Sodium in PDB 4e0k: Crystal Structure of the Amyloid-Fibril Forming Peptide Kdwsfy Derived From Human Beta 2 Microglobulin (58-63)

The structure of Crystal Structure of the Amyloid-Fibril Forming Peptide Kdwsfy Derived From Human Beta 2 Microglobulin (58-63), PDB code: 4e0k was solved by M.Zhao, C.Liu, M.R.Sawaya, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.98 / 0.97
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	62.370, 62.370, 11.730, 90.00, 90.00, 120.00
R / Rfree (%)	11.2 / 13.1

The binding sites of Sodium atom in the Crystal Structure of the Amyloid-Fibril Forming Peptide Kdwsfy Derived From Human Beta 2 Microglobulin (58-63) (pdb code 4e0k). 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 Crystal Structure of the Amyloid-Fibril Forming Peptide Kdwsfy Derived From Human Beta 2 Microglobulin (58-63), PDB code: 4e0k:

Sodium binding site 1 out of 1 in the Crystal Structure of the Amyloid-Fibril Forming Peptide Kdwsfy Derived From Human Beta 2 Microglobulin (58-63)


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 Amyloid-Fibril Forming Peptide Kdwsfy Derived From Human Beta 2 Microglobulin (58-63) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:48.9 occ:1.00 HB2 B:TRP3 2.5 7.5 1.0 OD1 B:ASP2 2.8 13.8 0.5 H B:TRP3 2.9 7.0 1.0 HD1 B:TRP3 3.0 9.2 1.0 CB B:TRP3 3.4 6.2 1.0 N B:TRP3 3.7 5.8 1.0 CD1 B:TRP3 3.7 7.7 1.0 CG B:ASP2 3.9 13.6 0.5 HB3 B:ASP2 4.0 11.7 0.5 CG B:TRP3 4.0 7.0 1.0 CA B:TRP3 4.0 5.5 1.0 HB3 B:TRP3 4.1 7.5 1.0 O B:TRP3 4.2 8.1 1.0 C B:TRP3 4.5 5.7 1.0 OD2 B:ASP2 4.5 15.5 0.5 HA B:ASP2 4.5 9.2 0.5 HA B:ASP2 4.5 9.8 0.5 C B:ASP2 4.8 6.1 1.0 CB B:ASP2 4.8 9.7 0.5 HZ3 A:TRP3 4.9 6.8 1.0 HA B:TRP3 4.9 6.6 1.0 CA B:ASP2 5.0 7.6 0.5 CA B:ASP2 5.0 8.2 0.5

C.Liu, M.Zhao, L.Jiang, P.N.Cheng, J.Park, M.R.Sawaya, A.Pensalfini, D.Gou, A.J.Berk, C.G.Glabe, J.Nowick, D.Eisenberg. Out-of-Register Beta-Sheets Suggest A Pathway to Toxic Amyloid Aggregates. Proc.Natl.Acad.Sci.Usa V. 109 20913 2012.
ISSN: ISSN 0027-8424
PubMed: 23213214
DOI: 10.1073/PNAS.1218792109