Sodium in PDB 8d2v: Zebrafish MFSD2A Isoform B in Inward Open Ligand 1B Conformation

The binding sites of Sodium atom in the Zebrafish MFSD2A Isoform B in Inward Open Ligand 1B Conformation (pdb code 8d2v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Zebrafish MFSD2A Isoform B in Inward Open Ligand 1B Conformation, PDB code: 8d2v:

Sodium binding site 1 out of 1 in the Zebrafish MFSD2A Isoform B in Inward Open Ligand 1B Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Zebrafish MFSD2A Isoform B in Inward Open Ligand 1B Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na610 b:56.8 occ:1.00 OH A:TYR425 2.7 92.1 1.0 OE2 A:GLU184 2.7 76.6 1.0 O26 A:ZGS601 2.8 75.9 1.0 OE1 A:GLN51 2.9 71.0 1.0 CD A:GLU184 3.8 76.6 1.0 CE2 A:TYR50 3.9 68.9 1.0 CD A:GLN51 3.9 71.0 1.0 C17 A:ZGS601 4.1 75.9 1.0 P25 A:ZGS601 4.1 75.9 1.0 CZ A:TYR425 4.1 92.1 1.0 O27 A:ZGS601 4.2 75.9 1.0 OE1 A:GLU184 4.3 76.6 1.0 CD2 A:TYR50 4.4 68.9 1.0 C18 A:ZGS601 4.6 75.9 1.0 NE2 A:GLN51 4.8 71.0 1.0 CG A:GLN51 4.8 71.0 1.0 CE2 A:TYR425 4.8 92.1 1.0 NH2 A:ARG180 4.8 89.3 1.0 NE2 A:HIS156 4.8 76.3 1.0 CZ A:TYR50 5.0 68.9 1.0 C23 A:ZGS601 5.0 75.9 1.0 CE1 A:TYR425 5.0 92.1 1.0 CE1 A:HIS156 5.0 76.3 1.0

C.Nguyen, H.T.Lei, L.T.F.Lai, M.J.Gallentino, X.Mu, D.Matthies, T.Gonen. Lipid Flipping in the MFSD2A Omega-3 Fatty-Acid Transporter Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-37702-7