Calcium in PDB 8axt: 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: 8axt 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) 72.73 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.96, 56.79, 146.72, 90, 94.55, 90
R / Rfree (%) 16.8 / 20.2

Other elements in 8axt:

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:

Chlorine (Cl) 5 atoms

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 8axt). 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: 8axt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8axt

Go back to Calcium Binding Sites List in 8axt
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:Ca701

b:21.7
occ:1.00
OD1 A:ASP300 2.1 15.3 1.0
O A:HOH968 2.1 13.8 1.0
O A:HOH1162 2.1 12.8 1.0
OE1 A:GLU299 2.1 14.4 1.0
OE2 A:GLU289 2.1 16.6 1.0
O A:HOH978 2.1 12.1 1.0
CD A:GLU289 3.1 15.9 1.0
H A:ASP300 3.2 15.9 1.0
CD A:GLU299 3.2 16.3 1.0
CG A:ASP300 3.3 17.5 1.0
OE1 A:GLU289 3.4 17.4 1.0
H A:VAL301 3.5 13.6 1.0
H A:TRP212 3.5 15.4 1.0
HA A:ARG211 3.6 15.0 1.0
OE2 A:GLU299 3.6 16.1 1.0
O A:HOH849 3.9 11.7 1.0
OD2 A:ASP300 3.9 15.5 1.0
N A:ASP300 4.0 13.3 1.0
HA A:GLU299 4.0 15.5 1.0
HB1 A:ALA293 4.0 21.9 1.0
O A:HOH1152 4.1 22.1 1.0
O A:VAL301 4.1 13.1 1.0
N A:TRP212 4.3 12.9 1.0
N A:VAL301 4.3 11.3 1.0
HG12 A:VAL301 4.4 15.6 1.0
HB2 A:ALA293 4.4 21.9 1.0
CG A:GLU289 4.4 11.2 1.0
HG3 A:GLU289 4.4 13.5 1.0
CB A:ASP300 4.5 14.4 1.0
HB2 A:TRP212 4.5 13.2 1.0
O A:VAL210 4.5 14.3 1.0
CA A:ARG211 4.5 12.5 1.0
CG A:GLU299 4.5 11.8 1.0
HG3 A:GLU299 4.5 14.2 1.0
O A:HOH1297 4.5 16.0 1.0
HG2 A:ARG211 4.6 13.7 1.0
CB A:ALA293 4.7 18.2 1.0
CA A:ASP300 4.7 14.5 1.0
HB3 A:ASP300 4.7 17.3 1.0
CA A:GLU299 4.8 12.9 1.0
HA A:GLU289 4.8 11.3 1.0
HB3 A:GLU289 4.9 12.3 1.0
C A:GLU299 4.9 12.3 1.0
C A:ARG211 4.9 11.8 1.0
HB3 A:TRP212 5.0 13.2 1.0

Calcium binding site 2 out of 2 in 8axt

Go back to Calcium Binding Sites List in 8axt
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:Ca701

b:20.8
occ:1.00
O B:HOH1016 2.0 14.3 1.0
O B:HOH963 2.1 12.6 1.0
OE1 B:GLU289 2.1 15.4 1.0
OD1 B:ASP300 2.1 14.4 1.0
OE1 B:GLU299 2.1 14.1 1.0
O B:HOH854 2.3 12.7 1.0
CD B:GLU289 3.0 17.1 1.0
H B:ASP300 3.1 20.9 1.0
CD B:GLU299 3.2 13.2 1.0
OE2 B:GLU289 3.3 17.9 1.0
CG B:ASP300 3.3 18.7 1.0
H B:VAL301 3.5 13.6 1.0
OE2 B:GLU299 3.6 13.8 1.0
HA B:ARG211 3.6 14.4 1.0
H B:TRP212 3.6 13.4 1.0
O B:HOH864 3.8 14.0 1.0
N B:ASP300 4.0 17.4 1.0
OD2 B:ASP300 4.0 17.7 1.0
HB1 B:ALA293 4.0 20.8 1.0
HA B:GLU299 4.1 16.1 1.0
O B:VAL301 4.1 13.8 1.0
O B:HOH999 4.1 24.2 1.0
HG12 B:VAL301 4.1 16.4 1.0
HB2 B:ALA293 4.2 20.8 1.0
N B:VAL301 4.3 11.3 1.0
CG B:GLU289 4.4 13.6 1.0
N B:TRP212 4.4 11.2 1.0
HG3 B:GLU289 4.4 16.3 1.0
CG B:GLU299 4.5 14.5 1.0
CB B:ASP300 4.5 16.3 1.0
O B:HOH1253 4.5 16.8 1.0
O B:VAL210 4.5 13.0 1.0
CA B:ARG211 4.5 12.0 1.0
HB2 B:TRP212 4.5 13.9 1.0
HG3 B:GLU299 4.6 17.4 1.0
CB B:ALA293 4.6 17.4 1.0
HG2 B:ARG211 4.6 14.1 1.0
CA B:ASP300 4.7 14.1 1.0
HB3 B:ASP300 4.8 19.6 1.0
HA B:GLU289 4.8 13.1 1.0
CA B:GLU299 4.8 13.4 1.0
HB3 B:GLU289 4.9 13.3 1.0
C B:GLU299 4.9 13.0 1.0
C B:ASP300 5.0 15.1 1.0
CG1 B:VAL301 5.0 13.6 1.0
HG2 B:GLU289 5.0 16.3 1.0
C B:ARG211 5.0 12.7 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 07:04:44 2024

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