Sodium in PDB 2agv: Crystal Structure of the Sr CA2+-Atpase with Bhq and Tg

All present enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with Bhq and Tg:
3.6.3.8;

The structure of Crystal Structure of the Sr CA2+-Atpase with Bhq and Tg, PDB code: 2agv was solved by C.Toyoshima, K.Obara, Y.Norimatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.98 / 2.40
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	71.385, 71.385, 591.017, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 26.3

The binding sites of Sodium atom in the Crystal Structure of the Sr CA2+-Atpase with Bhq and Tg (pdb code 2agv). 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 the Sr CA2+-Atpase with Bhq and Tg, PDB code: 2agv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Sr CA2+-Atpase with Bhq and Tg


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 Sr CA2+-Atpase with Bhq and Tg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1000 b:41.4 occ:1.00 O A:ALA714 2.4 40.0 1.0 OE1 A:GLU732 2.4 35.0 1.0 O A:LEU711 2.5 38.7 1.0 O A:LYS712 2.7 32.0 1.0 O A:HOH2097 2.8 46.7 1.0 O A:HOH2095 3.0 47.0 1.0 CD A:GLU732 3.2 35.9 1.0 C A:LYS712 3.3 35.0 1.0 OE2 A:GLU732 3.5 36.5 1.0 C A:ALA714 3.5 39.4 1.0 C A:LEU711 3.6 36.5 1.0 N A:GLY717 3.7 31.2 1.0 CA A:LYS712 3.7 37.0 1.0 NE2 A:GLN244 3.9 82.5 1.0 O A:GLU715 4.0 32.2 1.0 C A:GLU715 4.1 33.5 1.0 N A:ALA714 4.1 40.6 1.0 C A:LYS713 4.1 42.1 1.0 N A:LYS713 4.2 35.4 1.0 N A:LYS712 4.2 34.0 1.0 CA A:GLY717 4.2 28.3 1.0 CA A:ALA714 4.4 40.4 1.0 O A:LYS713 4.4 43.0 1.0 CG A:GLU732 4.4 36.9 1.0 N A:ILE716 4.4 32.6 1.0 CD A:GLN244 4.5 81.0 1.0 N A:GLU715 4.5 34.5 1.0 OE1 A:GLN244 4.5 82.1 1.0 CA A:GLU715 4.5 34.4 1.0 O A:ALA730 4.5 35.0 1.0 C A:ILE716 4.6 34.8 1.0 CA A:LYS713 4.6 39.3 1.0 CA A:ILE716 4.8 33.6 1.0 CB A:ALA714 4.8 42.4 1.0 CA A:LEU711 4.9 34.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Sr CA2+-Atpase with Bhq and Tg


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 Sr CA2+-Atpase with Bhq and Tg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1100 b:45.2 occ:1.00 OE1 B:GLU732 2.4 34.7 1.0 O B:ALA714 2.4 41.5 1.0 O B:LEU711 2.5 36.8 1.0 O B:LYS712 2.7 33.0 1.0 O B:HOH3097 2.8 49.6 1.0 O B:HOH3095 3.0 45.7 1.0 CD B:GLU732 3.2 37.3 1.0 C B:LYS712 3.3 34.5 1.0 OE2 B:GLU732 3.5 36.7 1.0 C B:ALA714 3.6 39.5 1.0 C B:LEU711 3.6 35.6 1.0 N B:GLY717 3.7 32.4 1.0 CA B:LYS712 3.7 36.6 1.0 NE2 B:GLN244 3.9 82.7 1.0 O B:GLU715 4.1 32.7 1.0 N B:ALA714 4.1 41.3 1.0 C B:GLU715 4.1 33.8 1.0 N B:LYS712 4.1 33.4 1.0 N B:LYS713 4.2 35.8 1.0 C B:LYS713 4.2 42.0 1.0 CA B:GLY717 4.2 28.5 1.0 CA B:ALA714 4.4 40.2 1.0 O B:LYS713 4.4 43.4 1.0 CG B:GLU732 4.4 37.5 1.0 N B:ILE716 4.5 33.6 1.0 O B:ALA730 4.5 38.3 1.0 N B:GLU715 4.5 35.0 1.0 CD B:GLN244 4.5 80.9 1.0 OE1 B:GLN244 4.5 81.9 1.0 CA B:GLU715 4.6 34.9 1.0 C B:ILE716 4.6 35.6 1.0 CA B:LYS713 4.6 39.2 1.0 CA B:ILE716 4.8 34.8 1.0 CB B:ALA714 4.8 42.2 1.0 CA B:LEU711 4.9 34.0 1.0

K.Obara, N.Miyashita, C.Xu, I.Toyoshima, Y.Sugita, G.Inesi, C.Toyoshima. Inaugural Article: Structural Role of Countertransport Revealed in CA2+ Pump Crystal Structure in the Absence of CA2+. Proc.Natl.Acad.Sci.Usa V. 102 14489 2005.
ISSN: ISSN 0027-8424
PubMed: 16150713
DOI: 10.1073/PNAS.0506222102