Sodium in PDB 4h5r: HSC70 Nbd with Na, Cl and Glycerol

The structure of HSC70 Nbd with Na, Cl and Glycerol, PDB code: 4h5r was solved by B.Stec, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.637, 102.462, 77.776, 90.00, 119.80, 90.00
R / Rfree (%)	20.5 / 23.9

The structure of HSC70 Nbd with Na, Cl and Glycerol also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the HSC70 Nbd with Na, Cl and Glycerol (pdb code 4h5r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the HSC70 Nbd with Na, Cl and Glycerol, PDB code: 4h5r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the HSC70 Nbd with Na, Cl and Glycerol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of HSC70 Nbd with Na, Cl and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:32.1 occ:1.00 O A:HOH501 1.9 18.0 1.0 O A:HOH502 1.9 19.2 1.0 O3 A:PO4402 2.1 20.0 1.0 O A:HOH503 2.3 20.1 1.0 O A:HOH505 2.4 34.0 1.0 O A:HOH504 2.5 20.9 1.0 P A:PO4402 3.3 20.4 1.0 O1 A:PO4402 3.4 18.1 1.0 O A:HOH608 3.6 27.3 1.0 OE1 A:GLU175 3.9 20.0 1.0 O A:HOH680 3.9 28.7 1.0 O A:HOH606 4.0 16.6 1.0 O2 A:PO4402 4.0 21.1 1.0 OD2 A:ASP199 4.1 20.7 1.0 OD1 A:ASP199 4.1 16.3 1.0 OD2 A:ASP10 4.3 16.4 1.0 OD1 A:ASP10 4.4 17.8 1.0 CG A:ASP199 4.5 18.0 1.0 O4 A:PO4402 4.5 20.6 1.0 CD A:GLU175 4.6 19.1 1.0 CL A:CL403 4.7 26.4 1.0 CG A:ASP10 4.8 18.4 1.0 CG1 A:VAL337 4.9 19.1 1.0

Sodium binding site 2 out of 2 in the HSC70 Nbd with Na, Cl and Glycerol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of HSC70 Nbd with Na, Cl and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:34.6 occ:1.00 O B:HOH501 1.8 18.1 1.0 O B:HOH502 2.1 20.4 1.0 O2 B:PO4402 2.2 19.8 1.0 O B:HOH503 2.4 21.0 1.0 O B:HOH504 2.5 21.6 1.0 P B:PO4402 3.4 20.1 1.0 O B:HOH505 3.4 35.2 1.0 O4 B:PO4402 3.4 17.9 1.0 O B:HOH646 3.7 32.9 1.0 O B:HOH723 3.8 29.9 1.0 OE1 B:GLU175 3.9 17.0 1.0 OD2 B:ASP199 3.9 19.6 1.0 OD1 B:ASP199 4.0 17.9 1.0 O1 B:PO4402 4.1 20.2 1.0 O B:HOH640 4.1 21.2 1.0 OD2 B:ASP10 4.3 16.1 1.0 OD1 B:ASP10 4.4 18.4 1.0 CG B:ASP199 4.4 18.1 1.0 O3 B:PO4402 4.5 22.2 1.0 CD B:GLU175 4.6 18.2 1.0 CG1 B:VAL337 4.8 17.6 1.0 CG B:ASP10 4.8 17.9 1.0 CL B:CL403 4.9 22.6 1.0

Z.Ziming, J.Cellitti, P.Teriete, M.Pellecchia, B.Stec. New Crystal Structures of Hsc-70 Atp Binding Domain Confirm the Role of Individual Binding Pockets and Suggests A New Method of Inhibition. To Be Published.