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Sodium in PDB 8qrp: ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1)

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 8qrp

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Sodium binding site 1 out of 3 in the ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:80.6
occ:1.00
O B:ASN386 2.3 82.1 1.0
OD2 B:ASP475 2.6 80.5 1.0
O B:GLY382 2.7 77.7 1.0
O B:ASN471 2.7 73.4 1.0
OD1 B:ASP475 3.2 81.6 1.0
CG B:ASP475 3.3 80.1 1.0
CA B:ALA383 3.4 67.9 1.0
C B:ASN471 3.5 68.5 1.0
C B:ASN386 3.5 79.0 1.0
C B:GLY382 3.5 70.0 1.0
O B:ALA383 3.7 75.7 1.0
C B:ALA383 3.7 72.6 1.0
N B:ALA383 3.9 69.7 1.0
SD B:MET387 3.9 85.7 1.0
CB B:ASN471 3.9 66.2 1.0
CA B:ASN471 4.1 60.7 1.0
OG B:SER353 4.1 79.2 1.0
N B:VAL472 4.3 66.1 1.0
N B:MET387 4.4 80.1 1.0
CA B:MET387 4.4 74.3 1.0
CA B:ASN386 4.4 67.6 1.0
CB B:SER353 4.5 67.5 1.0
CG B:MET387 4.5 78.3 1.0
CA B:VAL472 4.5 68.8 1.0
N B:ASN386 4.6 69.0 1.0
CB B:ASN386 4.6 73.0 1.0
N B:THR384 4.6 81.3 1.0
CB B:ALA383 4.7 65.9 1.0
CB B:ASP475 4.7 74.3 1.0
CA B:GLY382 4.8 60.3 1.0
CG1 B:VAL472 4.8 63.3 1.0
ND2 B:ASN386 4.8 79.9 1.0
CG B:ASN471 4.8 70.8 1.0
CB B:MET387 4.9 71.3 1.0

Sodium binding site 2 out of 3 in 8qrp

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Sodium binding site 2 out of 3 in the ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:88.7
occ:1.00
O B:SER425 2.3 92.0 1.0
O B:THR384 2.4 87.6 1.0
O B:ALA428 2.7 95.0 1.0
CG B:MET387 2.8 78.3 1.0
O B:VAL426 3.1 80.9 1.0
SD B:MET387 3.2 85.7 1.0
CE B:MET387 3.4 79.1 1.0
C B:THR384 3.4 79.0 1.0
C B:SER425 3.5 87.1 1.0
C B:VAL426 3.5 82.6 1.0
N B:ALA428 3.6 97.2 1.0
C B:ALA428 3.6 97.9 1.0
CB B:ALA428 3.7 89.3 1.0
CA B:VAL426 3.8 83.9 1.0
CA B:ALA428 3.8 98.3 1.0
CB B:MET387 4.1 71.3 1.0
N B:VAL426 4.1 80.7 1.0
O B:VAL385 4.2 77.4 1.0
N B:VAL385 4.2 73.2 1.0
CA B:VAL385 4.3 70.4 1.0
CA B:THR384 4.3 81.3 1.0
N B:GLY427 4.3 88.2 1.0
C B:VAL385 4.3 70.8 1.0
C B:GLY427 4.4 93.1 1.0
CA B:SER425 4.7 86.5 1.0
N B:ALA429 4.8 96.9 1.0
CA B:GLY427 4.9 90.0 1.0
N B:GLY430 5.0 85.2 1.0

Sodium binding site 3 out of 3 in 8qrp

Go back to Sodium Binding Sites List in 8qrp
Sodium binding site 3 out of 3 in the ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of ASCT2 Protomer in Lipid Nanodiscs with Bound Glutamine and Na+ Ions in the Outward-Facing State (Ofs.1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:97.6
occ:1.00
OG1 B:THR139 2.3 69.2 1.0
OD1 B:ASN386 2.3 74.2 1.0
OD1 B:ASP388 2.3 87.9 1.0
O B:PHE135 2.3 76.6 1.0
OG1 B:THR138 2.4 75.8 1.0
N B:THR139 2.6 65.3 1.0
CA B:THR139 3.3 63.5 1.0
C B:PHE135 3.3 68.2 1.0
CB B:THR138 3.3 67.2 1.0
CB B:THR139 3.3 62.6 1.0
C B:THR138 3.3 66.9 1.0
CG B:ASP388 3.3 82.9 1.0
CG B:ASN386 3.5 74.7 1.0
CA B:PHE135 3.6 62.9 1.0
CA B:THR138 3.7 69.9 1.0
OD2 B:ASP388 3.7 83.2 1.0
N B:THR138 4.0 77.2 1.0
O B:THR138 4.1 72.5 1.0
O B:PHE134 4.2 74.0 1.0
ND2 B:ASN386 4.3 79.9 1.0
CB B:PHE135 4.4 61.9 1.0
N B:LEU136 4.5 71.3 1.0
CG2 B:THR139 4.5 65.5 1.0
CB B:ASN386 4.5 73.0 1.0
CG2 B:THR138 4.6 65.5 1.0
CB B:ASP388 4.6 78.1 1.0
CA B:ASN386 4.6 67.6 1.0
N B:PHE135 4.7 68.5 1.0
C B:THR139 4.7 67.7 1.0
N B:ASP388 4.7 79.5 1.0
CA B:ASP388 4.8 74.7 1.0
N B:MET387 4.8 80.1 1.0
C B:PHE134 4.9 70.6 1.0
C B:LEU136 4.9 69.8 1.0
C B:ASN386 5.0 79.0 1.0

Reference:

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
Page generated: Wed Oct 9 13:13:40 2024

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