Sodium in PDB 8r34: Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates.

The binding sites of Sodium atom in the Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates. (pdb code 8r34). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates., PDB code: 8r34:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:62.9 occ:1.00 O A:ALA811 2.3 63.4 1.0 OG A:SER815 2.6 55.7 1.0 OD1 A:ASN606 3.1 65.5 1.0 C A:ALA811 3.4 64.4 1.0 OG A:SER814 3.4 58.0 1.0 CB A:MET597 3.6 56.6 1.0 CB A:SER815 3.6 61.0 1.0 CG A:GLN605 3.7 61.1 1.0 CA A:MET597 3.9 50.6 1.0 CA A:LEU812 3.9 58.7 1.0 O A:LEU812 3.9 63.2 1.0 CG A:ASN606 4.1 62.9 1.0 N A:LEU812 4.1 65.8 1.0 NE2 A:GLN605 4.1 62.0 1.0 C A:LEU812 4.1 59.7 1.0 N A:SER815 4.1 54.4 1.0 OG A:SER603 4.2 61.6 1.0 O A:GLY596 4.2 59.1 1.0 ND2 A:ASN606 4.4 61.0 1.0 CD A:GLN605 4.5 61.3 1.0 CA A:ALA811 4.5 59.7 1.0 CA A:SER815 4.5 59.4 1.0 CB A:SER814 4.7 52.5 1.0 C A:SER814 4.7 57.2 1.0 O A:MET597 4.7 61.3 1.0 N A:SER814 4.7 51.7 1.0 N A:MET597 4.8 55.3 1.0 C A:MET597 4.8 54.5 1.0 C A:GLY596 4.9 55.0 1.0 CB A:GLN605 4.9 60.2 1.0 CA A:SER814 4.9 53.0 1.0 CG A:MET597 5.0 55.0 1.0 CB A:ALA811 5.0 57.6 1.0

Sodium binding site 2 out of 4 in the Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:56.4 occ:1.00 O A:LEU820 3.0 53.0 1.0 O A:THR775 3.1 61.1 1.0 CB A:SER823 3.2 50.9 1.0 O A:HOH1014 3.2 50.4 1.0 O A:SER823 3.3 50.7 1.0 CA A:THR775 3.5 49.7 1.0 N A:LEU820 3.5 53.1 1.0 O A:GLY817 3.6 60.7 1.0 C A:THR775 3.7 57.8 1.0 ND2 A:ASN827 3.7 44.0 1.0 OG1 A:THR775 3.7 50.6 1.0 CB A:LEU820 3.8 51.0 1.0 CA A:MET818 3.8 45.8 1.0 C A:LEU820 3.9 54.7 1.0 CA A:LEU820 3.9 51.8 1.0 O A:HOH1002 3.9 49.2 1.0 OG A:SER823 3.9 58.8 1.0 C A:MET818 4.0 54.0 1.0 C A:SER823 4.0 52.4 1.0 CA A:SER823 4.0 44.6 1.0 N A:GLY819 4.0 50.8 1.0 CB A:THR775 4.1 52.3 1.0 O A:GLY774 4.1 57.0 1.0 C A:GLY817 4.1 51.5 1.0 N A:MET818 4.2 49.7 1.0 N A:SER823 4.4 46.3 1.0 O A:MET818 4.6 65.0 1.0 N A:THR775 4.6 55.4 1.0 C A:GLY819 4.6 49.3 1.0 C A:GLY774 4.8 58.8 1.0 CG A:ASN827 4.8 42.3 1.0 N A:PHE776 4.9 56.5 1.0 CA A:GLY819 4.9 43.8 1.0

Sodium binding site 3 out of 4 in the Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:61.6 occ:1.00 O B:ALA811 2.3 62.2 1.0 OG B:SER815 2.7 54.8 1.0 OD1 B:ASN606 3.1 65.0 1.0 C B:ALA811 3.4 63.6 1.0 OG B:SER814 3.5 58.9 1.0 CB B:MET597 3.5 57.1 1.0 CB B:SER815 3.6 60.8 1.0 CG B:GLN605 3.8 59.9 1.0 CA B:MET597 3.9 51.5 1.0 CA B:LEU812 3.9 58.6 1.0 O B:LEU812 3.9 62.7 1.0 CG B:ASN606 4.0 62.3 1.0 N B:LEU812 4.1 65.1 1.0 C B:LEU812 4.1 59.0 1.0 N B:SER815 4.1 53.0 1.0 O B:GLY596 4.2 57.2 1.0 OG B:SER603 4.2 60.9 1.0 NE2 B:GLN605 4.3 61.7 1.0 ND2 B:ASN606 4.3 60.3 1.0 CA B:ALA811 4.5 59.5 1.0 CA B:SER815 4.5 58.6 1.0 CD B:GLN605 4.6 60.0 1.0 C B:SER814 4.7 56.7 1.0 CB B:SER814 4.7 52.5 1.0 N B:SER814 4.7 51.8 1.0 O B:MET597 4.7 61.0 1.0 N B:MET597 4.8 54.9 1.0 C B:MET597 4.8 55.2 1.0 C B:GLY596 4.9 53.1 1.0 CB B:GLN605 4.9 60.0 1.0 CA B:SER814 4.9 52.5 1.0 CG B:MET597 4.9 55.0 1.0 CB B:ALA811 5.0 57.5 1.0

Sodium binding site 4 out of 4 in the Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryoem Structure of the Symmetric PHO90 Dimer From Yeast with Substrates. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na904 b:59.6 occ:1.00 O B:LEU820 3.0 54.8 1.0 O B:THR775 3.1 62.9 1.0 CB B:SER823 3.2 52.0 1.0 O B:HOH1015 3.2 50.7 1.0 O B:SER823 3.3 49.4 1.0 CA B:THR775 3.5 50.8 1.0 ND2 B:ASN827 3.5 45.8 1.0 N B:LEU820 3.5 54.9 1.0 O B:GLY817 3.6 60.6 1.0 C B:THR775 3.7 59.6 1.0 OG1 B:THR775 3.7 51.2 1.0 CB B:LEU820 3.8 51.7 1.0 CA B:MET818 3.8 45.9 1.0 C B:LEU820 3.9 55.8 1.0 O B:HOH1002 3.9 49.3 1.0 CA B:LEU820 3.9 52.8 1.0 OG B:SER823 3.9 59.7 1.0 C B:MET818 4.0 55.3 1.0 C B:SER823 4.0 52.5 1.0 N B:GLY819 4.0 51.6 1.0 CA B:SER823 4.0 46.2 1.0 CB B:THR775 4.1 53.8 1.0 O B:GLY774 4.1 57.2 1.0 C B:GLY817 4.1 52.0 1.0 N B:MET818 4.2 49.8 1.0 N B:SER823 4.4 48.6 1.0 O B:MET818 4.6 67.0 1.0 N B:THR775 4.6 56.2 1.0 C B:GLY819 4.6 51.0 1.0 CG B:ASN827 4.8 43.5 1.0 C B:GLY774 4.8 57.8 1.0 N B:PHE776 4.9 57.4 1.0 CA B:GLY819 4.9 45.0 1.0

S.Schneider, W.Kuehlbrandt, O.Yildiz. Complementary Structures of the Yeast Phosphate Transporter PHO90 Provide Insights Into Its Transport Mechanism Structure 2024.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2024.04.005