Sodium in PDB 8pxt: Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood

The structure of Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood, PDB code: 8pxt was solved by M.Jensen, 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)	62.32 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.23, 169.06, 171.97, 90, 90, 90
R / Rfree (%)	18 / 21

The structure of Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood (pdb code 8pxt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood, PDB code: 8pxt:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:54.9 occ:1.00 OE2 A:GLU450 2.5 51.4 1.0 O A:HOH936 2.6 65.4 1.0 HG3 A:GLU450 3.2 57.4 1.0 CD A:GLU450 3.4 47.1 1.0 HG2 A:GLU450 3.5 57.4 1.0 CG A:GLU450 3.6 47.8 1.0 OE1 A:GLU450 4.6 43.9 1.0

Sodium binding site 2 out of 4 in the Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:73.0 occ:1.00 H A:ALA20 2.5 93.2 1.0 OG A:SER91 2.5 68.0 1.0 O A:THR138 2.5 76.8 1.0 O A:ILE135 2.7 71.5 1.0 HE2 A:PHE140 2.9 77.1 1.0 HB A:ILE135 3.0 84.4 1.0 HA A:PRO139 3.1 97.4 1.0 HA A:PRO19 3.2 107.5 1.0 HB2 A:PRO19 3.2 102.0 1.0 N A:ALA20 3.3 77.6 1.0 HD2 A:PHE140 3.3 79.1 1.0 HB3 A:SER91 3.3 79.5 1.0 HB3 A:PRO19 3.4 102.0 1.0 CE2 A:PHE140 3.4 64.2 1.0 CB A:SER91 3.5 66.2 1.0 C A:THR138 3.6 77.5 1.0 HB3 A:ALA20 3.6 89.2 1.0 CB A:PRO19 3.6 84.9 1.0 CD2 A:PHE140 3.6 65.8 1.0 CA A:PRO19 3.7 89.5 1.0 C A:ILE135 3.8 68.8 1.0 CA A:PRO139 3.9 81.1 1.0 HB3 A:SER136 3.9 83.6 1.0 O A:SER91 3.9 73.3 1.0 CB A:ILE135 4.0 70.3 1.0 HB2 A:ALA20 4.0 89.2 1.0 C A:PRO19 4.0 85.9 1.0 N A:PRO139 4.1 85.0 1.0 CB A:ALA20 4.1 74.3 1.0 C A:SER91 4.1 74.6 1.0 HB2 A:SER91 4.1 79.5 1.0 HG22 A:ILE135 4.2 81.5 1.0 CA A:ALA20 4.2 76.3 1.0 HA A:SER92 4.3 98.1 1.0 H A:THR138 4.3 92.3 1.0 CA A:SER91 4.4 66.5 1.0 CA A:ILE135 4.4 71.4 1.0 H A:ILE135 4.5 86.9 1.0 H A:PHE140 4.5 83.4 1.0 CZ A:PHE140 4.5 61.3 1.0 CG2 A:ILE135 4.6 67.9 1.0 C A:PRO139 4.6 78.1 1.0 N A:SER92 4.6 74.4 1.0 O A:ALA20 4.7 73.2 1.0 N A:THR138 4.7 76.9 1.0 CA A:THR138 4.7 76.4 1.0 N A:PHE140 4.7 69.5 1.0 HZ A:PHE140 4.8 73.6 1.0 CG A:PHE140 4.8 63.9 1.0 CB A:SER136 4.8 69.6 1.0 HG21 A:ILE135 4.8 81.5 1.0 HB3 A:PRO139 4.9 105.0 1.0 N A:ILE135 4.9 72.4 1.0 N A:SER136 4.9 67.9 1.0 HA A:SER91 4.9 79.9 1.0 HG12 A:ILE135 4.9 84.7 1.0 CA A:SER92 4.9 81.7 1.0 CG1 A:ILE135 4.9 70.5 1.0 C A:ALA20 5.0 80.1 1.0 HG13 A:ILE135 5.0 84.7 1.0 HB2 A:SER136 5.0 83.6 1.0

