Calcium in PDB 4a0p: Crystal Structure of LRP6P3E3P4E4

The structure of Crystal Structure of LRP6P3E3P4E4, PDB code: 4a0p was solved by S.Chen, T.Malinauskas, A.R.Aricescu, C.Siebold, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.09 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.815, 42.699, 119.879, 90.00, 97.49, 90.00
R / Rfree (%)	18.135 / 21.098

The structure of Crystal Structure of LRP6P3E3P4E4 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of LRP6P3E3P4E4 (pdb code 4a0p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of LRP6P3E3P4E4, PDB code: 4a0p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of LRP6P3E3P4E4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of LRP6P3E3P4E4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1353 b:27.2 occ:1.00 OD2 A:ASP878 2.4 21.5 1.0 O A:HOH2435 2.4 25.8 1.0 O A:HOH2027 2.5 33.4 1.0 OD1 A:ASP878 2.5 19.5 1.0 O A:HOH2434 2.5 27.7 1.0 O A:HOH2050 2.6 36.0 1.0 O A:HOH2026 2.6 18.7 1.0 O A:HOH2147 2.7 25.7 1.0 CG A:ASP878 2.8 22.4 1.0 O A:HOH2052 3.9 16.7 1.0 O A:HOH2146 4.0 23.2 1.0 O A:LEU667 4.2 18.7 1.0 O A:HOH2085 4.2 22.9 1.0 CB A:ASP878 4.3 19.1 1.0 O A:HOH2110 4.5 19.0 1.0 O A:HOH2030 4.5 36.9 1.0 N A:LEU667 4.6 18.7 1.0 O A:ILE879 4.6 23.6 1.0 O A:HOH2113 4.7 43.8 1.0 O A:HOH2025 4.8 50.6 1.0 CB A:ALA666 5.0 18.6 1.0 CA A:ALA666 5.0 18.9 1.0 O A:MET710 5.0 15.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of LRP6P3E3P4E4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of LRP6P3E3P4E4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1354 b:24.3 occ:1.00 O A:PRO833 2.3 25.2 1.0 O A:HOH2129 2.3 33.6 1.0 OD1 A:ASN813 2.3 26.4 1.0 O A:LEU810 2.3 23.6 1.0 O A:HOH2127 2.4 26.1 1.0 O A:HOH2132 2.4 29.2 1.0 O A:HOH2128 2.4 43.2 1.0 C A:PRO833 3.4 25.4 1.0 CG A:ASN813 3.4 27.6 1.0 C A:LEU810 3.6 23.8 1.0 ND2 A:ASN813 3.9 30.2 1.0 CA A:PRO833 4.0 27.2 1.0 CA A:ASP811 4.3 29.0 1.0 N A:ASP811 4.4 24.3 1.0 O A:ASP811 4.5 30.3 1.0 N A:HIS834 4.5 24.0 1.0 CA A:LEU810 4.5 21.0 1.0 C A:ASP811 4.6 27.9 1.0 CB A:ASN813 4.7 28.9 1.0 ND1 A:HIS834 4.7 24.1 1.0 CB A:PRO833 4.8 29.3 1.0 CA A:HIS834 4.8 22.5 1.0 O A:HOH2133 5.0 59.6 1.0 CA A:ASN813 5.0 25.1 1.0 O A:LEU832 5.0 25.0 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of LRP6P3E3P4E4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of LRP6P3E3P4E4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1360 b:16.7 occ:1.00 O A:HOH2283 2.3 19.0 1.0 O A:HOH2437 2.4 20.1 1.0 O A:HOH2252 2.4 18.5 1.0 O A:HOH2281 2.5 21.6 1.0 O A:HOH2280 2.5 17.0 1.0 O A:HOH2253 2.5 21.1 1.0 O A:HOH2342 2.5 17.2 1.0 O A:HOH2375 3.8 18.9 1.0 OD1 A:ASP1018 4.2 17.8 1.0 O A:LEU1019 4.2 16.4 1.0 O A:HOH2376 4.3 19.9 1.0 O A:LEU1107 4.4 15.4 1.0 O A:HOH2256 4.4 19.0 1.0 CG2 A:VAL1063 4.4 21.2 1.0 OD2 A:ASP1018 4.4 18.1 1.0 O A:ILE970 4.4 18.4 1.0 O A:HOH2374 4.5 23.3 1.0 OD2 A:ASP1190 4.5 20.9 1.0 ND1 A:HIS1192 4.5 20.8 1.0 O A:HOH2341 4.5 18.9 1.0 O A:VAL1062 4.5 17.8 1.0 CL A:CL1355 4.8 16.9 1.0 CG A:ASP1018 4.8 22.5 1.0 CE1 A:HIS1192 5.0 19.4 1.0

S.Chen, D.Bubeck, B.T.Macdonald, W.X.Liang, J.H.Mao, T.Malinauskas, O.Llorca, A.R.Aricescu, C.Siebold, X.He, E.Y.Jones. Structural and Functional Studies of LRP6 Ectodomain Reveal A Platform For Wnt Signaling. Dev.Cell V. 21 848 2011.
ISSN: ISSN 1534-5807
PubMed: 22000855
DOI: 10.1016/J.DEVCEL.2011.09.007