Sodium in PDB 1wpg: Crystal Structure of the Sr CA2+-Atpase with MGF4

All present enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with MGF4:
3.6.3.8;

The structure of Crystal Structure of the Sr CA2+-Atpase with MGF4, PDB code: 1wpg was solved by C.Toyoshima, H.Nomura, T.Tsuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.210, 275.394, 109.945, 90.00, 90.01, 90.00
R / Rfree (%)	22.3 / 24.5

The structure of Crystal Structure of the Sr CA2+-Atpase with MGF4 also contains other interesting chemical elements:

Fluorine	(F)	16 atoms
Magnesium	(Mg)	12 atoms

The binding sites of Sodium atom in the Crystal Structure of the Sr CA2+-Atpase with MGF4 (pdb code 1wpg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Sr CA2+-Atpase with MGF4, PDB code: 1wpg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1000 b:32.0 occ:1.00 O A:ALA714 2.4 34.3 1.0 O A:LYS712 2.5 35.3 1.0 O A:LEU711 2.7 36.6 1.0 O A:HOH2127 2.8 43.2 1.0 OE1 A:GLU732 2.9 53.2 1.0 C A:LYS712 3.2 37.8 1.0 C A:ALA714 3.5 35.5 1.0 CA A:LYS712 3.6 38.5 1.0 CD A:GLU732 3.6 52.2 1.0 OE2 A:GLU732 3.8 54.0 1.0 C A:LEU711 3.8 35.4 1.0 N A:ALA714 4.0 37.1 1.0 N A:LYS712 4.1 37.6 1.0 CA A:ALA714 4.3 36.2 1.0 N A:LYS713 4.3 36.8 1.0 O A:GLU715 4.3 39.5 1.0 N A:GLY717 4.3 39.0 1.0 C A:LYS713 4.3 36.8 1.0 C A:GLU715 4.4 39.6 1.0 N A:GLU715 4.6 37.6 1.0 O A:ALA730 4.6 40.6 1.0 CA A:GLY717 4.7 37.5 1.0 N A:ILE716 4.7 38.3 1.0 CB A:ALA714 4.7 33.8 1.0 O A:LYS713 4.8 36.6 1.0 CA A:LYS713 4.8 35.5 1.0 CA A:GLU715 4.8 39.6 1.0 C A:ILE716 4.8 38.5 1.0 CG A:GLU732 4.9 48.4 1.0 CB A:LYS712 4.9 41.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1100 b:25.6 occ:1.00 O B:ALA714 2.4 28.1 1.0 OE2 B:GLU732 2.6 35.4 1.0 O B:LYS712 2.6 30.1 1.0 O B:LEU711 2.7 30.8 1.0 O B:HOH3127 2.7 25.4 1.0 OE1 B:GLN244 2.7 94.9 1.0 CD B:GLU732 3.3 37.5 1.0 C B:LYS712 3.3 29.5 1.0 OE1 B:GLU732 3.4 39.9 1.0 C B:ALA714 3.6 32.7 1.0 CD B:GLN244 3.7 97.1 1.0 CA B:LYS712 3.7 34.6 1.0 C B:LEU711 3.7 29.6 1.0 NE2 B:GLN244 4.0 95.7 1.0 O B:GLU715 4.1 34.3 1.0 N B:GLY717 4.1 29.6 1.0 N B:ALA714 4.1 30.3 1.0 N B:LYS712 4.2 30.9 1.0 C B:GLU715 4.3 33.6 1.0 CA B:ALA714 4.3 31.9 1.0 C B:LYS713 4.4 29.6 1.0 N B:LYS713 4.4 28.6 1.0 N B:GLU715 4.6 32.5 1.0 CA B:GLY717 4.6 27.1 1.0 O B:ALA730 4.6 30.7 1.0 CG B:GLU732 4.7 32.8 1.0 O B:LYS713 4.7 32.9 1.0 N B:ILE716 4.7 33.7 1.0 CA B:GLU715 4.7 33.6 1.0 CB B:ALA714 4.8 28.3 1.0 C B:ILE716 4.8 30.4 1.0 CA B:LYS713 4.9 30.2 1.0 CG B:GLN244 5.0 97.1 1.0 CA B:ILE716 5.0 31.