Calcium in PDB 3p5b: The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation

The structure of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation, PDB code: 3p5b was solved by P.Lo Surdo, M.J.Bottomley, A.Calzetta, E.C.Settembre, A.Cirillo, S.Pandit, Y.Ni, B.Hubbard, A.Sitlani, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.000, 109.701, 178.456, 90.00, 90.00, 90.00
R / Rfree (%)	27.1 / 29.8

The binding sites of Calcium atom in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation (pdb code 3p5b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation, PDB code: 3p5b:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:78.8 occ:1.00 OG1 A:THR335 2.7 52.1 1.0 O A:CYS358 2.7 54.2 1.0 O A:ALA330 2.7 54.9 1.0 O A:VAL333 3.0 57.2 1.0 OD2 A:ASP360 3.1 57.5 1.0 O A:ALA328 3.5 45.0 1.0 CB A:THR335 3.7 51.2 1.0 C A:ALA330 3.7 54.1 1.0 C A:CYS358 3.8 53.5 1.0 CG A:ASP360 3.9 57.9 1.0 CA A:PRO331 4.0 56.0 1.0 O A:PRO331 4.1 58.1 1.0 OD1 A:ASP360 4.1 59.9 1.0 N A:THR335 4.1 50.6 1.0 C A:VAL333 4.2 56.0 1.0 C A:PRO331 4.3 56.9 1.0 N A:PRO331 4.3 55.2 1.0 CA A:CYS358 4.4 54.3 1.0 CA A:THR335 4.5 50.4 1.0 C A:ALA328 4.6 44.3 1.0 CB A:CYS358 4.6 57.2 1.0 N A:ALA330 4.8 50.0 1.0 CG2 A:THR335 4.8 51.4 1.0 CA A:ALA330 4.9 52.1 1.0 C A:SER329 4.9 48.9 1.0 N A:VAL359 5.0 51.9 1.0 N A:VAL333 5.0 56.8 1.0 C A:ILE334 5.0 51.0 1.0

Calcium binding site 2 out of 3 in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca1 b:64.3 occ:1.00 OD2 L:ASP333 2.2 94.8 1.0 O L:LEU350 2.3 98.2 1.0 O L:ILE334 2.3 87.6 1.0 O L:GLY353 3.1 99.5 1.0 CG L:ASP333 3.1 94.1 1.0 C L:LEU350 3.3 97.5 1.0 OD1 L:ASP333 3.4 93.7 1.0 C L:ILE334 3.4 87.5 1.0 N L:LEU350 3.5 95.2 1.0 CA L:ASP335 3.8 86.9 1.0 CA L:LEU350 3.9 96.7 1.0 OE1 L:GLU336 3.9 85.7 1.0 N L:ASP335 4.0 87.4 1.0 C L:GLY353 4.1 99.7 1.0 O L:GLY352 4.3 0.6 1.0 N L:ILE334 4.4 88.9 1.0 OD1 L:ASP335 4.4 86.0 1.0 CB L:ASP333 4.5 93.2 1.0 CB L:LEU350 4.5 97.1 1.0 N L:GLU351 4.5 98.6 1.0 CA L:ILE334 4.5 87.4 1.0 CD L:GLU336 4.6 85.7 1.0 C L:ASN349 4.6 94.0 1.0 OE2 L:GLU336 4.6 85.3 1.0 N L:GLU336 4.6 87.0 1.0 CA L:GLY353 4.6 0.5 1.0 C L:ASP333 4.7 90.6 1.0 CB L:ASP335 4.7 87.0 1.0 C L:ASP335 4.8 86.5 1.0 C L:GLY352 4.8 0.6 1.0 CA L:ASN349 4.9 93.2 1.0 C L:GLU351 5.0 99.5 1.0 CA L:GLU351 5.0 99.7 1.0 N L:GLY353 5.0 0.8 1.0

Calcium binding site 3 out of 3 in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca3 b:0.8 occ:1.00 OD2 L:ASP310 3.0 89.8 1.0 OE1 L:GLU296 3.5 0.8 1.0 OE2 L:GLU296 3.6 0.2 1.0 O L:LEU311 3.7 94.3 1.0 CD L:GLU296 3.9 0.5 1.0 CA L:ASN295 3.9 97.0 1.0 O L:GLY314 4.0 92.4 1.0 CG L:ASP310 4.2 90.1 1.0 N L:ASN295 4.3 96.8 1.0 C L:LEU311 4.4 94.4 1.0 N L:GLU296 4.6 96.5 1.0 C L:ASN295 4.6 96.7 1.0 N L:LEU311 4.7 93.2 1.0 OD1 L:ASP310 4.8 89.0 1.0 OD1 L:ASN295 4.9 0.9 1.0 CB L:ASN295 4.9 98.2 1.0 O L:LYS312 4.9 95.3 1.0 C L:LYS312 4.9 95.5 1.0

P.Lo Surdo, M.J.Bottomley, A.Calzetta, E.C.Settembre, A.Cirillo, S.Pandit, Y.G.Ni, B.Hubbard, A.Sitlani, A.Carfi. Mechanistic Implications For Ldl Receptor Degradation From the PCSK9/Ldlr Structure at Neutral pH. Embo Rep. V. 12 1300 2011.
ISSN: ISSN 1469-221X
PubMed: 22081141
DOI: 10.1038/EMBOR.2011.205