Calcium in PDB 8ayr: Sialidases and Fucosidases of Akkermansia Muciniphila Are Key For Rapid Growth on Colonic Mucin and Nutrient Sharing Amongst Mucin- Associated Human Gut Microbiota

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: 8ayr 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)	34.51 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.19, 76.45, 84.5, 88.41, 89.08, 88.23
R / Rfree (%)	23.3 / 27.5

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 8ayr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 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: 8ayr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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:Ca801 b:98.8 occ:1.00 OD1 A:ASP389 2.3 80.1 1.0 O A:THR394 2.3 96.3 1.0 OG1 A:THR394 2.4 89.8 1.0 O A:GLN386 2.5 88.5 1.0 O A:LYS391 2.6 84.4 1.0 O A:CYS484 2.6 75.6 1.0 C A:THR394 3.2 87.7 1.0 CG A:ASP389 3.3 78.0 1.0 CB A:THR394 3.5 87.1 1.0 C A:GLN386 3.7 86.0 1.0 C A:LYS391 3.7 80.2 1.0 OD2 A:ASP389 3.7 78.5 1.0 C A:CYS484 3.7 78.1 1.0 CA A:THR394 3.7 85.2 1.0 N A:LYS391 3.8 84.0 1.0 N A:THR394 4.0 89.8 1.0 CA A:CYS484 4.1 79.6 1.0 CA A:LYS391 4.2 89.8 1.0 N A:TYR395 4.2 84.2 1.0 CA A:VAL387 4.2 82.1 1.0 CB A:CYS484 4.3 90.2 1.0 N A:ARG390 4.3 79.3 1.0 N A:VAL387 4.4 78.4 1.0 CB A:LYS391 4.4 84.6 1.0 C A:ARG390 4.4 80.3 1.0 C A:VAL387 4.5 84.8 1.0 CA A:TYR395 4.6 89.9 1.0 N A:ASP389 4.6 74.5 1.0 CB A:ASP389 4.7 82.0 1.0 C A:ASP389 4.7 77.6 1.0 CA A:GLN386 4.7 82.8 1.0 CG2 A:THR394 4.7 85.7 1.0 CA A:ARG390 4.8 84.2 1.0 N A:ARG392 4.8 76.9 1.0 N A:GLU485 4.8 80.5 1.0 CA A:ASP389 4.9 87.7 1.0 O A:VAL387 4.9 82.4 1.0 N A:LEU388 5.0 80.7 1.0 CB A:GLN386 5.0 91.7 1.0

Calcium binding site 2 out of 4 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 A:Ca802 b:89.0 occ:1.00 O A:LEU585 2.1 90.3 1.0 O A:ALA698 2.3 95.1 1.0 OG1 A:THR593 2.4 105.1 1.0 OE2 A:GLU699 2.4 98.9 1.0 O A:ASP590 2.4 99.4 1.0 OD1 A:ASP588 2.4 92.6 1.0 O A:THR593 2.8 96.7 1.0 CD A:GLU699 3.2 96.9 1.0 C A:LEU585 3.3 86.9 1.0 CG A:ASP588 3.4 92.3 1.0 C A:ALA698 3.5 96.4 1.0 C A:ASP590 3.6 97.2 1.0 C A:THR593 3.6 99.8 1.0 CG A:GLU699 3.6 99.0 1.0 CB A:THR593 3.7 98.3 1.0 OD2 A:ASP588 3.7 97.2 1.0 CA A:THR593 4.0 92.7 1.0 CA A:ALA586 4.1 88.0 1.0 N A:ALA586 4.1 87.0 1.0 N A:ASP590 4.2 96.6 1.0 N A:THR593 4.2 93.9 1.0 OE1 A:GLU699 4.2 92.4 1.0 CA A:LEU585 4.3 83.5 1.0 CA A:ASP590 4.4 96.6 1.0 N A:GLU699 4.4 103.7 1.0 CA A:GLU699 4.4 103.2 1.0 C A:ALA586 4.4 84.7 1.0 CA A:ALA698 4.5 94.6 1.0 N A:SER591 4.5 107.7 1.0 N A:ASP588 4.6 84.7 1.0 CB A:GLU699 4.6 101.6 1.0 CA A:SER591 4.6 102.1 1.0 N A:LEU594 4.6 94.0 1.0 CB A:ASP590 4.7 99.4 1.0 CB A:ASP588 4.7 85.1 1.0 N A:ILE587 4.8 86.9 1.0 CB A:LEU585 4.8 86.4 1.0 CG2 A:THR593 4.8 103.8 1.0 O A:ALA586 4.9 85.7 1.0 N A:GLY589 4.9 90.4 1.0 C A:SER591 4.9 103.3 1.0

