|
25.4
|
1.0
|
CD1
|
A:LEU767
|
4.0
|
23.7
|
1.0
|
CA
|
A:LEU705
|
4.0
|
29.3
|
1.0
|
CA
|
A:PHE771
|
4.1
|
21.1
|
1.0
|
N
|
A:THR770
|
4.3
|
17.3
|
1.0
|
CA
|
A:ASN704
|
4.3
|
21.3
|
1.0
|
CA
|
A:LEU767
|
4.4
|
19.9
|
1.0
|
N
|
A:GLY706
|
4.5
|
28.0
|
1.0
|
N
|
A:GLY872
|
4.5
|
22.1
|
1.0
|
ND2
|
A:ASN704
|
4.5
|
21.3
|
1.0
|
OG
|
A:SER871
|
4.5
|
21.4
|
1.0
|
O
|
A:ASN704
|
4.5
|
31.5
|
1.0
|
CB
|
A:ASN704
|
4.6
|
24.5
|
1.0
|
CB
|
A:LEU705
|
4.6
|
35.0
|
1.0
|
O
|
A:PHE768
|
4.7
|
17.4
|
1.0
|
N
|
A:PHE768
|
4.7
|
20.2
|
1.0
|
CG2
|
A:THR770
|
4.7
|
26.3
|
1.0
|
CA
|
A:GLY706
|
4.8
|
29.6
|
1.0
|
C
|
A:PHE768
|
4.8
|
18.7
|
1.0
|
CB
|
A:PHE771
|
4.8
|
20.9
|
1.0
|
CA
|
A:PHE768
|
4.9
|
20.4
|
1.0
|
O
|
A:PRO766
|
4.9
|
19.9
|
1.0
|
N
|
A:SER871
|
4.9
|
21.7
|
1.0
|
CG
|
A:LEU767
|
5.0
|
22.7
|
1.0
|
CA
|
A:GLY872
|
5.0
|
27.7
|
1.0
|
O
|
A:ILE870
|
5.0
|
23.8
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6ed1
Go back to
Sodium Binding Sites List in 6ed1
Sodium binding site 2 out
of 4 in the Bacteroides Dorei Beta-Glucuronidase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na901
b:15.2
occ:1.00
|
OD1
|
B:ASN704
|
2.1
|
15.2
|
1.0
|
O
|
B:THR770
|
2.3
|
20.0
|
1.0
|
O
|
B:LEU705
|
2.4
|
18.2
|
1.0
|
O
|
B:SER871
|
2.4
|
16.6
|
1.0
|
O
|
B:LEU767
|
2.5
|
23.1
|
1.0
|
OG1
|
B:THR770
|
2.5
|
21.0
|
1.0
|
C
|
B:THR770
|
3.1
|
18.3
|
1.0
|
CG
|
B:ASN704
|
3.4
|
18.1
|
1.0
|
C
|
B:LEU705
|
3.5
|
18.2
|
1.0
|
CD1
|
B:LEU767
|
3.5
|
19.0
|
1.0
|
C
|
B:SER871
|
3.5
|
18.6
|
1.0
|
CB
|
B:THR770
|
3.5
|
21.2
|
1.0
|
N
|
B:LEU705
|
3.5
|
18.1
|
1.0
|
C
|
B:LEU767
|
3.5
|
19.8
|
1.0
|
CA
|
B:THR770
|
3.8
|
20.2
|
1.0
|
C
|
B:ASN704
|
3.8
|
17.9
|
1.0
|
CA
|
B:SER871
|
4.0
|
15.8
|
1.0
|
CA
|
B:LEU767
|
4.0
|
12.5
|
1.0
|
CA
|
B:LEU705
|
4.0
|
17.3
|
1.0
|
N
|
B:PHE771
|
4.1
|
17.0
|
1.0
|
N
|
B:THR770
|
4.1
|
21.9
|
1.0
|
ND2
|
B:ASN704
|
4.2
|
16.2
|
1.0
|
CA
|
B:ASN704
|
4.2
|
16.5
|
1.0
|
CB
|
B:SER871
|
4.2
|
17.7
|
1.0
|
CB
|
B:ASN704
|
4.4
|
19.9
|
1.0
|
O
|
B:PRO766
|
4.4
|
23.7
