Sodium in PDB 5fq6: Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Protein crystallography data
The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq6
was solved by
A.J.Glenwright,
K.R.Pothula,
D.S.Chorev,
A.Basle,
C.V.Robinson,
U.Kleinekathoefer,
D.N.Bolam,
B.Van Den Berg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.80 /
2.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
222.027,
91.941,
261.219,
90.00,
98.23,
90.00
|
R / Rfree (%)
|
19.8 /
25.5
|
Other elements in 5fq6:
The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
(pdb code 5fq6). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq6:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 5fq6
Go back to
Sodium Binding Sites List in 5fq6
Sodium binding site 1 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1986
b:30.7
occ:1.00
|
O
|
B:ALA631
|
2.2
|
64.9
|
1.0
|
OD1
|
B:ASN633
|
2.2
|
53.9
|
1.0
|
O
|
A:ALA82
|
2.3
|
76.8
|
1.0
|
C
|
B:ALA631
|
3.3
|
58.5
|
1.0
|
CG
|
B:ASN633
|
3.4
|
59.6
|
1.0
|
C
|
A:ALA82
|
3.5
|
62.2
|
1.0
|
OG
|
B:SER630
|
3.9
|
80.1
|
1.0
|
CA
|
A:GLY83
|
4.0
|
64.5
|
1.0
|
C
|
B:GLY632
|
4.1
|
73.2
|
1.0
|
N
|
B:ASN633
|
4.1
|
61.3
|
1.0
|
CA
|
B:ASN633
|
4.1
|
64.0
|
1.0
|
CA
|
B:ALA631
|
4.1
|
59.6
|
1.0
|
CB
|
B:ALA631
|
4.1
|
64.5
|
1.0
|
N
|
A:GLY83
|
4.2
|
64.0
|
1.0
|
O
|
B:GLY632
|
4.2
|
86.7
|
1.0
|
N
|
B:ALA631
|
4.3
|
59.5
|
1.0
|
OD1
|
A:ASP87
|
4.3
|
82.9
|
1.0
|
ND2
|
B:ASN633
|
4.3
|
59.7
|
1.0
|
N
|
B:GLY632
|
4.4
|
64.1
|
1.0
|
CB
|
B:ASN633
|
4.4
|
58.9
|
1.0
|
O
|
B:GLY686
|
4.5
|
74.8
|
1.0
|
CG
|
A:GLU86
|
4.6
|
57.9
|
1.0
|
CA
|
B:GLY632
|
4.6
|
67.3
|
1.0
|
O
|
A:GLY83
|
4.6
|
74.5
|
1.0
|
CA
|
A:ALA82
|
4.6
|
55.3
|
1.0
|
CB
|
A:GLU86
|
4.7
|
54.7
|
1.0
|
C
|
A:GLY83
|
4.8
|
67.0
|
1.0
|
CB
|
A:ALA82
|
4.9
|
45.4
|
1.0
|
C
|
B:SER630
|
5.0
|
56.4
|
1.0
|
CB
|
B:SER630
|
5.0
|
69.3
|
1.0
|
|
Sodium binding site 2 out
of 4 in 5fq6
Go back to
Sodium Binding Sites List in 5fq6
Sodium binding site 2 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1986
b:34.5
occ:1.00
|
OD1
|
D:ASN633
|
2.0
|
54.1
|
1.0
|
O
|
C:ALA82
|
2.3
|
72.2
|
1.0
|
O
|
D:ALA631
|
2.4
|
54.7
|
1.0
|
CG
|
D:ASN633
|
3.2
|
58.8
|
1.0
|
OG
|
D:SER630
|
3.3
|
72.4
|
1.0
|
C
|
C:ALA82
|
3.4
|
64.7
|
1.0
|
C
|
D:ALA631
|
3.6
|
49.8
|
1.0
|
CA
|
C:GLY83
|
3.7
|
68.8
|
1.0
|
ND2
|
D:ASN633
|
3.8
|
57.6
|
1.0
|
N
|
C:GLY83
|
4.0
|
68.2
|
1.0
|
N
|
D:ALA631
|
4.3
|
48.9
|
1.0
|
CA
|
D:ALA631
|
4.3
|
45.9
|
1.0
|
N
|
D:ASN633
|
4.3
|
45.8
|
1.0
|
C
|
D:GLY632
|
4.4
|
49.2
|
1.0
|
CB
|
D:ASN633
|
4.4
|
55.1
|
1.0
|
CA
|
D:ASN633
|
4.4
|
53.1
|
1.0
|
CB
|
D:SER630
|
4.5
|
61.7
|
1.0
|
O
|
C:GLY83
|
4.5
|
78.9
|
1.0
|
CB
|
D:ALA631
|
4.5
|
53.3
|
1.0
|
OD1
|
C:ASP87
|
4.6
|
58.2
|
1.0
|
N
|
D:GLY632
|
4.6
|
54.7
|
1.0
|
C
|
C:GLY83
|
4.6
|
72.2
|
1.0
|
CA
|
C:ALA82
|
4.7
|
62.2
|
1.0
|
O
|
