Sodium in PDB 5oca: PCSK9:Fab Complex with Dextran Sulfate

The structure of PCSK9:Fab Complex with Dextran Sulfate, PDB code: 5oca was solved by S.S.Thirup, J.P.Vilstrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.29 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	264.721, 137.352, 69.885, 90.00, 102.84, 90.00
R / Rfree (%)	16.7 / 19.5

The binding sites of Sodium atom in the PCSK9:Fab Complex with Dextran Sulfate (pdb code 5oca). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the PCSK9:Fab Complex with Dextran Sulfate, PDB code: 5oca:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the PCSK9:Fab Complex with Dextran Sulfate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PCSK9:Fab Complex with Dextran Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:51.2 occ:1.00 O B:HOH959 2.5 49.1 1.0 OG1 B:THR335 2.6 32.6 1.0 O B:VAL333 2.8 41.7 1.0 O B:CYS358 2.9 36.8 1.0 OD2 B:ASP360 3.0 43.0 1.0 O B:HOH905 3.0 63.0 1.0 O B:ALA330 3.0 38.8 1.0 O B:ALA328 3.4 31.1 1.0 CB B:THR335 3.5 32.2 1.0 O B:PRO331 3.8 56.3 1.0 C B:VAL333 3.9 39.3 1.0 CG B:ASP360 4.0 43.2 1.0 C B:CYS358 4.0 36.4 1.0 N B:THR335 4.0 32.2 1.0 C B:ALA330 4.1 37.1 1.0 CA B:PRO331 4.2 53.3 1.0 C B:PRO331 4.3 54.6 1.0 O B:HOH843 4.4 43.1 1.0 CA B:THR335 4.4 25.9 1.0 OD1 B:ASP360 4.4 49.8 1.0 CA B:CYS358 4.6 37.4 1.0 CG2 B:THR335 4.6 31.1 1.0 C B:ALA328 4.7 30.2 1.0 N B:PRO331 4.7 43.0 1.0 N B:VAL333 4.7 38.8 1.0 CB B:CYS358 4.7 28.6 1.0 CA B:VAL333 4.8 33.9 1.0 C B:ILE334 4.8 34.3 1.0 N B:ILE334 4.9 35.2 1.0 CA B:ILE334 4.9 35.3 1.0 CB B:VAL333 4.9 36.5 1.0 C B:SER329 4.9 37.5 1.0 N B:ALA330 5.0 34.6 1.0

Sodium binding site 2 out of 2 in the PCSK9:Fab Complex with Dextran Sulfate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of PCSK9:Fab Complex with Dextran Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:55.7 occ:1.00 O B:HOH933 2.6 42.4 1.0 O B:ILE369 2.9 37.6 1.0 O B:ALA239 3.0 44.0 1.0 CA B:GLY370 3.2 33.1 1.0 O B:GLY232 3.3 42.2 1.0 CA B:VAL233 3.3 33.3 1.0 CB B:ALA239 3.4 44.4 1.0 N B:VAL233 3.4 38.9 1.0 C B:GLY232 3.4 41.5 1.0 C B:ALA239 3.5 49.7 1.0 O B:HOH903 3.5 42.5 1.0 CG2 B:VAL233 3.7 35.0 1.0 C B:ILE369 3.8 38.9 1.0 N B:GLY370 4.0 36.0 1.0 CA B:ALA239 4.1 49.4 1.0 CB B:VAL233 4.1 35.0 1.0 N B:GLY240 4.1 43.5 1.0 CA B:GLY232 4.3 35.4 1.0 C B:GLY370 4.3 38.4 1.0 CA B:GLY240 4.4 41.4 1.0 N B:ALA371 4.4 40.1 1.0 C B:VAL233 4.5 37.1 1.0 O B:VAL233 4.7 38.3 1.0 O B:HIS229 4.8 36.0 1.0 OE2 B:GLU195 4.9 47.5 1.0 CG1 B:VAL233 4.9 33.5 1.0 N B:ALA239 5.0 53.0 1.0

C.Gustafsen, D.Olsen, J.Vilstrup, S.Lund, A.Reinhardt, N.Wellner, T.Larsen, C.B.F.Andersen, K.Weyer, J.P.Li, P.H.Seeberger, S.Thirup, P.Madsen, S.Glerup. Heparan Sulfate Proteoglycans Present PCSK9 to the Ldl Receptor. Nat Commun V. 8 503 2017.
ISSN: ESSN 2041-1723
PubMed: 28894089
DOI: 10.1038/S41467-017-00568-7