|
1.0
|
O
|
B:ASN704
|
4.4
|
15.2
|
1.0
|
CA
|
B:PHE771
|
4.4
|
17.2
|
1.0
|
CB
|
B:LEU705
|
4.6
|
14.4
|
1.0
|
N
|
B:GLY706
|
4.6
|
19.0
|
1.0
|
N
|
B:GLY872
|
4.7
|
14.9
|
1.0
|
CB
|
B:GLN707
|
4.7
|
19.1
|
1.0
|
CG
|
B:LEU767
|
4.7
|
14.6
|
1.0
|
N
|
B:PHE768
|
4.7
|
21.6
|
1.0
|
N
|
B:GLN707
|
4.8
|
17.9
|
1.0
|
CG2
|
B:THR770
|
4.8
|
21.6
|
1.0
|
CB
|
B:LEU767
|
4.9
|
11.3
|
1.0
|
CA
|
B:GLY872
|
5.0
|
15.2
|
1.0
|
OG
|
B:SER871
|
5.0
|
20.8
|
1.0
|
CA
|
B:GLY706
|
5.0
|
25.8
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6ed1
Go back to
Sodium Binding Sites List in 6ed1
Sodium binding site 3 out
of 4 in the Bacteroides Dorei Beta-Glucuronidase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na901
b:21.2
occ:1.00
|
OD1
|
C:ASN704
|
2.1
|
20.6
|
1.0
|
O
|
C:LEU705
|
2.3
|
18.4
|
1.0
|
O
|
C:LEU767
|
2.5
|
21.8
|
1.0
|
OG1
|
C:THR770
|
2.5
|
21.6
|
1.0
|
O
|
C:SER871
|
2.6
|
18.5
|
1.0
|
O
|
C:THR770
|
2.9
|
16.9
|
1.0
|
CG
|
C:ASN704
|
3.3
|
21.9
|
1.0
|
CB
|
C:THR770
|
3.4
|
19.6
|
1.0
|
C
|
C:THR770
|
3.4
|
16.0
|
1.0
|
C
|
C:LEU705
|
3.4
|
23.7
|
1.0
|
C
|
C:LEU767
|
3.5
|
22.1
|
1.0
|
C
|
C:SER871
|
3.6
|
17.7
|
1.0
|
N
|
C:LEU705
|
3.7
|
17.5
|
1.0
|
C
|
C:ASN704
|
3.8
|
22.4
|
1.0
|
CD1
|
C:LEU767
|
3.8
|
22.2
|
1.0
|
CA
|
C:THR770
|
3.8
|
16.1
|
1.0
|
CA
|
C:SER871
|
4.0
|
17.1
|
1.0
|
CA
|
C:LEU767
|
4.0
|
18.5
|
1.0
|
CA
|
C:LEU705
|
4.1
|
20.3
|
1.0
|
CA
|
C:ASN704
|
4.1
|
20.3
|
1.0
|
ND2
|
C:ASN704
|
4.1
|
20.6
|
1.0
|
N
|
C:THR770
|
4.1
|
16.3
|
1.0
|
CB
|
C:SER871
|
4.2
|
16.8
|
1.0
|
CB
|
C:ASN704
|
4.2
|
17.4
|
1.0
|
O
|
C:ASN704
|
4.3
|
21.7
|
1.0
|
N
|
C:PHE771
|
4.3
|
14.9
|
1.0
|
CG
|
C:LEU767
|
4.6
|
23.6
|
1.0
|
N
|
C:GLY706
|
4.6
|
20.9
|
1.0
|
O
|
C:PRO766
|
4.6
|
18.4
|
1.0
|
OG
|
C:SER871
|
4.6
|
16.0
|
1.0
|
CB
|
C:LEU705
|
4.6
|
19.4
|
1.0
|
CA
|
C:PHE771
|
4.7
|
17.0
|
1.0
|
N
|
C:GLY872
|
4.7
|
21.1
|
1.0
|
N
|
C:PHE768
|
4.7
|
21.0
|
1.0
|
CG2
|
C:THR770
|
4.7
|
18.4
|
1.0
|
N
|
C:GLN707
|
4.8
|
26.6
|
1.0
|
CB
|
C:LEU767
|
4.9
|
21.5
|
1.0
