Sodium in PDB 8qro: ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)

The binding sites of Sodium atom in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) (pdb code 8qro). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs), PDB code: 8qro:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:70.0 occ:1.00 O A:ASN386 2.3 75.8 1.0 OD2 A:ASP475 2.4 77.2 1.0 O A:GLY382 2.8 71.8 1.0 O A:ASN471 3.0 72.2 1.0 CG A:ASP475 3.0 76.0 1.0 OD1 A:ASP475 3.0 77.1 1.0 CA A:ALA383 3.3 66.5 1.0 C A:GLY382 3.3 66.1 1.0 C A:ASN386 3.5 75.0 1.0 N A:ALA383 3.6 65.3 1.0 C A:ASN471 3.6 62.8 1.0 C A:ALA383 3.9 69.8 1.0 CB A:ASN471 4.1 63.0 1.0 O A:ALA383 4.1 75.5 1.0 CA A:ASN471 4.3 61.6 1.0 CB A:ASN386 4.3 64.5 1.0 CA A:ASN386 4.3 65.7 1.0 CB A:ASP475 4.3 74.5 1.0 N A:VAL472 4.3 62.6 1.0 ND2 A:ASN386 4.4 70.5 1.0 CA A:GLY382 4.4 57.6 1.0 CB A:ALA383 4.4 60.1 1.0 N A:ASN386 4.5 64.2 1.0 N A:MET387 4.5 76.3 1.0 OG A:SER353 4.5 79.6 1.0 CA A:VAL472 4.5 69.6 1.0 CG A:MET387 4.5 71.8 1.0 CE A:MET387 4.6 73.7 1.0 CA A:MET387 4.7 67.8 1.0 N A:THR384 4.7 65.6 1.0 CB A:SER353 4.7 74.5 1.0 CG A:ASN386 4.8 69.7 1.0 N A:ASP475 5.0 72.7 1.0

Sodium binding site 2 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:74.6 occ:1.00 O A:SER425 2.3 78.8 1.0 O A:THR384 2.4 68.7 1.0 O A:VAL426 2.6 65.1 1.0 O A:ALA428 2.6 90.9 1.0 C A:VAL426 3.1 75.9 1.0 CA A:VAL426 3.4 73.2 1.0 C A:SER425 3.4 80.3 1.0 C A:THR384 3.5 63.2 1.0 N A:ALA428 3.5 90.9 1.0 SD A:MET387 3.5 80.2 1.0 C A:ALA428 3.6 90.8 1.0 CG A:MET387 3.6 71.8 1.0 CB A:ALA428 3.8 87.6 1.0 CA A:ALA428 3.8 91.7 1.0 CE A:MET387 3.8 73.7 1.0 N A:VAL426 3.9 73.2 1.0 N A:GLY427 4.0 86.7 1.0 C A:GLY427 4.1 83.4 1.0 N A:VAL385 4.3 61.5 1.0 CA A:VAL385 4.3 60.5 1.0 O A:VAL385 4.4 64.0 1.0 CA A:THR384 4.4 66.0 1.0 C A:VAL385 4.5 60.4 1.0 CA A:GLY427 4.6 80.4 1.0 CA A:SER425 4.7 81.9 1.0 CB A:MET387 4.7 72.7 1.0 N A:ALA429 4.8 84.8 1.0 CB A:VAL426 4.8 70.3 1.0 O A:GLY427 4.9 84.2 1.0 CG2 A:THR384 5.0 64.8 1.0