Calcium binding site 3 out of 4 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 3 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:Ca801 b:122.8 occ:0.00 O B:ALA698 2.1 133.0 1.0 O B:LEU585 2.3 118.0 1.0 OE2 B:GLU699 2.3 122.5 1.0 OG1 B:THR593 2.3 124.7 1.0 O B:ASP590 2.4 119.8 1.0 O B:THR593 2.4 123.7 1.0 OD1 B:ASP588 2.4 119.4 1.0 CD B:GLU699 3.1 124.4 1.0 C B:THR593 3.3 121.8 1.0 C B:ALA698 3.3 127.7 1.0 CG B:ASP588 3.3 117.8 1.0 CB B:THR593 3.5 120.9 1.0 C B:LEU585 3.5 121.8 1.0 C B:ASP590 3.5 133.8 1.0 OD2 B:ASP588 3.6 123.8 1.0 CG B:GLU699 3.6 118.7 1.0 CA B:THR593 3.8 125.3 1.0 N B:THR593 3.9 125.9 1.0 OE1 B:GLU699 4.0 122.0 1.0 N B:ASP590 4.2 115.5 1.0 N B:GLU699 4.2 116.8 1.0 CA B:ALA698 4.3 122.3 1.0 CA B:ALA586 4.3 118.3 1.0 N B:ALA586 4.3 117.0 1.0 CA B:GLU699 4.3 123.6 1.0 N B:LEU594 4.4 123.1 1.0 CA B:ASP590 4.4 126.4 1.0 N B:SER591 4.4 146.7 1.0 CA B:LEU585 4.5 115.8 1.0 CA B:SER591 4.5 151.8 1.0 CB B:GLU699 4.6 121.1 1.0 C B:ALA586 4.6 118.4 1.0 CG2 B:THR593 4.6 120.0 1.0 N B:ASP588 4.7 113.3 1.0 C B:SER591 4.7 155.0 1.0 CB B:ASP588 4.7 123.1 1.0 CB B:ASP590 4.8 126.2 1.0 CB B:LEU585 4.8 120.7 1.0 N B:GLY589 5.0 126.0 1.0 N B:ILE587 5.0 112.6 1.0 CB B:ALA698 5.0 119.9 1.0 CA B:LEU594 5.0 119.3 1.0

Calcium binding site 4 out of 4 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 4 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:Ca802 b:75.8 occ:0.00 O B:THR394 2.3 72.2 1.0 OD1 B:ASP389 2.3 82.9 1.0 O B:CYS484 2.4 73.8 1.0 OG1 B:THR394 2.4 73.7 1.0 O B:GLN386 2.4 83.0 1.0 O B:LYS391 2.6 75.5 1.0 C B:THR394 3.3 69.6 1.0 CG B:ASP389 3.5 75.2 1.0 C B:CYS484 3.5 71.7 1.0 C B:GLN386 3.6 81.3 1.0 CB B:THR394 3.6 73.8 1.0 N B:LYS391 3.7 73.5 1.0 C B:LYS391 3.7 72.5 1.0 CA B:THR394 3.9 79.5 1.0 OD2 B:ASP389 3.9 74.8 1.0 CA B:CYS484 4.0 76.8 1.0 CA B:VAL387 4.0 71.2 1.0 N B:ARG390 4.1 78.7 1.0 CA B:LYS391 4.1 75.7 1.0 N B:THR394 4.2 76.1 1.0 CB B:CYS484 4.2 73.2 1.0 C B:ARG390 4.2 77.0 1.0 N B:VAL387 4.3 79.9 1.0 N B:TYR395 4.3 66.0 1.0 C B:VAL387 4.3 80.8 1.0 N B:ASP389 4.5 72.3 1.0 CB B:LYS391 4.5 76.4 1.0 C B:ASP389 4.5 75.6 1.0 CA B:ARG390 4.5 76.0 1.0 CA B:TYR395 4.6 78.3 1.0 O B:VAL387 4.6 80.8 1.0 N B:GLU485 4.6 70.8 1.0 CB B:ASP389 4.7 63.5 1.0 CA B:GLN386 4.7 79.2 1.0 N B:LEU388 4.8 76.9 1.0 CA B:ASP389 4.8 67.7 1.0 CG2 B:THR394 4.8 74.0 1.0 N B:ARG392 4.9 72.6 1.0 CA B:GLU485 4.9 71.9 1.0 O B:ARG390 5.0 85.1 1.0

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.