|
CA
|
C:GLY706
|
4.9
|
18.5
|
1.0
|
CB
|
C:GLN707
|
5.0
|
20.0
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6ed1
Go back to
Sodium Binding Sites List in 6ed1
Sodium binding site 4 out
of 4 in the Bacteroides Dorei Beta-Glucuronidase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na901
b:17.9
occ:1.00
|
O
|
D:SER871
|
2.2
|
19.4
|
1.0
|
OD1
|
D:ASN704
|
2.3
|
19.5
|
1.0
|
OG1
|
D:THR770
|
2.4
|
21.6
|
1.0
|
O
|
D:LEU705
|
2.6
|
23.4
|
1.0
|
O
|
D:LEU767
|
2.8
|
22.9
|
1.0
|
O
|
D:THR770
|
3.1
|
21.6
|
1.0
|
N
|
D:LEU705
|
3.2
|
22.1
|
1.0
|
C
|
D:SER871
|
3.2
|
20.8
|
1.0
|
C
|
D:ASN704
|
3.3
|
18.3
|
1.0
|
CB
|
D:THR770
|
3.3
|
17.7
|
1.0
|
CG
|
D:ASN704
|
3.5
|
22.1
|
1.0
|
C
|
D:LEU705
|
3.5
|
21.4
|
1.0
|
CA
|
D:ASN704
|
3.7
|
13.2
|
1.0
|
C
|
D:THR770
|
3.7
|
21.1
|
1.0
|
O
|
D:ASN704
|
3.8
|
21.1
|
1.0
|
C
|
D:LEU767
|
3.8
|
20.7
|
1.0
|
CA
|
D:LEU705
|
3.9
|
21.1
|
1.0
|
CA
|
D:SER871
|
3.9
|
17.3
|
1.0
|
CD1
|
D:LEU767
|
3.9
|
16.4
|
1.0
|
CA
|
D:THR770
|
4.1
|
17.7
|
1.0
|
CB
|
D:ASN704
|
4.1
|
15.8
|
1.0
|
CA
|
D:LEU767
|
4.1
|
18.8
|
1.0
|
CB
|
D:SER871
|
4.2
|
18.7
|
1.0
|
CG
|
D:LEU767
|
4.3
|
21.6
|
1.0
|
N
|
D:GLY872
|
4.3
|
20.7
|
1.0
|
CB
|
D:LEU705
|
4.5
|
17.9
|
1.0
|
CA
|
D:GLY872
|
4.5
|
18.6
|
1.0
|
ND2
|
D:ASN704
|
4.5
|
21.5
|
1.0
|
CG2
|
D:THR770
|
4.5
|
19.2
|
1.0
|
N
|
D:THR770
|
4.5
|
25.9
|
1.0
|
N
|
D:PHE771
|
4.6
|
15.4
|
1.0
|
N
|
D:GLY706
|
4.7
|
21.6
|
1.0
|
O
|
D:PRO766
|
4.7
|
20.4
|
1.0
|
CB
|
D:LEU767
|
4.9
|
17.1
|
1.0
|
CB
|
D:GLN707
|
4.9
|
18.7
|
1.0
|
N
|
D:GLN707
|
4.9
|
22.6
|
1.0
|
CA
|
D:PHE771
|
5.0
|
17.3
|
1.0
|
N
|
D:PHE768
|
5.0
|
19.4
|
1.0
|
|
Reference:
K.A.Biernat,
S.J.Pellock,
A.P.Bhatt,
M.M.Bivins,
W.G.Walton,
B.N.T.Tran,
L.Wei,
M.C.Snider,
A.P.Cesmat,
A.Tripathy,
D.A.Erie,
M.R.Redinbo.
Structure, Function, and Inhibition of Drug Reactivating Human Gut Microbial Beta-Glucuronidases. Sci Rep V. 9 825 2019.
ISSN: ESSN 2045-2322
PubMed: 30696850
DOI: 10.1038/S41598-018-36069-W
Page generated: Tue Oct 8 08:22:51 2024
|