Sodium in PDB 3e89: Crystal Structure of the the Open Nak Channel-Low Na+ Complex

The structure of Crystal Structure of the the Open Nak Channel-Low Na+ Complex, PDB code: 3e89 was solved by Y.Jiang, A.Alam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.81 / 1.80
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	68.050, 68.050, 89.251, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.8

The structure of Crystal Structure of the the Open Nak Channel-Low Na+ Complex also contains other interesting chemical elements:

Caesium

(Cs)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the the Open Nak Channel-Low Na+ Complex (pdb code 3e89). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the the Open Nak Channel-Low Na+ Complex, PDB code: 3e89:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the the Open Nak Channel-Low Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the the Open Nak Channel-Low Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:42.0 occ:0.25 CS A:CS1 2.5 18.3 0.8 O A:VAL64 2.9 20.9 1.0 C A:VAL64 4.0 17.9 1.0 O A:HOH508 4.0 32.1 1.0 CA A:GLY65 4.2 19.0 1.0 N A:GLY65 4.6 14.9 1.0 O A:THR63 4.6 19.5 1.0 C A:GLY65 4.7 23.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the the Open Nak Channel-Low Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the the Open Nak Channel-Low Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6 b:22.9 occ:0.25 OG1 A:THR63 2.4 18.3 1.0 O A:HOH507 2.7 53.8 0.2 CB A:THR63 3.3 23.0 1.0 O A:THR63 4.1 19.5 1.0 CG2 A:THR63 4.2 18.1 1.0 C A:THR63 4.5 19.1 1.0 CA A:THR63 4.6 19.7 1.0 O A:THR62 4.8 19.7 1.0 CS A:CS1 4.9 18.3 0.8

Sodium binding site 3 out of 4 in the Crystal Structure of the the Open Nak Channel-Low Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the the Open Nak Channel-Low Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:40.9 occ:0.25 CS B:CS2 2.8 27.7 0.7 O B:VAL64 3.2 32.3 1.0 CA B:GLY65 4.2 37.9 1.0 C B:VAL64 4.2 32.3 1.0 N B:GLY65 4.6 33.7 1.0 C B:GLY65 4.7 38.4 1.0 O B:THR63 4.9 25.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the the Open Nak Channel-Low Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the the Open Nak Channel-Low Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5 b:33.8 occ:0.25 OG1 B:THR63 2.5 28.9 1.0 O B:HOH540 2.9 35.6 0.2 CB B:THR63 3.4 27.5 1.0 O B:THR63 4.0 25.7 1.0 CG2 B:THR63 4.3 20.3 1.0 C B:THR63 4.5 27.4 1.0 CA B:THR63 4.6 26.9 1.0 O B:THR62 4.8 23.6 1.0 CS B:CS2 4.8 27.7 0.7

A.Alam, Y.Jiang. Structural Analysis of Ion Selectivity in the Nak Channel Nat.Struct.Mol.Biol. V. 16 35 2009.
ISSN: ISSN 1545-9993
PubMed: 19098915
DOI: 10.1038/NSMB.1537