Sodium in PDB 8k66: Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom

The binding sites of Sodium atom in the Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom (pdb code 8k66). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom, PDB code: 8k66:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom


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 Oryza Sativa HKT2;1 at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:30.0 occ:1.00 O A:LEU86 2.1 7.6 1.0 O A:ASN242 2.3 10.8 1.0 O A:ASN467 2.4 10.8 1.0 O A:HIS366 2.6 9.0 1.0 O A:VAL468 2.9 9.5 1.0 O A:VAL243 3.1 9.2 1.0 C A:LEU86 3.2 7.6 1.0 C A:ASN467 3.3 10.8 1.0 O A:SER367 3.4 10.8 1.0 C A:ASN242 3.4 10.8 1.0 C A:VAL468 3.5 9.5 1.0 CA A:VAL468 3.6 9.5 1.0 C A:VAL243 3.7 9.2 1.0 CA A:VAL243 3.7 9.2 1.0 C A:HIS366 3.8 9.0 1.0 N A:VAL468 3.8 9.5 1.0 C A:SER367 3.9 10.8 1.0 NA A:NA608 4.0 30.0 1.0 CB A:LEU86 4.0 7.6 1.0 N A:VAL243 4.0 9.2 1.0 CA A:SER367 4.1 10.8 1.0 CA A:LEU86 4.2 7.6 1.0 N A:SER87 4.2 8.6 1.0 CA A:SER87 4.2 8.6 1.0 C A:SER87 4.3 8.6 1.0 N A:SER367 4.4 10.8 1.0 O A:SER87 4.4 8.6 1.0 CA A:ASN467 4.5 10.8 1.0 CB A:ASN467 4.6 10.8 1.0 CA A:ASN242 4.6 10.8 1.0 CB A:SER88 4.6 5.8 1.0 N A:GLY469 4.7 7.5 1.0 CB A:ASN242 4.7 10.8 1.0 N A:GLY368 4.8 9.2 1.0 N A:SER88 4.8 5.8 1.0 N A:GLY244 4.9 7.6 1.0 CB A:HIS366 4.9 9.0 1.0 CA A:HIS366 5.0 9.0 1.0 CB A:VAL468 5.0 9.5 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom


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 Oryza Sativa HKT2;1 at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:30.0 occ:1.00 O A:HOH741 2.8 30.0 1.0 CB A:HIS366 3.5 9.0 1.0 O A:ASN467 3.5 10.8 1.0 O A:ASN242 3.5 10.8 1.0 CB A:ASN242 3.5 10.8 1.0 O A:HIS366 3.6 9.0 1.0 NA A:NA607 4.0 30.0 1.0 CD1 A:LEU86 4.0 7.6 1.0 C A:HIS366 4.2 9.0 1.0 O A:HOH733 4.3 30.0 1.0 CB A:LEU86 4.3 7.6 1.0 CB A:ASN467 4.4 10.8 1.0 CA A:HIS366 4.4 9.0 1.0 C A:ASN242 4.4 10.8 1.0 CG A:HIS366 4.5 9.0 1.0 CG A:ASN242 4.5 10.8 1.0 O A:HOH710 4.5 30.0 1.0 OD1 A:ASN273 4.5 9.2 1.0 OD1 A:ASN242 4.6 10.8 1.0 C A:ASN467 4.6 10.8 1.0 O A:LEU86 4.6 7.6 1.0 CA A:ASN242 4.6 10.8 1.0 O A:ALA241 4.6 9.0 1.0 CG A:ASN273 4.7 9.2 1.0 OE1 A:GLU114 4.7 10.3 1.0 O A:GLY466 4.7 10.8 1.0 O A:HOH720 4.8 30.0 1.0 ND2 A:ASN273 4.8 9.2 1.0 ND1 A:HIS366 4.8 9.0 1.0 CG A:LEU86 4.9 7.6 1.0 N A:HIS366 4.9 9.0 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom


