Sodium in PDB 1s3x: The Crystal Structure of the Human HSP70 Atpase Domain

The structure of The Crystal Structure of the Human HSP70 Atpase Domain, PDB code: 1s3x was solved by M.Sriram, J.Osipiuk, B.Freeman, R.I.Morimoto, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	145.470, 63.340, 45.950, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 21.9

The structure of The Crystal Structure of the Human HSP70 Atpase Domain also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the The Crystal Structure of the Human HSP70 Atpase Domain (pdb code 1s3x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of the Human HSP70 Atpase Domain, PDB code: 1s3x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of the Human HSP70 Atpase Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Human HSP70 Atpase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na387 b:27.1 occ:1.00 OG1 A:THR204 2.8 15.1 1.0 O2 A:PO4384 2.8 18.7 1.0 OD2 A:ASP206 2.8 28.5 1.0 O A:THR204 2.8 7.4 1.0 OD1 A:ASP199 3.2 17.4 1.0 OD2 A:ASP199 3.2 23.5 1.0 CG A:ASP199 3.3 16.4 1.0 O A:ASP199 3.4 10.4 1.0 C A:THR204 3.4 10.3 1.0 O A:HOH415 3.5 11.5 1.0 N A:GLY201 3.7 9.2 1.0 CB A:THR204 3.9 14.0 1.0 O A:HOH429 3.9 10.3 1.0 CG A:ASP206 3.9 25.2 1.0 C A:ASP199 4.0 8.7 1.0 P A:PO4384 4.0 14.7 1.0 O4 A:PO4384 4.1 13.5 1.0 N A:PHE205 4.1 8.6 1.0 N A:ASP206 4.2 14.0 1.0 CA A:GLY201 4.2 8.5 1.0 CA A:THR204 4.2 11.0 1.0 CB A:ASP199 4.2 11.7 1.0 CA A:PHE205 4.3 10.4 1.0 O A:HOH463 4.3 24.9 1.0 CB A:ASP206 4.4 17.9 1.0 CA A:CA386 4.5 25.9 1.0 C A:LEU200 4.5 8.7 1.0 C A:PHE205 4.5 10.4 1.0 N A:LEU200 4.5 7.7 1.0 CA A:LEU200 4.6 9.0 1.0 O A:HOH424 4.6 22.9 1.0 N A:THR204 4.6 10.4 1.0 O A:HOH692 4.7 21.4 1.0 O3B A:ADP383 4.8 12.6 1.0 CA A:ASP199 4.8 10.4 1.0 O1 A:PO4384 4.8 15.7 1.0 CA A:ASP206 5.0 12.7 1.0 OD1 A:ASP206 5.0 28.6 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of the Human HSP70 Atpase Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Human HSP70 Atpase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na388 b:22.8 occ:1.00 O A:HOH655 2.5 12.8 1.0 O1B A:ADP383 2.6 12.0 1.0 OD2 A:ASP10 2.7 16.0 1.0 O A:HOH636 2.9 47.3 1.0 O A:TYR15 2.9 9.0 1.0 CG A:ASP10 3.4 11.7 1.0 O3A A:ADP383 3.5 10.5 1.0 PB A:ADP383 3.5 11.1 1.0 C A:TYR15 3.7 6.1 1.0 O A:HOH657 3.7 20.6 1.0 OD1 A:ASP10 3.8 13.2 1.0 CA A:CA386 4.0 25.9 1.0 CA A:GLY12 4.0 6.7 1.0 O1A A:ADP383 4.0 10.5 1.0 PA A:ADP383 4.1 7.9 1.0 N A:GLY12 4.2 7.6 1.0 O A:HOH565 4.2 18.2 1.0 O2A A:ADP383 4.2 7.5 1.0 O2B A:ADP383 4.2 11.1 1.0 CA A:SER16 4.3 6.5 1.0 N A:SER16 4.3 7.1 1.0 O A:ASP10 4.3 7.5 1.0 CB A:ASP10 4.4 6.4 1.0 CB A:TYR15 4.5 6.8 1.0 O A:ASP366 4.5 10.1 1.0 O A:HOH402 4.5 10.4 1.0 CA A:TYR15 4.6 5.4 1.0 C A:SER16 4.6 4.3 1.0 N A:CYS17 4.7 6.2 1.0 C A:ASP10 4.9 7.8 1.0 O3B A:ADP383 4.9 12.6 1.0 N A:TYR15 4.9 5.3 1.0

M.Sriram, J.Osipiuk, B.Freeman, R.I.Morimoto, A.Joachimiak. Human HSP70 Molecular Chaperone Binds Two Calcium Ions Within the Atpase Domain Structure V. 5 403 1997.
ISSN: ISSN 0969-2126
PubMed: 9083109
DOI: 10.1016/S0969-2126(97)00197-4