Sodium in PDB 2ygo: Wif Domain-Egf-Like Domain 1 of Human Wnt Inhibitory Factor 1 in Complex with 1,2-Dipalmitoylphosphatidylcholine

The structure of Wif Domain-Egf-Like Domain 1 of Human Wnt Inhibitory Factor 1 in Complex with 1,2-Dipalmitoylphosphatidylcholine, PDB code: 2ygo was solved by T.Malinauskas, A.R.Aricescu, W.Lu, C.Siebold, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.422 / 1.85
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	50.996, 134.260, 60.403, 90.00, 90.00, 90.00
R / Rfree (%)	18.39 / 21.68

The binding sites of Sodium atom in the Wif Domain-Egf-Like Domain 1 of Human Wnt Inhibitory Factor 1 in Complex with 1,2-Dipalmitoylphosphatidylcholine (pdb code 2ygo). 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 Wif Domain-Egf-Like Domain 1 of Human Wnt Inhibitory Factor 1 in Complex with 1,2-Dipalmitoylphosphatidylcholine, PDB code: 2ygo:

Sodium binding site 1 out of 1 in the Wif Domain-Egf-Like Domain 1 of Human Wnt Inhibitory Factor 1 in Complex with 1,2-Dipalmitoylphosphatidylcholine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wif Domain-Egf-Like Domain 1 of Human Wnt Inhibitory Factor 1 in Complex with 1,2-Dipalmitoylphosphatidylcholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1215 b:0.3 occ:1.00 O A:CYS186 2.4 87.1 1.0 O A:HOH2151 2.4 49.4 1.0 O A:HOH2137 2.5 76.1 1.0 O A:HOH2138 2.7 77.3 1.0 O A:GLY190 2.7 74.0 1.0 C A:CYS186 3.3 90.1 1.0 CB A:CYS186 3.4 78.0 1.0 N A:CYS186 3.5 97.6 1.0 CA A:CYS186 3.6 84.5 1.0 C A:GLY190 3.8 61.4 1.0 CA A:PHE191 4.5 79.3 1.0 N A:ARG187 4.6 77.8 1.0 N A:PHE191 4.6 56.6 1.0 SG A:CYS186 4.6 73.2 1.0 CD1 A:PHE191 4.7 89.8 1.0 CA A:GLY190 4.8 66.5 1.0 N A:GLY190 4.8 83.5 1.0 C A:GLY185 4.8 0.2 1.0 CE1 A:PHE191 5.0 80.7 1.0

T.Malinauskas, A.R.Aricescu, W.Lu, C.Siebold, E.Y.Jones. Modular Mechanism of Wnt Signaling Inhibition By Wnt Inhibitory Factor 1 Nat.Struct.Mol.Biol. V. 18 886 2011.
ISSN: ISSN 1545-9993
PubMed: 21743455
DOI: 10.1038/NSMB.2081