Calcium in PDB 5vll: Short PCSK9 Delta-P' Complex with Peptide PEP3

The structure of Short PCSK9 Delta-P' Complex with Peptide PEP3, PDB code: 5vll 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)	29.34 / 2.37
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.566, 70.566, 158.487, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 24.4

The binding sites of Calcium atom in the Short PCSK9 Delta-P' Complex with Peptide PEP3 (pdb code 5vll). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Short PCSK9 Delta-P' Complex with Peptide PEP3, PDB code: 5vll:

Calcium binding site 1 out of 1 in the Short PCSK9 Delta-P' Complex with Peptide PEP3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Short PCSK9 Delta-P' Complex with Peptide PEP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:55.7 occ:1.00 O A:HOH638 2.4 38.8 1.0 O A:PRO331 2.5 39.4 1.0 O A:VAL333 2.5 38.1 1.0 OD2 A:ASP360 2.5 43.5 1.0 OD1 A:ASP360 2.7 41.0 1.0 CG A:ASP360 3.0 40.1 1.0 O A:HOH672 3.0 45.1 1.0 C A:PRO331 3.5 40.6 1.0 C A:VAL333 3.7 39.8 1.0 N A:VAL333 4.2 39.8 1.0 O A:CYS358 4.2 43.9 1.0 CA A:PRO331 4.2 36.0 1.0 O A:ALA330 4.2 37.8 1.0 O A:HOH653 4.3 45.8 1.0 N A:GLU332 4.4 37.8 1.0 CB A:ASP360 4.5 33.9 1.0 C A:GLU332 4.6 43.7 1.0 NE A:ARG412 4.6 46.2 1.0 CA A:VAL333 4.6 38.7 1.0 OG1 A:THR335 4.6 31.7 1.0 N A:ILE334 4.7 35.8 1.0 CA A:GLU332 4.7 37.9 1.0 N A:THR335 4.7 35.6 1.0 CA A:ILE334 4.7 34.7 1.0 NH1 A:ARG412 4.9 40.8 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