Sodium in PDB 3w5d: Crystal Structure of the Calcium Pump in the E2+Pi State

The structure of Crystal Structure of the Calcium Pump in the E2+Pi State, PDB code: 3w5d was solved by C.Toyoshima, S.Iwasawa, H.Ogawa, A.Hirata, J.Tsueda, G.Inesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.248, 71.248, 587.086, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 27.1

The binding sites of Sodium atom in the Crystal Structure of the Calcium Pump in the E2+Pi State (pdb code 3w5d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Calcium Pump in the E2+Pi State, PDB code: 3w5d:

Sodium binding site 1 out of 1 in the Crystal Structure of the Calcium Pump in the E2+Pi State


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 Calcium Pump in the E2+Pi State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:47.2 occ:1.00 OE1 A:GLU732 2.1 54.8 1.0 O A:HOH1101 2.3 50.0 1.0 O A:HOH1102 2.4 41.6 1.0 O A:ALA714 2.5 58.1 1.0 O A:LEU711 2.6 56.2 1.0 CD A:GLU732 2.8 52.7 1.0 OE2 A:GLU732 2.8 50.9 1.0 O A:LYS712 3.1 55.0 1.0 C A:LYS712 3.6 53.5 1.0 C A:ALA714 3.7 57.0 1.0 N A:GLY717 3.7 47.8 1.0 C A:LEU711 3.7 53.8 1.0 CA A:LYS712 3.8 53.9 1.0 OE1 A:GLN244 4.0 0.1 1.0 O A:GLU715 4.1 53.8 1.0 CG A:GLU732 4.2 57.5 1.0 C A:GLU715 4.2 48.5 1.0 CA A:GLY717 4.2 46.7 1.0 O A:ALA730 4.3 46.5 1.0 N A:LYS712 4.3 52.5 1.0 N A:ALA714 4.5 54.4 1.0 CA A:GLU715 4.5 49.4 1.0 N A:GLU715 4.5 51.9 1.0 C A:LYS713 4.6 58.0 1.0 N A:LYS713 4.6 49.3 1.0 N A:ILE716 4.6 47.3 1.0 CA A:ALA714 4.6 56.1 1.0 C A:ILE716 4.6 50.5 1.0 O A:LYS713 4.7 62.1 1.0 N A:GLU732 4.7 58.6 1.0 CA A:ILE716 4.8 48.1 1.0 CA A:LEU711 5.0 47.6 1.0

C.Toyoshima, S.Iwasawa, H.Ogawa, A.Hirata, J.Tsueda, G.Inesi. Crystal Structures of the Calcium Pump and Sarcolipin in the MG2+-Bound E1 State. Nature V. 495 260 2013.
ISSN: ISSN 0028-0836
PubMed: 23455422
DOI: 10.1038/NATURE11899