Calcium in PDB 8axs: Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota
Protein crystallography data
The structure of Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota, PDB code: 8axs
was solved by
H.Sakanaka,
T.S.Nielsen,
M.J.Pichler,
E.Nordberg Karlsson,
M.Abou Hachem,
J.P.Morth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.25 /
1.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.07,
51.78,
118.44,
90,
93.07,
90
|
R / Rfree (%)
|
16.6 /
18.8
|
Other elements in 8axs:
The structure of Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota
(pdb code 8axs). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota, PDB code: 8axs:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 8axs
Go back to
Calcium Binding Sites List in 8axs
Calcium binding site 1 out
of 2 in the Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca709
b:16.1
occ:1.00
|
O
|
A:HOH906
|
2.3
|
18.1
|
1.0
|
OE2
|
A:GLU299
|
2.3
|
17.9
|
1.0
|
OD1
|
A:ASP300
|
2.4
|
17.1
|
1.0
|
O
|
A:HOH1028
|
2.4
|
17.7
|
1.0
|
O
|
A:HOH989
|
2.4
|
15.5
|
1.0
|
OE1
|
A:GLU289
|
2.5
|
16.9
|
1.0
|
OE2
|
A:GLU289
|
2.5
|
16.7
|
1.0
|
CD
|
A:GLU289
|
2.8
|
17.2
|
1.0
|
H
|
A:ASP300
|
3.4
|
18.8
|
1.0
|
CD
|
A:GLU299
|
3.4
|
16.3
|
1.0
|
HA
|
A:ARG211
|
3.5
|
20.4
|
1.0
|
CG
|
A:ASP300
|
3.6
|
17.9
|
1.0
|
H
|
A:TRP212
|
3.7
|
17.9
|
1.0
|
H
|
A:VAL301
|
3.7
|
19.3
|
1.0
|
OE1
|
A:GLU299
|
3.8
|
15.2
|
1.0
|
HB1
|
A:ALA293
|
4.0
|
25.4
|
1.0
|
O
|
A:HOH869
|
4.0
|
17.7
|
1.0
|
HB1
|
A:ALA293
|
4.0
|
24.9
|
0.0
|
O
|
A:VAL301
|
4.1
|
17.3
|
1.0
|
N
|
A:ASP300
|
4.2
|
15.7
|
1.0
|
OD2
|
A:ASP300
|
4.3
|
17.4
|
1.0
|
CG
|
A:GLU289
|
4.3
|
15.0
|
1.0
|
HG2
|
A:ARG211
|
4.3
|
21.2
|
1.0
|
HA
|
A:GLU299
|
4.4
|
23.0
|
1.0
|
O
|
A:HOH1356
|
4.4
|
17.2
|
1.0
|
CA
|
A:ARG211
|
4.4
|
17.0
|
1.0
|
N
|
A:TRP212
|
4.4
|
14.9
|
1.0
|
HG12
|
A:VAL301
|
4.5
|
21.0
|
1.0
|
O
|
A:VAL210
|
4.5
|
18.1
|
0.6
|
N
|
A:VAL301
|
4.5
|
16.1
|
1.0
|
HG3
|
A:GLU289
|
4.6
|
18.0
|
1.0
|
HB2
|
A:TRP212
|
4.6
|
20.1
|
1.0
|
CB
|
A:ASP300
|
4.6
|
17.0
|
1.0
|
O
|
A:VAL210
|
4.6
|
17.9
|
0.4
|
HG3
|
A:GLU299
|
4.7
|
20.1
|
1.0
|
CG
|
A:GLU299
|
4.7
|
16.8
|
1.0
|
HA
|
A:GLU289
|
4.8
|
18.6
|
1.0
|
HB3
|
A:ASP300
|
4.8
|
20.4
|
1.0
|
HG2
|
A:GLU289
|
4.8
|
18.0
|
1.0
|
O
|
A:HOH1088
|
4.8
|
16.5
|
1.0
|
CB
|
A:ALA293
|
4.8
|
21.1
|
1.0
|
CA
|
A:ASP300
|
4.9
|
16.5
|
1.0
|
CB
|
A:ALA293
|
4.9
|
20.7
