Sodium in PDB 5vlp: PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7

The structure of PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7, PDB code: 5vlp was solved by C.Eigenbrot, M.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.60 / 2.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.865, 142.168, 239.365, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.9

The binding sites of Sodium atom in the PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7 (pdb code 5vlp). 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 Complex with Ldlr Antagonist Peptide and FAB7G7, PDB code: 5vlp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:39.2 occ:1.00 O A:GLY106 2.6 45.5 1.0 C A:GLY106 3.2 43.6 1.0 CA A:GLY106 3.7 41.6 1.0 N A:TYR107 4.1 36.6 1.0 CA A:TYR107 4.6 34.9 1.0 N A:LEU108 5.0 37.1 1.0 C A:TYR107 5.0 40.2 1.0

Sodium binding site 2 out of 2 in the PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of PCSK9 Complex with Ldlr Antagonist Peptide and FAB7G7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:59.5 occ:1.00 OD1 A:ASP360 2.8 57.3 1.0 O A:ALA330 2.9 42.0 1.0 O A:CYS358 2.9 37.7 1.0 OG1 A:THR335 3.1 37.1 1.0 O A:VAL333 3.2 44.1 1.0 O A:ALA328 3.5 42.9 1.0 O A:PRO331 3.8 48.0 1.0 CA A:PRO331 3.8 44.2 1.0 CB A:THR335 3.8 37.6 1.0 C A:ALA330 3.8 44.5 1.0 CG A:ASP360 3.9 54.7 1.0 C A:CYS358 4.0 38.9 1.0 C A:PRO331 4.0 47.6 1.0 N A:PRO331 4.2 43.9 1.0 OD2 A:ASP360 4.3 61.5 1.0 C A:VAL333 4.4 43.0 1.0 CG2 A:VAL333 4.4 42.5 1.0 N A:THR335 4.4 35.1 1.0 CA A:CYS358 4.5 36.9 1.0 C A:ALA328 4.7 41.9 1.0 CB A:CYS358 4.7 37.4 1.0 C A:SER329 4.8 44.9 1.0 CG2 A:THR335 4.8 32.0 1.0 CA A:THR335 4.8 33.6 1.0 O A:SER329 4.8 47.0 1.0 N A:ALA330 4.9 39.9 1.0 N A:VAL333 4.9 39.7 1.0 N A:GLU332 5.0 42.1 1.0

Y.Zhang, M.Ultsch, N.J.Skelton, D.J.Burdick, M.H.Beresini, W.Li, M.Kong-Beltran, A.Peterson, J.Quinn, C.Chiu, Y.Wu, S.Shia, P.Moran, P.Di Lello, C.Eigenbrot, D.Kirchhofer. Discovery of A Cryptic Peptide-Binding Site on PCSK9 and Design of Antagonists. Nat. Struct. Mol. Biol. V. 24 848 2017.
ISSN: ESSN 1545-9985
PubMed: 28825733
DOI: 10.1038/NSMB.3453