Calcium in PDB 3m0c: The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor

The structure of The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor, PDB code: 3m0c was solved by G.Spraggon, E.N.Hampton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	279.64 / 7.01
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	322.906, 322.906, 76.733, 90.00, 90.00, 120.00
R / Rfree (%)	34.1 / 36.2

The binding sites of Calcium atom in the The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor (pdb code 3m0c). 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 X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor, PDB code: 3m0c:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:0.2 occ:1.00 OD2 C:ASP310 2.1 0.8 1.0 O C:LEU311 2.4 0.1 1.0 O C:GLY314 2.6 0.7 1.0 OE1 C:GLU296 2.7 0.1 1.0 O C:THR294 2.7 0.3 1.0 CG C:ASP310 3.3 0.8 1.0 C C:LEU311 3.5 0.7 1.0 C C:GLY314 3.6 0.4 1.0 N C:LEU311 3.6 0.5 1.0 C C:THR294 3.7 0.6 1.0 CD C:GLU296 3.8 0.9 1.0 OD1 C:ASP310 4.0 0.7 1.0 C C:ASP310 4.0 0.8 1.0 N C:GLY314 4.0 0.8 1.0 CA C:GLY314 4.1 0.4 1.0 CA C:LEU311 4.2 0.8 1.0 OE2 C:GLU296 4.2 0.7 1.0 CA C:ASP310 4.3 0.7 1.0 CB C:ASP310 4.3 0.1 1.0 N C:THR294 4.4 0.6 1.0 O C:LYS312 4.4 0.7 1.0 CA C:ASN295 4.4 0.4 1.0 N C:ASN295 4.5 0.8 1.0 N C:GLY293 4.6 0.0 1.0 C C:LYS312 4.6 0.7 1.0 N C:GLU296 4.6 0.6 1.0 N C:LYS312 4.6 0.4 1.0 CA C:THR294 4.7 0.6 1.0 O C:ASP310 4.7 0.8 1.0 C C:ILE313 4.7 0.6 1.0 O C:GLU291 4.8 0.2 1.0 N C:TYR315 4.8 0.6 1.0 C C:GLY293 4.9 0.6 1.0 CA C:LYS312 4.9 0.8 1.0 CB C:TYR315 5.0 0.6 1.0

Calcium binding site 2 out of 3 in the The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1002 b:0.1 occ:1.00 O C:LEU350 2.4 0.7 1.0 OD2 C:ASP333 3.0 0.5 1.0 C C:LEU350 3.1 0.2 1.0 CG C:ASP333 3.1 0.3 1.0 N C:ASP335 3.1 0.9 1.0 CA C:GLU351 3.2 0.5 1.0 CA C:ASP335 3.2 0.4 1.0 CB C:ASP333 3.3 0.1 1.0 N C:GLU351 3.4 0.3 1.0 CG C:GLU351 3.6 0.3 1.0 CB C:GLU351 3.6 0.2 1.0 OD1 C:ASP333 3.8 0.4 1.0 OD1 C:ASN349 3.9 0.2 1.0 OD1 C:ASP335 3.9 0.5 1.0 CB C:ASP335 4.0 0.7 1.0 C C:ILE334 4.1 0.5 1.0 O C:ASP333 4.1 0.9 1.0 C C:ASP333 4.1 0.0 1.0 CA C:LEU350 4.3 0.3 1.0 CG C:ASP335 4.3 0.2 1.0 CA C:ASP333 4.4 0.4 1.0 C C:ASP335 4.4 0.9 1.0 N C:GLU336 4.5 0.1 1.0 C C:GLU351 4.5 0.5 1.0 ND2 C:ASN349 4.5 0.4 1.0 CG C:ASN349 4.5 0.6 1.0 N C:ILE334 4.5 1.0 1.0 O C:ILE334 4.7 0.7 1.0 N C:GLY352 4.7 0.4 1.0 N C:LEU350 4.7 0.4 1.0 OE2 C:GLU336 4.8 0.8 1.0 CD C:GLU351 4.8 0.8 1.0 CA C:ILE334 4.9 0.1 1.0

Calcium binding site 3 out of 3 in the The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1003 b:0.2 occ:1.00 OD1 C:ASP286 2.5 0.2 1.0 O C:LYS273 2.6 0.6 1.0 OE2 C:GLU287 2.7 0.6 1.0 OD2 C:ASP280 2.8 0.2 1.0 CG C:LYS273 2.9 0.5 1.0 OD1 C:ASN276 3.0 0.1 1.0 OD2 C:ASP286 3.1 0.9 1.0 CG C:ASP286 3.2 0.2 1.0 CD C:LYS273 3.4 0.5 1.0 CG C:ASP280 3.6 0.3 1.0 CB C:ASP280 3.6 0.7 1.0 C C:LYS273 3.7 0.8 1.0 CD C:GLU287 3.7 0.1 1.0 O C:ALA278 3.8 1.0 1.0 CG C:ASN276 3.9 0.7 1.0 CB C:LYS273 4.0 0.3 1.0 ND2 C:ASN276 4.2 0.6 1.0 CG C:GLU287 4.2 0.2 1.0 CE C:LYS273 4.3 0.5 1.0 CB C:ALA278 4.3 0.6 1.0 CA C:LYS273 4.4 0.2 1.0 N C:CYS275 4.5 0.0 1.0 C C:ALA278 4.5 0.1 1.0 N C:ASP280 4.5 0.6 1.0 N C:ASN276 4.5 0.8 1.0 CB C:ASP286 4.6 0.7 1.0 CA C:ASP280 4.7 0.8 1.0 OE1 C:GLU287 4.7 0.6 1.0 N C:VAL274 4.7 0.0 1.0 OD1 C:ASP280 4.8 0.8 1.0 O C:ASN276 4.8 0.6 1.0 CA C:ALA278 4.9 0.3 1.0

J.Li, J.A.Gavigan, G.Zheng, W.Huang, D.Yowe, S.Geisse, J.L.Harris, S.A.Lesley, G.Spraggon. The X-Ray Crystal Structure of PCSK9 in Complex with the Ldl Receptor To Be Published.