|
0.0
|
HB2
|
A:ALA293
|
4.9
|
25.4
|
1.0
|
O
|
A:ALA293
|
4.9
|
25.1
|
1.0
|
O
|
A:ALA293
|
4.9
|
23.6
|
0.0
|
HB2
|
A:ALA293
|
5.0
|
24.9
|
0.0
|
C
|
A:ARG211
|
5.0
|
18.0
|
1.0
|
O
|
A:HOH956
|
5.0
|
17.2
|
1.0
|
|
Calcium binding site 2 out
of 2 in 8axs
Go back to
Calcium Binding Sites List in 8axs
Calcium binding site 2 out
of 2 in the Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca608
b:15.8
occ:1.00
|
OD1
|
B:ASP300
|
2.3
|
16.0
|
1.0
|
O
|
B:HOH740
|
2.4
|
16.2
|
1.0
|
OE2
|
B:GLU299
|
2.4
|
16.8
|
1.0
|
O
|
B:HOH842
|
2.4
|
17.1
|
1.0
|
OE1
|
B:GLU289
|
2.4
|
15.9
|
1.0
|
O
|
B:HOH864
|
2.5
|
14.9
|
1.0
|
OE2
|
B:GLU289
|
2.5
|
15.8
|
1.0
|
CD
|
B:GLU289
|
2.8
|
15.7
|
1.0
|
H
|
B:ASP300
|
3.4
|
19.0
|
1.0
|
HA
|
B:ARG211
|
3.4
|
19.1
|
1.0
|
CD
|
B:GLU299
|
3.5
|
17.4
|
1.0
|
CG
|
B:ASP300
|
3.6
|
15.8
|
1.0
|
H
|
B:TRP212
|
3.6
|
19.0
|
1.0
|
H
|
B:VAL301
|
3.7
|
17.8
|
1.0
|
OE1
|
B:GLU299
|
3.8
|
14.8
|
1.0
|
HB1
|
B:ALA293
|
4.0
|
23.7
|
1.0
|
O
|
B:HOH780
|
4.0
|
15.0
|
1.0
|
HB1
|
B:ALA293
|
4.0
|
23.6
|
0.0
|
O
|
B:VAL301
|
4.2
|
16.4
|
1.0
|
N
|
B:ASP300
|
4.2
|
15.8
|
1.0
|
OD2
|
B:ASP300
|
4.3
|
18.1
|
1.0
|
HA
|
B:GLU299
|
4.3
|
21.3
|
1.0
|
CG
|
B:GLU289
|
4.3
|
14.6
|
1.0
|
O
|
B:VAL210
|
4.3
|
17.8
|
0.4
|
HG2
|
B:ARG211
|
4.4
|
21.7
|
1.0
|
O
|
B:HOH1264
|
4.4
|
16.5
|
1.0
|
CA
|
B:ARG211
|
4.4
|
15.9
|
1.0
|
N
|
B:TRP212
|
4.4
|
15.8
|
1.0
|
HG12
|
B:VAL301
|
4.5
|
20.3
|
1.0
|
N
|
B:VAL301
|
4.5
|
14.9
|
1.0
|
HG3
|
B:GLU289
|
4.6
|
17.5
|
1.0
|
O
|
B:VAL210
|
4.6
|
16.6
|
0.6
|
HB2
|
B:TRP212
|
4.6
|
20.3
|
1.0
|
CB
|
B:ASP300
|
4.6
|
15.6
|
1.0
|
HA
|
B:GLU289
|
4.7
|
18.9
|
1.0
|
HB3
|
B:ASP300
|
4.7
|
18.8
|
1.0
|
CG
|
B:GLU299
|
4.8
|
16.6
|
1.0
|
HG3
|
B:GLU299
|
4.8
|
19.9
|
1.0
|
HG2
|
B:GLU289
|
4.8
|
17.5
|
1.0
|
CB
|
B:ALA293
|
4.8
|
19.8
|
1.0
|
CB
|
B:ALA293
|
4.9
|
19.7
|
0.0
|
O
|
B:HOH913
|
4.9
|
14.5
|
1.0
|
CA
|
B:ASP300
|
4.9
|
16.6
|
1.0
|
HB2
|
B:ALA293
|
4.9
|
23.7
|
1.0
|
C
|
B:ARG211
|
4.9
|
17.3
|
1.0
|
HB2
|
B:ALA293
|
4.9
|
23.6
|
0.0
|
O
|
B:ALA293
|
4.9
|
21.9
|
0.0
|
O
|
B:ALA293
|
5.0
|
24.0
|
1.0
|
O
|
B:HOH967
|
5.0
|
15.7
|
1.0
|
|
Reference:
H.Sakanaka,
T.S.Nielsen,
M.J.Pichler,
E.Nordberg Karlsson,
M.Abou Hachem,
J.P.Morth.
Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin-Associated Human Gut Microbiota To Be Published.
Page generated: Fri Jul 19 07:04:34 2024
|