Sodium binding site 3 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:83.2 occ:1.00 OG1 A:THR138 2.2 67.9 1.0 OD1 A:ASP388 2.3 75.6 1.0 OG1 A:THR139 2.3 63.9 1.0 OD1 A:ASN386 2.3 76.9 1.0 O A:PHE135 2.3 70.8 1.0 N A:THR139 2.6 67.4 1.0 CB A:THR138 3.1 68.0 1.0 CA A:THR139 3.2 63.8 1.0 CG A:ASP388 3.2 77.3 1.0 C A:THR138 3.2 66.9 1.0 CB A:THR139 3.2 62.8 1.0 C A:PHE135 3.3 62.7 1.0 CG A:ASN386 3.4 69.7 1.0 CA A:THR138 3.6 66.3 1.0 OD2 A:ASP388 3.7 74.7 1.0 CA A:PHE135 3.7 58.1 1.0 ND2 A:ASN386 4.0 70.5 1.0 N A:THR138 4.0 69.1 1.0 O A:THR138 4.0 69.3 1.0 CB A:ASP388 4.3 74.8 1.0 O A:PHE134 4.4 67.4 1.0 CG2 A:THR139 4.5 67.0 1.0 CB A:PHE135 4.5 56.3 1.0 CG2 A:THR138 4.5 66.2 1.0 N A:ASP388 4.5 69.6 1.0 N A:LEU136 4.5 62.9 1.0 CB A:ASN386 4.6 64.5 1.0 CA A:ASP388 4.6 70.2 1.0 C A:THR139 4.7 68.2 1.0 N A:MET387 4.7 76.3 1.0 CA A:ASN386 4.8 65.7 1.0 N A:PHE135 4.9 65.5 1.0 C A:LEU136 5.0 63.9 1.0 C A:MET387 5.0 66.3 1.0

Sodium binding site 4 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:70.0 occ:1.00 O B:ASN386 2.3 75.8 1.0 OD2 B:ASP475 2.4 77.2 1.0 O B:GLY382 2.8 71.8 1.0 O B:ASN471 3.0 72.2 1.0 CG B:ASP475 3.0 76.0 1.0 OD1 B:ASP475 3.0 77.1 1.0 CA B:ALA383 3.3 66.5 1.0 C B:GLY382 3.3 66.1 1.0 C B:ASN386 3.5 75.0 1.0 N B:ALA383 3.6 65.3 1.0 C B:ASN471 3.6 62.8 1.0 C B:ALA383 3.9 69.8 1.0 CB B:ASN471 4.1 63.0 1.0 O B:ALA383 4.1 75.5 1.0 CA B:ASN471 4.3 61.6 1.0 CB B:ASN386 4.3 64.5 1.0 CA B:ASN386 4.3 65.7 1.0 CB B:ASP475 4.3 74.5 1.0 N B:VAL472 4.3 62.6 1.0 ND2 B:ASN386 4.4 70.5 1.0 CA B:GLY382 4.4 57.6 1.0 CB B:ALA383 4.4 60.1 1.0 N B:ASN386 4.5 64.2 1.0 N B:MET387 4.5 76.3 1.0 OG B:SER353 4.5 79.6 1.0 CA B:VAL472 4.5 69.6 1.0 CG B:MET387 4.5 71.8 1.0 CE B:MET387 4.6 73.7 1.0 CA B:MET387 4.7 67.8 1.0 N B:THR384 4.7 65.6 1.0 CB B:SER353 4.7 74.5 1.0 CG B:ASN386 4.8 69.7 1.0 N B:ASP475 5.0 72.7 1.0

Sodium binding site 5 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:74.6 occ:1.00 O B:SER425 2.3 78.8 1.0 O B:THR384 2.4 68.7 1.0 O B:VAL426 2.6 65.1 1.0 O B:ALA428 2.6 90.9 1.0 C B:VAL426 3.1 75.9 1.0 CA B:VAL426 3.4 73.2 1.0 C B:SER425 3.4 80.3 1.0 C B:THR384 3.5 63.2 1.0 N B:ALA428 3.5 90.9 1.0 SD B:MET387 3.5 80.2 1.0 C B:ALA428 3.6 90.8 1.0 CG B:MET387 3.6 71.8 1.0 CB B:ALA428 3.8 87.6 1.0 CA B:ALA428 3.8 91.7 1.0 CE B:MET387 3.8 73.7 1.0 N B:VAL426 3.9 73.2 1.0 N B:GLY427 4.0 86.7 1.0 C B:GLY427 4.1 83.4 1.0 N B:VAL385 4.3 61.5 1.0 CA B:VAL385 4.3 60.5 1.0 O B:VAL385 4.4 64.0 1.0 CA B:THR384 4.4 66.0 1.0 C B:VAL385 4.5 60.4 1.0 CA B:GLY427 4.6 80.4 1.0 CA B:SER425 4.7 81.9 1.0 CB B:MET387 4.7 72.7 1.0 N B:ALA429 4.8 84.8 1.0 CB B:VAL426 4.8 70.3 1.0 O B:GLY427 4.9 84.2 1.0 CG2 B:THR384 5.0 64.8 1.0

