Sodium in PDB 3v5u: Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661

The structure of Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661, PDB code: 3v5u was solved by Y.Jiang, J.Liao, H.Li, W.Zeng, D.Sauer, R.Belmares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.67 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.490, 72.879, 96.206, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21

The structure of Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661 (pdb code 3v5u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661, PDB code: 3v5u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:20.5 occ:1.00 OE2 A:GLU213 2.3 19.3 1.0 O A:ALA47 2.4 19.2 1.0 OG A:SER236 2.4 17.6 1.0 OG1 A:THR50 2.4 19.4 1.0 OG A:SER51 2.5 17.2 1.0 N A:SER51 3.0 16.9 1.0 CB A:SER236 3.1 18.5 1.0 CD A:GLU213 3.2 22.8 1.0 C A:THR50 3.3 20.5 1.0 CB A:SER51 3.3 18.4 1.0 C A:ALA47 3.4 22.2 1.0 CA A:SER51 3.4 20.4 1.0 CB A:THR50 3.5 17.8 1.0 CG A:GLU213 3.5 20.0 1.0 CA A:ALA47 3.7 16.4 1.0 CA A:SER236 3.7 19.3 1.0 CA A:THR50 3.8 20.1 1.0 O A:THR50 3.9 20.9 1.0 NA A:NA704 4.1 23.5 0.8 N A:THR50 4.2 20.1 1.0 OE1 A:GLU213 4.3 23.7 1.0 O A:MET46 4.3 22.0 1.0 OD1 A:ASN232 4.4 29.5 1.0 CB A:ALA47 4.5 17.0 1.0 CA A:CA702 4.5 21.7 0.5 N A:ILE48 4.6 20.6 1.0 N A:SER236 4.7 17.7 1.0 C A:SER236 4.8 18.4 1.0 CG2 A:THR50 4.8 19.6 1.0 N A:ALA47 4.8 17.5 1.0 O A:SER236 4.9 14.6 1.0 O A:ASN232 4.9 18.7 1.0 C A:SER51 5.0 21.9 1.0 OD1 A:ASP240 5.0 19.6 1.0 CB A:GLU213 5.0 16.3 1.0

Sodium binding site 2 out of 3 in the Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:24.1 occ:1.00 OG A:SER77 2.3 23.5 1.0 OE2 A:GLU54 2.4 22.3 1.0 O A:ALA206 2.4 20.2 1.0 OG1 A:THR209 2.5 22.0 1.0 OG A:SER210 2.5 24.9 1.0 N A:SER210 3.0 20.0 1.0 CB A:SER77 3.1 20.5 1.0 CD A:GLU54 3.2 24.4 1.0 CB A:SER210 3.3 21.4 1.0 C A:THR209 3.3 22.6 1.0 C A:ALA206 3.4 22.8 1.0 CA A:SER210 3.4 22.0 1.0 CG A:GLU54 3.5 21.3 1.0 CB A:THR209 3.5 20.6 1.0 CA A:ALA206 3.8 25.5 1.0 CA A:THR209 3.8 21.5 1.0 CA A:SER77 3.8 18.5 1.0 O A:THR209 3.9 21.5 1.0 NA A:NA704 4.2 23.5 0.8 N A:THR209 4.2 21.9 1.0 OD1 A:ASN73 4.3 27.8 1.0 CB A:ALA206 4.3 20.1 1.0 OE1 A:GLU54 4.3 22.3 1.0 CA A:CA702 4.5 21.7 0.5 O A:ASN73 4.6 21.1 1.0 N A:PHE207 4.6 22.0 1.0 N A:SER77 4.7 17.3 1.0 O A:VAL205 4.8 25.4 1.0 CG2 A:THR209 4.8 22.1 1.0 C A:SER77 4.9 17.4 1.0 C A:SER210 5.0 22.9 1.0 CB A:GLU54 5.0 21.2 1.0

Sodium binding site 3 out of 3 in the Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Sodium/Calcium Exchanger From Methanocaldococcus Jannaschii Dsm 2661 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:23.5 occ:0.83 OD2 A:ASP240 2.7 21.3 1.0 OE2 A:GLU54 2.7 22.3 1.0 OE2 A:GLU213 2.8 19.3 1.0 OD1 A:ASN81 2.9 23.4 1.0 CD A:GLU213 3.2 22.8 1.0 CD A:GLU54 3.3 24.4 1.0 CG A:ASP240 3.4 20.9 1.0 OD1 A:ASP240 3.4 19.6 1.0 CA A:CA702 3.7 21.7 0.5 OG A:SER51 3.7 17.2 1.0 CG A:ASN81 3.7 20.5 1.0 OE1 A:GLU213 3.8 23.7 1.0 ND2 A:ASN81 3.8 19.0 1.0 OG A:SER210 3.8 24.9 1.0 CG A:GLU213 3.8 20.0 1.0 OE1 A:GLU54 3.9 22.3 1.0 CB A:SER236 4.0 18.5 1.0 CB A:SER77 4.0 20.5 1.0 CG A:GLU54 4.1 21.3 1.0 NA A:NA701 4.1 20.5 1.0 NA A:NA703 4.2 24.1 1.0 O A:SER236 4.5 14.6 1.0 OG A:SER236 4.5 17.6 1.0 OG A:SER77 4.6 23.5 1.0 O A:SER77 4.7 17.3 1.0 CB A:GLU213 4.8 16.3 1.0 CB A:SER51 4.8 18.4 1.0 C A:SER236 4.8 18.4 1.0 CB A:ASP240 4.9 15.5 1.0 CA A:SER236 4.9 19.3 1.0 CB A:SER210 4.9 21.4 1.0 CA A:SER51 4.9 20.4 1.0 CA A:SER210 4.9 22.0 1.0 C A:SER77 4.9 17.4 1.0 CA A:SER77 5.0 18.5 1.0

J.Liao, H.Li, W.Zeng, D.B.Sauer, R.Belmares, Y.Jiang. Structural Insight Into the Ion-Exchange Mechanism of the Sodium/Calcium Exchanger. Science V. 335 686 2012.
ISSN: ISSN 0036-8075
PubMed: 22323814
DOI: 10.1126/SCIENCE.1215759