D:GLY632
|
4.7
|
47.2
|
1.0
|
C
|
D:SER630
|
4.7
|
50.7
|
1.0
|
CA
|
D:GLY632
|
4.7
|
47.7
|
1.0
|
OD2
|
C:ASP87
|
4.8
|
71.3
|
1.0
|
O
|
D:GLY686
|
4.9
|
72.7
|
1.0
|
CB
|
C:ALA82
|
4.9
|
67.3
|
1.0
|
CB
|
C:GLU86
|
5.0
|
48.1
|
1.0
|
CG
|
C:GLU86
|
5.0
|
56.1
|
1.0
|
|
Sodium binding site 3 out
of 4 in 5fq6
Go back to
Sodium Binding Sites List in 5fq6
Sodium binding site 3 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na1986
b:33.0
occ:1.00
|
OD1
|
I:ASN633
|
2.2
|
51.0
|
1.0
|
O
|
I:ALA631
|
2.4
|
68.7
|
1.0
|
O
|
H:ALA82
|
2.5
|
68.5
|
1.0
|
CG
|
I:ASN633
|
3.3
|
48.0
|
1.0
|
C
|
I:ALA631
|
3.6
|
50.3
|
1.0
|
OG
|
I:SER630
|
3.6
|
46.4
|
1.0
|
C
|
H:ALA82
|
3.6
|
50.4
|
1.0
|
CA
|
H:GLY83
|
3.8
|
45.2
|
1.0
|
ND2
|
I:ASN633
|
3.8
|
44.8
|
1.0
|
N
|
H:GLY83
|
4.1
|
45.2
|
1.0
|
N
|
I:ALA631
|
4.3
|
44.5
|
1.0
|
CA
|
I:ALA631
|
4.4
|
48.0
|
1.0
|
C
|
I:GLY632
|
4.4
|
46.6
|
1.0
|
N
|
I:ASN633
|
4.4
|
40.1
|
1.0
|
CB
|
I:SER630
|
4.5
|
47.8
|
1.0
|
N
|
I:GLY632
|
4.6
|
43.9
|
1.0
|
CB
|
I:ASN633
|
4.6
|
38.4
|
1.0
|
O
|
H:GLY83
|
4.6
|
62.0
|
1.0
|
CB
|
I:ALA631
|
4.6
|
52.7
|
1.0
|
CA
|
I:GLY632
|
4.7
|
37.5
|
1.0
|
C
|
H:GLY83
|
4.7
|
55.2
|
1.0
|
O
|
I:GLY632
|
4.7
|
60.9
|
1.0
|
CA
|
I:ASN633
|
4.7
|
42.8
|
1.0
|
OD2
|
H:ASP87
|
4.7
|
80.8
|
1.0
|
OD1
|
H:ASP87
|
4.8
|
75.4
|
1.0
|
C
|
I:SER630
|
4.8
|
54.5
|
1.0
|
CA
|
H:ALA82
|
4.9
|
44.2
|
1.0
|
|
Sodium binding site 4 out
of 4 in 5fq6
Go back to
Sodium Binding Sites List in 5fq6
Sodium binding site 4 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Na1986
b:42.6
occ:1.00
|
O
|
M:ALA631
|
2.2
|
70.5
|
1.0
|
OD1
|
M:ASN633
|
2.2
|
60.5
|
1.0
|
O
|
L:ALA82
|
2.4
|
74.6
|
1.0
|
C
|
M:ALA631
|
3.4
|
55.5
|
1.0
|
CG
|
M:ASN633
|
3.4
|
50.2
|
1.0
|
C
|
L:ALA82
|
3.6
|
62.6
|
1.0
|
C
|
M:GLY632
|
4.0
|
56.1
|
1.0
|
CA
|
L:GLY83
|
4.1
|
62.1
|
1.0
|
O
|
M:GLY632
|
4.1
|
62.7
|
1.0
|
ND2
|
M:ASN633
|
4.2
|
40.1
|
1.0
|
CA
|
M:ALA631
|
4.2
|
58.4
|
1.0
|
N
|
M:ASN633
|
4.2
|
55.1
|
1.0
|
CB
|
M:ALA631
|
4.2
|
60.5
|
1.0
|
N
|
L:GLY83
|
4.3
|
61.0
|
1.0
|
N
|
M:GLY632
|
4.3
|
52.0
|
1.0
|
CA
|
M:ASN633
|
4.3
|
56.0
|
1.0
|
N
|
M:ALA631
|
4.4
|
55.0
|
1.0
|
OG
|
M:SER630
|
4.4
|
63.2
|
1.0
|
CA
|
M:GLY632
|
4.4
|
52.2
|
1.0
|
CB
|
M:ASN633
|
4.5
|
46.3
|
1.0
|
O
|
M:GLY686
|
4.6
|
67.6
|
1.0
|
O
|
L:GLY83
|
4.6
|
69.5
|
1.0
|
CA
|
L:ALA82
|
4.7
|
61.2
|
1.0
|
CG
|
L:GLU86
|
4.9
|
48.9
|
1.0
|
CB
|
L:ALA82
|
4.9
|
46.8
|
1.0
|
CB
|
L:GLU86
|
4.9
|
51.5
|
1.0
|
C
|
L:GLY83
|
4.9
|
67.4
|
1.0
|
C
|
M:SER630
|
4.9
|
52.3
|
1.0
|
OD1
|
L:ASP87
|
5.0
|
92.9
|
1.0
|
|
Reference:
A.J.Glenwright,
K.R.Pothula,
S.P.Bhamidimarri,
D.S.Chorev,
A.Basle,
S.J.Firbank,
H.Zheng,
C.V.Robinson,
M.Winterhalter,
U.Kleinekathofer,
D.N.Bolam,
B.Van Den Berg.
Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828
Page generated: Mon Oct 7 21:04:56 2024
|