Calcium in PDB 2w2m: Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr

The structure of Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr, PDB code: 2w2m was solved by M.J.Bottomley, A.Cirillo, L.Orsatti, L.Ruggeri, T.S.Fisher, J.C.Santoro, R.T.Cummings, R.M.Cubbon, P.Lo Surdo, A.Calzetta, A.Noto, J.Baysarowich, M.Mattu, F.Talamo, R.De Francesco, C.P.Sparrow, A.Sitlani, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.004, 83.004, 211.566, 90.00, 90.00, 90.00
R / Rfree (%)	21.524 / 25.421

The binding sites of Calcium atom in the Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr (pdb code 2w2m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr, PDB code: 2w2m:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1448 b:61.2 occ:1.00 OG1 A:THR335 2.7 22.2 1.0 OD2 A:ASP360 2.7 25.1 1.0 O A:VAL333 2.7 26.4 1.0 O A:CYS358 3.1 24.8 1.0 O A:ALA330 3.3 28.6 1.0 O A:HOH2075 3.6 42.1 1.0 CB A:THR335 3.6 21.9 1.0 O A:ALA328 3.7 22.4 1.0 CG A:ASP360 3.8 23.7 1.0 C A:VAL333 3.8 26.4 1.0 N A:THR335 4.0 22.4 1.0 NH2 A:ARG412 4.1 39.9 1.0 OD1 A:ASP360 4.1 26.4 1.0 C A:CYS358 4.2 24.8 1.0 CA A:THR335 4.5 21.9 1.0 C A:ALA330 4.5 28.3 1.0 CA A:VAL333 4.6 27.2 1.0 C A:ILE334 4.7 23.4 1.0 N A:ILE334 4.7 25.2 1.0 N A:VAL333 4.7 28.3 1.0 CB A:VAL333 4.7 27.1 1.0 CA A:CYS358 4.7 25.1 1.0 CA A:ILE334 4.8 23.9 1.0 CG2 A:THR335 4.8 22.0 1.0 C A:ALA328 4.9 22.5 1.0

Calcium binding site 2 out of 3 in the Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1334 b:30.5 occ:1.00 O E:LEU311 2.3 26.6 1.0 O E:THR294 2.4 27.0 1.0 OD2 E:ASP310 2.4 28.2 1.0 O E:GLY314 2.4 26.8 1.0 O E:HOH2010 2.5 34.0 1.0 OE1 E:GLU296 2.5 26.7 1.0 O E:HOH2013 2.6 31.1 1.0 C E:GLY314 3.4 27.1 1.0 CD E:GLU296 3.5 26.6 1.0 C E:LEU311 3.5 26.6 1.0 CG E:ASP310 3.6 26.3 1.0 C E:THR294 3.6 27.0 1.0 OE2 E:GLU296 3.7 27.5 1.0 N E:GLY314 3.8 27.0 1.0 CA E:GLY314 3.9 27.1 1.0 O E:LYS312 4.0 27.0 1.0 N E:LEU311 4.0 26.4 1.0 OD1 E:ASP310 4.1 27.4 1.0 N E:THR294 4.2 27.7 1.0 C E:LYS312 4.2 27.2 1.0 C E:ASP310 4.3 26.2 1.0 CA E:LEU311 4.4 26.2 1.0 C E:ILE313 4.4 27.0 1.0 O E:HOH2025 4.5 18.7 1.0 CA E:THR294 4.5 27.4 1.0 N E:LYS312 4.5 27.1 1.0 N E:ASN295 4.5 26.5 1.0 CA E:ASP310 4.6 26.2 1.0 N E:TYR315 4.6 26.9 1.0 O A:HOH2014 4.6 28.4 1.0 CA E:ASN295 4.6 26.1 1.0 N E:GLU296 4.6 25.8 1.0 CB E:ASP310 4.7 26.3 1.0 CA E:LYS312 4.7 27.4 1.0 N E:ILE313 4.8 27.0 1.0 O E:ALA291 4.8 28.0 1.0 CB E:TYR315 4.8 26.4 1.0 CA E:ILE313 4.9 27.1 1.0 O E:ASP310 4.9 26.4 1.0 CG E:GLU296 4.9 25.8 1.0 N E:GLY293 5.0 28.4 1.0 CA E:TYR315 5.0 26.9 1.0

Calcium binding site 3 out of 3 in the Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wt PCSK9-Deltac Bound to Wt Egf-A of Ldlr within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1335 b:92.3 occ:1.00 C E:ASP333 4.1 40.6 1.0 O E:ASP333 4.1 40.5 1.0 O E:GLY322 4.2 38.2 1.0 CA E:ASP333 4.9 40.6 1.0

M.J.Bottomley, A.Cirillo, L.Orsatti, L.Ruggeri, T.S.Fisher, J.C.Santoro, R.T.Cummings, R.M.Cubbon, P.Lo Surdo, A.Calzetta, A.Noto, J.Baysarowich, M.Mattu, F.Talamo, R.De Francesco, C.P.Sparrow, A.Sitlani, A.Carfi. Structural and Biochemical Characterization of the Wild Type PCSK9/Egf-Ab Complex and Natural Fh Mutants. J.Biol.Chem. V. 284 1313 2009.
ISSN: ISSN 0021-9258
PubMed: 19001363
DOI: 10.1074/JBC.M808363200