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1200 b:25.1 occ:1.00 O C:ALA714 2.4 27.5 1.0 OE2 C:GLU732 2.6 32.9 1.0 O C:LYS712 2.6 32.6 1.0 O C:HOH4127 2.6 28.2 1.0 O C:LEU711 2.7 28.9 1.0 OE1 C:GLN244 2.7 94.4 1.0 CD C:GLU732 3.3 38.1 1.0 C C:LYS712 3.4 31.0 1.0 OE1 C:GLU732 3.4 36.9 1.0 C C:ALA714 3.6 31.9 1.0 CD C:GLN244 3.6 96.8 1.0 CA C:LYS712 3.7 35.3 1.0 C C:LEU711 3.8 29.3 1.0 NE2 C:GLN244 4.0 95.7 1.0 O C:GLU715 4.1 33.4 1.0 N C:GLY717 4.1 29.7 1.0 N C:ALA714 4.1 30.1 1.0 N C:LYS712 4.2 31.7 1.0 C C:GLU715 4.3 32.8 1.0 CA C:ALA714 4.3 31.9 1.0 N C:LYS713 4.4 29.7 1.0 C C:LYS713 4.4 29.6 1.0 CA C:GLY717 4.6 26.7 1.0 N C:GLU715 4.6 31.9 1.0 CG C:GLU732 4.6 33.4 1.0 O C:ALA730 4.6 30.8 1.0 N C:ILE716 4.7 33.3 1.0 CA C:GLU715 4.7 32.6 1.0 O C:LYS713 4.8 31.7 1.0 C C:ILE716 4.8 29.6 1.0 CB C:ALA714 4.8 30.5 1.0 CA C:LYS713 4.9 30.1 1.0 CG C:GLN244 5.0 96.8 1.0 CA C:ILE716 5.0 31.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1300 b:33.3 occ:1.00 O D:ALA714 2.4 33.9 1.0 O D:LYS712 2.5 36.2 1.0 O D:LEU711 2.7 36.2 1.0 O D:HOH5127 2.8 44.3 1.0 OE1 D:GLU732 2.8 52.0 1.0 C D:LYS712 3.2 38.3 1.0 C D:ALA714 3.6 34.3 1.0 CA D:LYS712 3.6 39.5 1.0 CD D:GLU732 3.6 50.8 1.0 OE2 D:GLU732 3.7 52.6 1.0 C D:LEU711 3.8 35.7 1.0 N D:ALA714 4.0 36.9 1.0 N D:LYS712 4.1 37.8 1.0 O D:GLU715 4.2 40.4 1.0 N D:GLY717 4.2 39.3 1.0 CA D:ALA714 4.3 36.0 1.0 N D:LYS713 4.3 37.6 1.0 C D:GLU715 4.3 38.7 1.0 C D:LYS713 4.4 37.2 1.0 N D:GLU715 4.6 36.9 1.0 O D:ALA730 4.6 39.7 1.0 CA D:GLY717 4.7 37.6 1.0 N D:ILE716 4.7 37.3 1.0 CB D:ALA714 4.7 33.0 1.0 CA D:GLU715 4.8 39.3 1.0 C D:ILE716 4.8 38.2 1.0 CA D:LYS713 4.8 36.5 1.0 O D:LYS713 4.8 36.3 1.0 CG D:GLU732 4.9 47.1 1.0 CB D:LYS712 4.9 42.3 1.0 CA D:ILE716 5.0 37.5 1.0

C.Toyoshima, H.Nomura, T.Tsuda. Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues Nature V. 432 361 2004.
ISSN: ISSN 0028-0836
PubMed: 15448704
DOI: 10.1038/NATURE02981