Sodium in PDB 5vyy: Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim

The structure of Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim, PDB code: 5vyy was solved by N.S.Que, D.T.Gewirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.51 / 1.79
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.075, 92.055, 85.262, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.9

The structure of Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim (pdb code 5vyy). 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 Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim, PDB code: 5vyy:

Sodium binding site 1 out of 1 in the Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human HSP90-Alpha Bound to Resorcinylic Inhibitor Bnim within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:36.0 occ:0.50 O A:ASP193 2.5 35.8 1.0 O A:HOH428 2.6 43.1 1.0 HE21 A:GLN194 3.3 37.8 1.0 HB2 A:ASP193 3.4 49.3 1.0 NE2 A:GLN194 3.6 31.5 1.0 C A:ASP193 3.7 38.0 1.0 HE22 A:GLN194 3.8 37.8 1.0 O A:HOH513 4.0 31.4 1.0 CB A:ASP193 4.1 41.1 1.0 HA A:GLN194 4.1 40.2 1.0 CD A:GLN194 4.2 32.0 1.0 OD2 A:ASP193 4.3 54.8 1.0 CG A:ASP193 4.3 45.7 1.0 OE1 A:GLN194 4.4 29.7 1.0 CA A:ASP193 4.4 40.9 1.0 OE1 A:GLU196 4.5 34.2 1.0 HA A:ASP193 4.6 49.1 1.0 O A:HOH514 4.7 35.2 1.0 N A:GLN194 4.7 32.0 1.0 CA A:GLN194 4.9 33.5 1.0 HB3 A:ASP193 4.9 49.3 1.0 OD1 A:ASP193 4.9 45.4 1.0 HG2 A:GLN194 5.0 38.7 1.0

N.L.S.Que, V.M.Crowley, A.S.Duerfeldt, J.Zhao, C.N.Kent, B.S.J.Blagg, D.T.Gewirth. Structure Based Design of A GRP94-Selective Inhibitor: Exploiting A Key Residue in GRP94 to Optimize Paralog-Selective Binding. J. Med. Chem. V. 61 2793 2018.
ISSN: ISSN 1520-4804
PubMed: 29528635
DOI: 10.1021/ACS.JMEDCHEM.7B01608