Sodium in PDB 9mxc: Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3)

All present enzymatic activity of Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3):
2.7.7.48; 3.4.22.28; 3.4.22.29; 3.6.1.15;

The binding sites of Sodium atom in the Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3) (pdb code 9mxc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3), PDB code: 9mxc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1301 b:46.2 occ:1.00 HG1 A:THR1007 2.0 56.0 1.0 O A:ALA1008 2.3 58.2 1.0 O A:ASN1050 2.6 56.3 1.0 OG1 A:THR1007 2.8 56.0 1.0 OD1 A:ASP1010 3.1 54.4 1.0 HB3 A:ASN1050 3.2 52.7 1.0 C A:ALA1008 3.5 43.7 1.0 HB A:THR1007 3.6 51.4 1.0 HA A:THR1009 3.6 62.4 1.0 C A:ASN1050 3.7 46.7 1.0 H A:ASN1050 3.8 58.5 1.0 CB A:THR1007 3.8 51.4 1.0 H A:ASP1010 3.9 57.9 1.0 CG A:ASP1010 3.9 44.2 1.0 N A:ASP1010 4.0 57.9 1.0 CB A:ASN1050 4.1 52.7 1.0 C A:THR1009 4.2 54.9 1.0 CA A:THR1009 4.2 62.4 1.0 CA A:ASN1050 4.2 55.9 1.0 N A:THR1009 4.3 53.6 1.0 C A:THR1007 4.4 47.6 1.0 N A:ASN1050 4.4 58.5 1.0 N A:ALA1008 4.4 51.1 1.0 OD2 A:ASP1010 4.5 49.0 1.0 O A:THR1007 4.5 55.5 1.0 HA A:GLN1051 4.5 53.1 1.0 CA A:ALA1008 4.6 60.0 1.0 HA A:ASP1010 4.6 55.5 1.0 HG21 A:THR1007 4.7 44.1 1.0 CA A:THR1007 4.7 60.7 1.0 H A:ALA1008 4.7 51.1 1.0 CA A:ASP1010 4.8 55.5 1.0 O A:THR1009 4.8 49.9 1.0 N A:GLN1051 4.8 52.1 1.0 CG A:ASN1050 4.8 51.5 1.0 HB2 A:ASN1050 4.8 52.7 1.0 CG2 A:THR1007 4.9 44.1 1.0 CB A:ASP1010 4.9 50.6 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2301 b:49.5 occ:1.00 OD2 B:ASP2163 2.1 55.4 1.0 O A:HOH1440 3.1 34.5 1.0 CG B:ASP2163 3.2 54.9 1.0 HG1 B:THR2165 3.2 67.3 1.0 OG1 B:THR2165 3.4 67.3 1.0 HD11 B:LEU2161 3.5 80.6 1.0 HG21 B:THR2165 3.5 50.3 1.0 OD1 B:ASP2163 3.5 99.9 1.0 HH11 A:ARG1252 3.5 49.0 1.0 HD2 B:HIS2130 3.6 54.1 1.0 HD2 A:PRO1253 3.6 57.0 1.0 HE2 B:PHE2173 3.6 50.4 1.0 HD13 B:LEU2161 3.9 80.6 1.0 HG2 A:PRO1253 4.0 51.8 1.0 HZ B:PHE2173 4.1 46.7 1.0 HB2 B:LEU2161 4.1 63.9 1.0 HB2 A:PRO1253 4.1 52.7 1.0 CD1 B:LEU2161 4.2 80.6 1.0 CG2 B:THR2165 4.2 50.3 1.0 HE A:ARG1252 4.2 47.3 1.0 HG22 B:THR2165 4.2 50.3 1.0 NH1 A:ARG1252 4.2 49.0 1.0 HG21 B:ILE2127 