Sodium in PDB 5nkq: Crystal Structure of A Dual Topology Fluoride Ion Channel.

The structure of Crystal Structure of A Dual Topology Fluoride Ion Channel., PDB code: 5nkq was solved by R.Stockbridge, C.Miller, S.Newstead, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.95 / 2.17
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.590, 84.060, 85.960, 109.41, 101.40, 101.37
R / Rfree (%)	21.7 / 24.3

The structure of Crystal Structure of A Dual Topology Fluoride Ion Channel. also contains other interesting chemical elements:

Fluorine

(F)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of A Dual Topology Fluoride Ion Channel. (pdb code 5nkq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Dual Topology Fluoride Ion Channel., PDB code: 5nkq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


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 A Dual Topology Fluoride Ion Channel. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:39.1 occ:1.00 O A:THR80 2.3 31.0 1.0 O B:THR80 2.3 34.6 1.0 O A:GLY77 2.3 36.6 1.0 O B:GLY77 2.3 39.3 1.0 C B:THR80 3.3 36.3 1.0 C A:THR80 3.3 31.7 1.0 C A:GLY77 3.4 32.2 1.0 C B:GLY77 3.5 35.8 1.0 CA B:THR81 3.8 33.1 1.0 CA A:THR81 3.8 34.7 1.0 N B:THR81 3.9 30.2 1.0 N A:THR81 4.0 31.0 1.0 CA B:GLY78 4.1 33.1 1.0 CA A:GLY78 4.2 27.0 1.0 OG1 A:THR80 4.2 31.0 1.0 N A:GLY78 4.2 28.2 1.0 N B:GLY78 4.2 34.8 1.0 O B:GLY78 4.2 30.6 1.0 C B:GLY78 4.3 29.5 1.0 OG1 B:THR80 4.3 31.8 1.0 C A:GLY78 4.3 32.4 1.0 CA A:GLY77 4.3 29.8 1.0 CB B:THR81 4.4 34.3 1.0 CA A:THR80 4.4 30.6 1.0 CA B:THR80 4.4 26.5 1.0 CB A:THR81 4.4 32.9 1.0 N A:THR80 4.5 29.2 1.0 O A:GLY78 4.5 33.2 1.0 N B:THR80 4.5 26.5 1.0 CA B:GLY77 4.5 32.9 1.0 CB A:THR80 4.9 29.6 1.0 N A:LEU79 4.9 27.2 1.0 CB B:THR80 4.9 26.5 1.0 N B:LEU79 5.0 28.3 1.0 C B:THR81 5.0 34.0 1.0 NH2 A:ARG23 5.0 33.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


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 A Dual Topology Fluoride Ion Channel. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:38.3 occ:1.00 O D:THR80 2.3 32.1 1.0 O C:THR80 2.3 33.3 1.0 O D:GLY77 2.3 36.8 1.0 O C:GLY77 2.3 39.0 1.0 C C:THR80 3.3 32.3 1.0 C D:THR80 3.3 32.3 1.0 C D:GLY77 3.5 33.6 1.0 C C:GLY77 3.5 34.9 1.0 CA D:THR81 3.7 34.3 1.0 CA C:THR81 3.8 32.3 1.0 N D:THR81 3.9 32.8 1.0 N C:THR81 3.9 32.1 1.0 OG1 C:THR80 4.1 29.0 1.0 OG1 D:THR80 4.2 34.7 1.0 CA D:GLY78 4.2 31.5 1.0 CA C:GLY78 4.2 30.9 1.0 N D:GLY78 4.3 33.3 1.0 N C:GLY78 4.3 32.0 1.0 O C:GLY78 4.3 31.8 1.0 O D:GLY78 4.3 34.5 1.0 C D:GLY78 4.3 31.9 1.0 C C:GLY78 4.3 30.8 1.0 CB D:THR81 4.4 40.0 1.0 CA C:THR80 4.4 31.4 1.0 CA D:THR80 4.4 27.9 1.0 CA C:GLY77 4.4 33.5 1.0 N C:THR80 4.4 31.9 1.0 CA D:GLY77 4.4 32.7 1.0 CB C:THR81 4.5 34.1 1.0 N D:THR80 4.5 27.6 1.0 CB C:THR80 4.8 31.2 1.0 CB D:THR80 4.9 27.9 1.0 C D:THR81 4.9 39.9 1.0 C C:THR81 4.9 35.4 1.0 OG1 D:THR81 5.0 42.8 1.0 O C:LEU76 5.0 34.7 1.0 N D:LEU79 5.0 33.6 1.0

R.B.Stockbridge, L.Kolmakova-Partensky, T.Shane, A.Koide, S.Koide, C.Miller, S.Newstead. Crystal Structures of A Double-Barrelled Fluoride Ion Channel. Nature V. 525 548 2015.
ISSN: ESSN 1476-4687
PubMed: 26344196
DOI: 10.1038/NATURE14981