Sodium in PDB 4uzq: Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A

All present enzymatic activity of Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A:
3.1.1.1;

The structure of Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A, PDB code: 4uzq was solved by M.Zebisch, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.44 / 1.50
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.513, 69.350, 120.967, 90.00, 92.28, 90.00
R / Rfree (%)	12.789 / 17.775

The structure of Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A (pdb code 4uzq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A, PDB code: 4uzq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1455 b:12.8 occ:1.00 OD1 A:ASN348 2.2 11.2 1.0 O A:ILE283 2.2 13.4 1.0 O A:THR345 2.3 9.1 1.0 O A:HOH2230 2.4 16.5 1.0 C A:ILE283 3.3 12.0 1.0 CG A:ASN348 3.4 9.5 1.0 C A:THR345 3.5 9.1 1.0 CG2 A:ILE283 3.7 21.1 1.0 CA A:ASN348 3.9 8.1 1.0 N A:ASN348 4.0 7.9 1.0 CG2 A:THR345 4.1 12.8 1.0 N A:THR284 4.2 11.3 1.0 CA A:THR284 4.2 9.7 1.0 CB A:ASN348 4.3 8.8 1.0 CA A:VAL346 4.3 10.7 1.0 N A:VAL346 4.3 8.0 1.0 CA A:ILE283 4.3 14.0 1.0 CA A:THR345 4.4 9.2 1.0 O A:HOH2256 4.4 35.2 1.0 ND2 A:ASN348 4.4 12.3 1.0 C A:VAL346 4.5 10.1 1.0 CB A:ILE283 4.6 17.6 1.0 O A:VAL346 4.7 10.2 1.0 CB A:THR345 4.9 12.9 1.0 C A:THR284 4.9 10.3 1.0 OG1 A:THR277 4.9 11.8 1.0

Sodium binding site 2 out of 2 in the Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Wnt Deacylase Notum in Complex with O-Palmitoleoyl Serine - Crystal Form IX - 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1456 b:16.3 occ:1.00 O A:HOH2235 2.4 20.0 1.0 O A:HOH2054 2.4 15.8 1.0 OG A:SER439 2.4 13.7 1.0 O A:HOH2058 2.5 15.8 1.0 O A:HOH2222 2.5 14.9 1.0 CB A:SER439 3.6 12.7 1.0 N A:SER439 3.8 8.5 1.0 O A:HOH2269 4.2 41.0 1.0 CA A:SER439 4.2 11.3 1.0 O A:HOH2219 4.4 8.4 1.0 C A:ASP438 4.7 9.4 1.0 C A:SER439 4.7 11.8 1.0 CA A:ASP438 4.8 11.1 1.0 N A:CYS440 4.8 14.5 1.0 O A:VAL437 4.8 10.7 1.0 OD1 A:ASP438 5.0 16.4 1.0

S.Kakugawa, P.F.Langton, M.Zebisch, S.A.Howell, T.-H.Chang, Y.Liu, T.Feizi, G.Bineva, N.O'reilly, A.P.Snijders, E.Y.Jones, J.-P.Vincent. Notum Deacylates Wnt Proteins to Suppress Signalling Activity Nature 2015.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14259