Calcium in PDB 5vla: Short PCSK9 Delta-P' Complex with FUSION2 Peptide

The structure of Short PCSK9 Delta-P' Complex with FUSION2 Peptide, PDB code: 5vla 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)	26.31 / 2.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.267, 70.267, 157.254, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 26.7

The binding sites of Calcium atom in the Short PCSK9 Delta-P' Complex with FUSION2 Peptide (pdb code 5vla). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Short PCSK9 Delta-P' Complex with FUSION2 Peptide, PDB code: 5vla:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Short PCSK9 Delta-P' Complex with FUSION2 Peptide


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 FUSION2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:27.5 occ:1.00 O A:PRO331 2.3 26.3 1.0 O A:HOH623 2.4 25.0 1.0 O A:HOH690 2.4 29.4 1.0 O A:HOH688 2.4 32.6 1.0 O A:VAL333 2.4 24.1 1.0 OD2 A:ASP360 2.5 32.2 1.0 O A:HOH650 2.6 30.9 1.0 OD1 A:ASP360 2.6 25.7 1.0 CG A:ASP360 2.9 27.3 1.0 C A:PRO331 3.5 30.3 1.0 C A:VAL333 3.7 26.9 1.0 N A:VAL333 4.2 26.9 1.0 CA A:PRO331 4.3 27.7 1.0 O A:ALA330 4.3 29.3 1.0 CB A:ASP360 4.4 23.2 1.0 O A:HOH712 4.4 30.6 1.0 O A:CYS358 4.5 28.7 1.0 O A:HOH605 4.5 22.7 1.0 C A:GLU332 4.5 31.6 1.0 NE A:ARG412 4.5 30.1 1.0 N A:GLU332 4.5 28.2 1.0 OG1 A:THR335 4.6 25.8 1.0 CA A:VAL333 4.6 25.6 1.0 N A:ILE334 4.6 23.4 1.0 CA A:ILE334 4.6 22.6 1.0 N A:THR335 4.7 25.4 1.0 CA A:GLU332 4.8 28.3 1.0 O A:HOH617 4.8 31.5 1.0 NH1 A:ARG412 5.0 27.4 1.0

Calcium binding site 2 out of 2 in the Short PCSK9 Delta-P' Complex with FUSION2 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Short PCSK9 Delta-P' Complex with FUSION2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:86.9 occ:1.00 O A:HOH631 2.5 37.2 1.0 O A:HOH635 2.5 48.6 1.0 O A:HOH708 2.7 33.9 1.0 O A:HOH691 3.2 52.6 1.0 O A:VAL435 4.5 37.9 1.0 OD1 A:ASP422 4.5 43.1 1.0 OE2 A:GLU426 4.8 64.0 1.0 O A:THR437 4.8 28.2 1.0 O A:ARG434 4.8 38.0 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