Sodium in PDB 3w5a: Crystal Structure of the Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State

The structure of Crystal Structure of the Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State, PDB code: 3w5a 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 / 3.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	352.883, 55.729, 187.951, 90.00, 119.02, 90.00
R / Rfree (%)	24.8 / 28.3

The structure of Crystal Structure of the Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State (pdb code 3w5a). 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 Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State, PDB code: 3w5a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ 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 and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1006 b:37.9 occ:1.00 O A:LEU711 2.4 45.2 1.0 OE1 A:GLU732 2.6 54.4 1.0 O A:ALA714 2.6 45.7 1.0 OE2 A:GLU732 2.7 52.0 1.0 O A:LYS712 2.8 40.5 1.0 CD A:GLU732 3.0 51.1 1.0 C A:LYS712 3.2 42.1 1.0 CA A:LYS712 3.4 46.0 1.0 C A:LEU711 3.5 43.9 1.0 C A:ALA714 3.7 43.2 1.0 N A:LYS712 4.0 45.9 1.0 N A:LYS713 4.1 42.5 1.0 N A:ALA714 4.1 42.5 1.0 N A:GLY717 4.1 38.7 1.0 C A:LYS713 4.3 40.9 1.0 O A:ALA730 4.4 49.3 1.0 CA A:ALA714 4.4 43.7 1.0 CG A:GLU732 4.5 48.0 1.0 O A:GLU715 4.5 41.8 1.0 CA A:GLY717 4.5 35.1 1.0 O A:LYS713 4.6 37.7 1.0 C A:GLU715 4.6 42.2 1.0 CA A:LYS713 4.7 43.6 1.0 CB A:LYS712 4.8 50.4 1.0 N A:GLU715 4.8 42.8 1.0 CA A:LEU711 4.8 41.7 1.0 CG A:LYS712 4.9 56.8 1.0 CB A:ALA714 4.9 42.5 1.0 CA A:GLU715 4.9 44.0 1.0 C A:ILE716 5.0 38.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State


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 Calcium Pump and Sarcolipin From Rabbit Fast Twitch Skeletal Muscle in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1007 b:33.2 occ:1.00 O B:ALA714 2.1 50.0 1.0 OE1 B:GLU732 2.6 48.9 1.0 OE2 B:GLU732 2.8 55.5 1.0 O B:LYS712 2.8 47.7 1.0 CD B:GLU732 3.0 51.1 1.0 O B:LEU711 3.0 50.4 1.0 C B:ALA714 3.3 48.4 1.0 C B:LYS712 3.5 48.9 1.0 O B:GLU715 3.8 44.1 1.0 CA B:LYS712 3.9 53.4 1.0 C B:GLU715 4.0 44.0 1.0 N B:ALA714 4.1 51.1 1.0 C B:LEU711 4.1 50.8 1.0 CA B:ALA714 4.2 50.1 1.0 N B:GLU715 4.2 46.7 1.0 N B:GLY717 4.2 40.7 1.0 C B:LYS713 4.2 49.5 1.0 CA B:GLU715 4.3 46.1 1.0 O B:LYS713 4.4 49.5 1.0 N B:LYS713 4.4 48.2 1.0 CG B:GLU732 4.5 48.5 1.0 N B:LYS712 4.5 53.2 1.0 N B:ILE716 4.6 41.9 1.0 CB B:ALA714 4.7 49.6 1.0 CA B:GLY717 4.8 40.6 1.0 C B:ILE716 4.9 39.8 1.0 CA B:LYS713 4.9 50.8 1.0 CA B:ILE716 5.0 40.6 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