Sodium binding site 6 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:83.2 occ:1.00 OG1 B:THR138 2.2 67.9 1.0 OD1 B:ASP388 2.3 75.6 1.0 OG1 B:THR139 2.3 63.9 1.0 OD1 B:ASN386 2.3 76.9 1.0 O B:PHE135 2.3 70.8 1.0 N B:THR139 2.6 67.4 1.0 CB B:THR138 3.1 68.0 1.0 CA B:THR139 3.2 63.8 1.0 CG B:ASP388 3.2 77.3 1.0 C B:THR138 3.2 66.9 1.0 CB B:THR139 3.2 62.8 1.0 C B:PHE135 3.3 62.7 1.0 CG B:ASN386 3.4 69.7 1.0 CA B:THR138 3.6 66.3 1.0 OD2 B:ASP388 3.7 74.7 1.0 CA B:PHE135 3.7 58.1 1.0 ND2 B:ASN386 4.0 70.5 1.0 N B:THR138 4.0 69.1 1.0 O B:THR138 4.0 69.3 1.0 CB B:ASP388 4.3 74.8 1.0 O B:PHE134 4.4 67.4 1.0 CG2 B:THR139 4.5 67.0 1.0 CB B:PHE135 4.5 56.3 1.0 CG2 B:THR138 4.5 66.2 1.0 N B:ASP388 4.5 69.6 1.0 N B:LEU136 4.5 62.9 1.0 CB B:ASN386 4.6 64.5 1.0 CA B:ASP388 4.6 70.2 1.0 C B:THR139 4.7 68.2 1.0 N B:MET387 4.7 76.3 1.0 CA B:ASN386 4.8 65.7 1.0 N B:PHE135 4.9 65.5 1.0 C B:LEU136 5.0 63.9 1.0 C B:MET387 5.0 66.3 1.0

Sodium binding site 7 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:70.0 occ:1.00 O C:ASN386 2.3 75.8 1.0 OD2 C:ASP475 2.4 77.2 1.0 O C:GLY382 2.8 71.8 1.0 O C:ASN471 3.0 72.2 1.0 CG C:ASP475 3.0 76.0 1.0 OD1 C:ASP475 3.0 77.1 1.0 CA C:ALA383 3.3 66.5 1.0 C C:GLY382 3.3 66.1 1.0 C C:ASN386 3.5 75.0 1.0 N C:ALA383 3.6 65.3 1.0 C C:ASN471 3.6 62.8 1.0 C C:ALA383 3.9 69.8 1.0 CB C:ASN471 4.1 63.0 1.0 O C:ALA383 4.1 75.5 1.0 CA C:ASN471 4.3 61.6 1.0 CB C:ASN386 4.3 64.5 1.0 CA C:ASN386 4.3 65.7 1.0 CB C:ASP475 4.3 74.5 1.0 N C:VAL472 4.3 62.6 1.0 ND2 C:ASN386 4.4 70.5 1.0 CA C:GLY382 4.4 57.6 1.0 CB C:ALA383 4.4 60.1 1.0 N C:ASN386 4.5 64.2 1.0 N C:MET387 4.5 76.3 1.0 OG C:SER353 4.5 79.6 1.0 CA C:VAL472 4.5 69.6 1.0 CG C:MET387 4.5 71.8 1.0 CE C:MET387 4.6 73.7 1.0 CA C:MET387 4.7 67.8 1.0 N C:THR384 4.7 65.6 1.0 CB C:SER353 4.7 74.5 1.0 CG C:ASN386 4.8 69.7 1.0 N C:ASP475 5.0 72.7 1.0