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 Oryza Sativa HKT2;1 at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na707 b:30.0 occ:1.00 O B:LEU86 2.0 7.6 1.0 O B:ASN467 2.3 8.1 1.0 O B:ASN242 2.4 7.2 1.0 O B:HIS366 2.6 7.5 1.0 O B:VAL468 2.9 8.2 1.0 O B:VAL243 2.9 6.7 1.0 C B:LEU86 3.2 7.6 1.0 C B:ASN467 3.2 8.1 1.0 O B:SER367 3.5 10.8 1.0 C B:VAL468 3.5 8.2 1.0 CA B:VAL468 3.6 8.2 1.0 C B:ASN242 3.6 7.2 1.0 C B:VAL243 3.7 6.7 1.0 N B:VAL468 3.8 8.2 1.0 CA B:VAL243 3.8 6.7 1.0 C B:HIS366 3.8 7.5 1.0 NA B:NA708 3.9 30.0 1.0 C B:SER367 3.9 10.8 1.0 CB B:LEU86 4.0 7.6 1.0 CA B:SER367 4.1 10.8 1.0 CA B:LEU86 4.1 7.6 1.0 N B:SER87 4.1 8.6 1.0 N B:VAL243 4.2 6.7 1.0 CA B:SER87 4.2 8.6 1.0 C B:SER87 4.2 8.6 1.0 O B:SER87 4.4 8.6 1.0 CA B:ASN467 4.4 8.1 1.0 N B:SER367 4.5 10.8 1.0 CB B:ASN467 4.5 8.1 1.0 CB B:SER88 4.6 5.8 1.0 N B:GLY469 4.7 7.2 1.0 CA B:ASN242 4.8 7.2 1.0 N B:SER88 4.8 5.8 1.0 CB B:ASN242 4.8 7.2 1.0 N B:GLY368 4.8 8.9 1.0 N B:GLY244 4.9 7.0 1.0 CB B:HIS366 4.9 7.5 1.0 CA B:HIS366 5.0 7.5 1.0 CB B:VAL468 5.0 8.2 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of Oryza Sativa HKT2;1 at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na708 b:30.0 occ:1.00 O B:HOH845 2.8 30.0 1.0 CB B:HIS366 3.5 7.5 1.0 O B:ASN467 3.5 8.1 1.0 CB B:ASN242 3.6 7.2 1.0 O B:HIS366 3.6 7.5 1.0 O B:ASN242 3.6 7.2 1.0 NA B:NA707 3.9 30.0 1.0 CD1 B:LEU86 4.1 7.6 1.0 C B:HIS366 4.2 7.5 1.0 O B:HOH832 4.3 30.0 1.0 CB B:LEU86 4.3 7.6 1.0 CB B:ASN467 4.4 8.1 1.0 CA B:HIS366 4.4 7.5 1.0 CG B:ASN242 4.5 7.2 1.0 CG B:HIS366 4.5 7.5 1.0 C B:ASN242 4.5 7.2 1.0 OD1 B:ASN242 4.5 7.2 1.0 OD1 B:ASN273 4.6 7.5 1.0 O B:LEU86 4.6 7.6 1.0 C B:ASN467 4.6 8.1 1.0 CA B:ASN242 4.7 7.2 1.0 O B:ALA241 4.7 6.2 1.0 CG B:ASN273 4.7 7.5 1.0 O B:GLY466 4.7 10.8 1.0 OE1 B:GLU114 4.7 10.1 1.0 O B:HOH816 4.8 30.0 1.0 O B:HOH822 4.8 30.0 1.0 ND1 B:HIS366 4.8 7.5 1.0 ND2 B:ASN273 4.8 7.5 1.0 CG B:LEU86 4.9 7.6 1.0 N B:HIS366 4.9 7.5 1.0

X.Wang, X.Shen, Y.Qu, H.Zhang, C.Wang, F.Yang, H.Shen. Structural Insights Into Ion Selectivity and Transport Mechanism of Plant Hkt Transporters To Be Published.