Sodium in PDB 2ahy: Na+ Complex of the Nak Channel

The structure of Na+ Complex of the Nak Channel, PDB code: 2ahy was solved by N.Shi, S.Ye, A.Alam, L.Chen, Y.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.528, 85.482, 129.572, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 26.1

The structure of Na+ Complex of the Nak Channel also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

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

Sodium binding site 1 out of 4 in the Na+ Complex of the Nak Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Na+ Complex of the Nak Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na111 b:10.5 occ:0.50 O A:THR63 2.7 55.1 1.0 O B:THR63 2.7 61.8 1.0 O A:VAL64 2.7 55.7 1.0 O B:VAL64 2.8 50.2 1.0 C A:VAL64 3.5 49.1 1.0 C B:VAL64 3.5 44.7 1.0 C A:THR63 3.9 44.3 1.0 C B:THR63 3.9 46.5 1.0 NA A:NA112 3.9 32.8 0.5 CA A:VAL64 4.1 48.5 1.0 CA B:VAL64 4.1 44.1 1.0 N B:GLY65 4.4 42.4 1.0 N A:GLY65 4.4 45.2 1.0 NA A:NA115 4.4 64.1 0.5 N A:VAL64 4.5 44.0 1.0 N B:VAL64 4.5 44.8 1.0 CA B:GLY65 4.7 32.6 1.0 CA A:GLY65 4.7 35.5 1.0

Sodium binding site 2 out of 4 in the Na+ Complex of the Nak Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Na+ Complex of the Nak Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na112 b:32.8 occ:0.50 OG1 A:THR63 2.6 41.7 1.0 OG1 B:THR63 2.7 47.5 1.0 O B:THR63 3.1 61.8 1.0 O A:THR63 3.1 55.1 1.0 CB B:THR63 3.3 41.8 1.0 CB A:THR63 3.4 44.4 1.0 C A:THR63 3.8 44.3 1.0 C B:THR63 3.8 46.5 1.0 NA A:NA111 3.9 10.5 0.5 NA A:NA113 4.1 85.4 0.5 CA B:THR63 4.2 44.3 1.0 CA A:THR63 4.2 44.0 1.0 CG2 B:THR63 4.5 39.0 1.0 CG2 A:THR63 4.6 35.5 1.0 N A:VAL64 4.6 44.0 1.0 N B:VAL64 4.7 44.8 1.0 O A:THR62 4.9 51.8 1.0 O B:THR62 4.9 45.9 1.0 CA A:VAL64 5.0 48.5 1.0

Sodium binding site 3 out of 4 in the Na+ Complex of the Nak Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Na+ Complex of the Nak Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na113 b:85.4 occ:0.50 O B:HOH112 3.7 0.9 1.0 O B:HOH111 3.9 94.9 1.0 NA A:NA112 4.1 32.8 0.5 OG1 A:THR63 4.1 41.7 1.0 OG1 B:THR63 4.2 47.5 1.0

Sodium binding site 4 out of 4 in the Na+ Complex of the Nak Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Na+ Complex of the Nak Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na115 b:64.1 occ:0.50 O B:VAL64 4.2 50.2 1.0 O A:VAL64 4.3 55.7 1.0 NA A:NA111 4.4 10.5 0.5 C B:GLY65 4.6 50.2 1.0 CA B:GLY65 4.6 32.6 1.0 C A:GLY65 4.6 47.6 1.0 O B:ASP66 4.6 55.0 1.0 O A:ASP66 4.7 54.5 1.0 CA A:GLY65 4.7 35.5 1.0 C A:ASP66 4.7 43.5 1.0 C B:ASP66 4.7 46.9 1.0 CA A:GLY67 4.7 54.1 1.0 N A:GLY67 4.8 47.4 1.0 N B:ASP66 4.8 49.9 1.0 CA B:GLY67 4.8 52.0 1.0 N A:ASP66 4.8 50.1 1.0 N B:GLY67 4.8 47.4 1.0 O A:GLY65 5.0 59.4 1.0 O B:GLY65 5.0 51.4 1.0

N.Shi, S.Ye, A.Alam, L.Chen, Y.Jiang. Atomic Structure of A Na+- and K+-Conducting Channel. Nature V. 440 570 2006.
ISSN: ISSN 0028-0836
PubMed: 16467789
DOI: 10.1038/NATURE04508