Sodium binding site 8 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:74.6 occ:1.00 O C:SER425 2.3 78.8 1.0 O C:THR384 2.4 68.7 1.0 O C:VAL426 2.6 65.1 1.0 O C:ALA428 2.6 90.9 1.0 C C:VAL426 3.1 75.9 1.0 CA C:VAL426 3.4 73.2 1.0 C C:SER425 3.4 80.3 1.0 C C:THR384 3.5 63.2 1.0 N C:ALA428 3.5 90.9 1.0 SD C:MET387 3.5 80.2 1.0 C C:ALA428 3.6 90.8 1.0 CG C:MET387 3.6 71.8 1.0 CB C:ALA428 3.8 87.6 1.0 CA C:ALA428 3.8 91.7 1.0 CE C:MET387 3.8 73.7 1.0 N C:VAL426 3.9 73.2 1.0 N C:GLY427 4.0 86.7 1.0 C C:GLY427 4.1 83.4 1.0 N C:VAL385 4.3 61.5 1.0 CA C:VAL385 4.3 60.5 1.0 O C:VAL385 4.4 64.0 1.0 CA C:THR384 4.4 66.0 1.0 C C:VAL385 4.5 60.4 1.0 CA C:GLY427 4.6 80.4 1.0 CA C:SER425 4.7 81.9 1.0 CB C:MET387 4.7 72.7 1.0 N C:ALA429 4.8 84.8 1.0 CB C:VAL426 4.8 70.3 1.0 O C:GLY427 4.9 84.2 1.0 CG2 C:THR384 5.0 64.8 1.0

Sodium binding site 9 out of 9 in the ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of ASCT2 Trimer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na603 b:83.2 occ:1.00 OG1 C:THR138 2.2 67.9 1.0 OD1 C:ASP388 2.3 75.6 1.0 OG1 C:THR139 2.3 63.9 1.0 OD1 C:ASN386 2.3 76.9 1.0 O C:PHE135 2.3 70.8 1.0 N C:THR139 2.6 67.4 1.0 CB C:THR138 3.1 68.0 1.0 CA C:THR139 3.2 63.8 1.0 CG C:ASP388 3.2 77.3 1.0 C C:THR138 3.2 66.9 1.0 CB C:THR139 3.2 62.8 1.0 C C:PHE135 3.3 62.7 1.0 CG C:ASN386 3.4 69.7 1.0 CA C:THR138 3.6 66.3 1.0 OD2 C:ASP388 3.7 74.7 1.0 CA C:PHE135 3.7 58.1 1.0 ND2 C:ASN386 4.0 70.5 1.0 N C:THR138 4.0 69.1 1.0 O C:THR138 4.0 69.3 1.0 CB C:ASP388 4.3 74.8 1.0 O C:PHE134 4.4 67.4 1.0 CG2 C:THR139 4.5 67.0 1.0 CB C:PHE135 4.5 56.3 1.0 CG2 C:THR138 4.5 66.2 1.0 N C:ASP388 4.5 69.6 1.0 N C:LEU136 4.5 62.9 1.0 CB C:ASN386 4.6 64.5 1.0 CA C:ASP388 4.6 70.2 1.0 C C:THR139 4.7 68.2 1.0 N C:MET387 4.7 76.3 1.0 CA C:ASN386 4.8 65.7 1.0 N C:PHE135 4.9 65.5 1.0 C C:LEU136 5.0 63.9 1.0 C C:MET387 5.0 66.3 1.0

A.M.Borowska, M.G.Chiariello, A.A.Garaeva, J.Rheinberger, S.J.Marrink, C.Paulino, D.J.Slotboom. Structural Basis of the Obligatory Exchange Mode of Human Neutral Amino Acid Transporter ASCT2. Nat Commun V. 15 6570 2024.
ISSN: ESSN 2041-1723
PubMed: 39095408
DOI: 10.1038/S41467-024-50888-8