4.3 50.3 1.0 CD2 B:HIS2130 4.3 54.1 1.0 CB B:THR2165 4.3 62.0 1.0 HB3 B:LEU2161 4.5 63.9 1.0 CE2 B:PHE2173 4.5 50.4 1.0 HD13 B:ILE2127 4.5 51.5 1.0 CB B:ASP2163 4.5 48.9 1.0 CD A:PRO1253 4.5 57.0 1.0 NE2 B:HIS2130 4.6 57.5 1.0 HB3 A:ARG1252 4.6 56.1 1.0 CG A:PRO1253 4.6 51.8 1.0 HB B:THR2165 4.7 62.0 1.0 HB2 B:ASP2163 4.7 48.9 1.0 CZ B:PHE2173 4.7 46.7 1.0 CB B:LEU2161 4.8 63.9 1.0 HB3 B:ASP2163 4.8 48.9 1.0 HH12 A:ARG1252 4.8 49.0 1.0 NE A:ARG1252 4.8 47.3 1.0 HG22 B:ILE2127 4.8 50.3 1.0 CZ A:ARG1252 4.9 47.5 1.0 HD12 B:LEU2161 4.9 80.6 1.0 CB A:PRO1253 4.9 52.7 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of Human Enterovirus D68 Usa/Il/14-18952 in Complex with Fc-MFSD6(L3) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3301 b:40.3 occ:1.00 O C:ASN3179 2.1 221.2 1.0 H C:ASP3181 2.3 64.5 1.0 H C:ASN3179 2.4 70.3 1.0 C C:ASN3179 2.7 104.1 1.0 N C:ASN3179 2.9 70.3 1.0 HB2 C:ASN3179 3.0 97.1 1.0 HB3 C:ASN3179 3.0 97.1 1.0 CA C:ASN3179 3.0 95.1 1.0 CB C:ASN3179 3.2 97.1 1.0 HB3 C:ALA3187 3.2 55.6 1.0 O C:ASP3181 3.3 62.3 1.0 N C:ASP3181 3.3 64.5 1.0 HB1 C:ALA3187 3.3 55.6 1.0 HA C:PHE3178 3.3 62.6 1.0 HE21 C:GLN3089 3.6 127.5 1.0 N C:ASN3180 3.6 58.6 1.0 CB C:ALA3187 3.7 55.6 1.0 C C:ASP3181 3.7 46.6 1.0 HG2 C:GLN3089 3.8 244.5 1.0 HA C:ASN3180 3.8 52.3 1.0 HB2 C:ALA3187 3.8 55.6 1.0 C C:PHE3178 3.8 61.6 1.0 O C:MET3177 3.9 77.8 1.0 HD23 C:LEU3090 4.0 57.3 1.0 CA C:ASP3181 4.0 61.2 1.0 CA C:ASN3180 4.1 52.3 1.0 CA C:PHE3178 4.1 62.6 1.0 HA C:ASN3179 4.1 95.1 1.0 C C:ASN3180 4.1 50.8 1.0 HB3 C:ASP3181 4.2 61.2 1.0 H C:ASN3180 4.3 58.6 1.0 HA C:ALA3182 4.4 56.6 1.0 N C:ALA3182 4.5 54.7 1.0 HB3 C:SER3184 4.6 54.8 1.0 NE2 C:GLN3089 4.6 127.5 1.0 HD12 C:LEU3090 4.6 55.7 1.0 HG3 C:GLN3089 4.7 244.5 1.0 CG C:GLN3089 4.7 244.5 1.0 CG C:ASN3179 4.7 75.7 1.0 CB C:ASP3181 4.8 61.2 1.0 O C:PHE3178 4.8 92.8 1.0 C C:MET3177 4.8 49.0 1.0 N C:PHE3178 5.0 65.1 1.0 HA C:ASP3181 5.0 61.2 1.0 HB3 C:PHE3178 5.0 127.2 1.0

L.Xu, G.Pintilie, L.Varanese, J.E.Carette, W.Chiu. MFSD6 Is An Entry Receptor For Enterovirus D68 Nature 2025.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-025-08908-0