Sodium in PDB 6s08: Crystal Structure of Properdin (Tsr Domains N1 & 456)

The structure of Crystal Structure of Properdin (Tsr Domains N1 & 456), PDB code: 6s08 was solved by R.M.Van Den Bos, N.M.Pearce, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.61 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.995, 114.860, 39.822, 90.00, 99.56, 90.00
R / Rfree (%)	21.2 / 24.8

The binding sites of Sodium atom in the Crystal Structure of Properdin (Tsr Domains N1 & 456) (pdb code 6s08). 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 Properdin (Tsr Domains N1 & 456), PDB code: 6s08:

Sodium binding site 1 out of 1 in the Crystal Structure of Properdin (Tsr Domains N1 & 456)


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 Properdin (Tsr Domains N1 & 456) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:27.7 occ:1.00 O A:ILE335 2.7 19.8 1.0 O A:ILE340 2.8 15.5 1.0 O A:GLN338 2.9 18.3 1.0 N A:SER372 3.1 14.1 1.0 O A:HOH635 3.5 10.9 1.0 C A:ILE335 3.6 21.0 1.0 CA A:TYR371 3.6 14.1 1.0 CG1 A:ILE335 3.7 20.9 1.0 C A:TYR371 3.8 14.1 1.0 CD1 A:ILE335 3.8 20.4 1.0 CB A:ILE335 3.8 21.2 1.0 C A:ILE340 3.8 15.9 1.0 O A:SER372 3.9 15.5 1.0 CA A:SER372 4.0 14.7 1.0 C A:GLN338 4.0 19.0 1.0 CB A:SER372 4.1 14.7 1.0 N A:ILE340 4.1 17.1 1.0 CB A:TYR371 4.1 14.3 1.0 CD1 A:TYR371 4.2 13.8 1.0 CA A:ILE335 4.3 22.0 1.0 CA A:ILE340 4.4 16.6 1.0 C A:SER372 4.4 15.7 1.0 N A:SER336 4.4 21.2 1.0 N A:GLN338 4.5 20.5 1.0 CA A:SER336 4.6 21.5 1.0 CB A:ILE340 4.6 16.5 1.0 CG A:TYR371 4.6 14.3 1.0 CA A:GLN338 4.8 20.0 1.0 N A:PRO341 4.8 15.8 1.0 N A:TYR371 4.9 14.5 1.0 O A:CYS370 4.9 14.7 1.0

R.M.Van Den Bos, N.M.Pearce, J.Granneman, T.H.C.Brondijk, P.Gros. Insights Into Enhanced Complement Activation By Structures of Properdin and Its Complex with the C-Terminal Domain of C3B. Front Immunol V. 10 2097 2019.
ISSN: ESSN 1664-3224
PubMed: 31552043
DOI: 10.3389/FIMMU.2019.02097