Sodium binding site 3 out of 4 in the Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood within 5.0Å range: probe atom residue distance (Å) B Occ C:Na703 b:59.9 occ:1.00 OG1 C:THR625 2.5 48.7 1.0 O C:ASN589 2.5 49.3 1.0 HB C:THR625 2.9 57.1 1.0 CB C:THR625 3.2 47.9 1.0 HB3 C:TYR587 3.2 55.2 1.0 OG1 C:THR623 3.2 54.5 1.0 H C:ASN589 3.3 54.1 1.0 HA C:ASN589 3.3 57.5 1.0 O C:THR623 3.3 48.6 1.0 HG1 C:THR623 3.3 65.5 1.0 C C:ASN589 3.4 50.8 1.0 H C:THR625 3.4 55.4 1.0 N C:ASN589 3.5 45.3 1.0 O C:TYR587 3.5 46.9 1.0 HB2 C:TYR587 3.6 55.2 1.0 CA C:ASN589 3.6 47.8 1.0 N C:THR625 3.6 46.5 1.0 HA C:TYR624 3.7 54.7 1.0 CB C:TYR587 3.8 46.0 1.0 C C:THR623 3.9 46.3 1.0 C C:TYR587 3.9 44.7 1.0 CA C:THR625 4.0 48.5 1.0 C C:TYR624 4.1 47.9 1.0 CA C:TYR624 4.2 45.9 1.0 C C:GLU588 4.3 46.1 1.0 N C:TYR624 4.3 46.6 1.0 HA C:GLU588 4.3 52.9 1.0 HG21 C:THR625 4.4 60.3 1.0 CB C:THR623 4.4 47.7 1.0 CG2 C:THR625 4.4 50.2 1.0 N C:GLU588 4.5 44.4 1.0 CA C:TYR587 4.5 44.9 1.0 HB C:THR623 4.6 57.0 1.0 CA C:GLU588 4.6 44.3 1.0 HA C:THR625 4.7 58.3 1.0 N C:SER590 4.7 52.0 1.0 HA C:SER590 4.8 63.5 1.0 CA C:THR623 4.8 51.7 1.0 O C:TYR624 4.8 48.2 1.0 HG23 C:THR625 5.0 60.3 1.0

Sodium binding site 4 out of 4 in the Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Targeting Extended Blood Antigens By Akkermansia Muciniphila Enzymes Unveils A Missing Link For Generating Universal Donor Blood within 5.0Å range: probe atom residue distance (Å) B Occ C:Na704 b:55.1 occ:1.00 O C:HOH938 2.3 43.1 1.0 O C:SER271 2.4 41.1 1.0 O C:PRO268 2.4 41.9 1.0 O C:HOH981 2.5 50.8 1.0 O C:HOH963 2.5 52.3 1.0 HG1 C:THR274 3.1 55.2 1.0 OG1 C:THR274 3.4 45.9 1.0 HA C:PHE269 3.5 51.9 1.0 C C:PRO268 3.5 43.8 1.0 C C:SER271 3.6 41.8 1.0 H C:THR274 3.7 46.8 1.0 HB C:THR274 3.7 50.6 1.0 HA C:LEU272 3.8 47.1 1.0 H C:SER271 3.8 48.5 1.0 CB C:THR274 4.1 42.1 1.0 HB3 C:PRO268 4.1 55.6 1.0 CA C:PHE269 4.2 43.2 1.0 N C:PHE269 4.3 43.4 1.0 HB2 C:PRO268 4.3 55.6 1.0 CA C:LEU272 4.4 39.5 1.0 C C:LEU272 4.4 39.6 1.0 CA C:PRO268 4.4 41.8 1.0 N C:LEU272 4.4 39.5 1.0 N C:THR274 4.5 39.0 1.0 N C:SER271 4.5 40.4 1.0 CB C:PRO268 4.5 46.3 1.0 HA C:PRO268 4.5 50.2 1.0 O C:LEU272 4.6 40.3 1.0 C C:PHE269 4.6 43.6 1.0 CA C:SER271 4.6 39.4 1.0 HB3 C:SER271 4.6 48.1 1.0 O C:HOH880 4.7 40.0 1.0 N C:LYS273 4.8 41.8 1.0 O C:PHE269 4.9 39.5 1.0 CA C:THR274 4.9 44.5 1.0

M.Jensen, L.Stenfelt, J.R.Hagman, M.J.Pichler, J.Weikum, T.S.Nielsen, A.Hult, J.P.Morth, M.L.Olsson, M.Abou Hachem. Akkermansia Muciniphila Exoglycosidases Target Extended Blood Group Antigens to Generate Abo-Universal Blood Nature Microbiology 2024.