Calcium in PDB 8dvm: Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6

The structure of Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6, PDB code: 8dvm was solved by A.K.Thakur, N.P.D.Liau, J.Sudhamsu, R.N.Hannoush, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.54 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.462, 102.978, 108.775, 90, 90, 90
R / Rfree (%)	18.6 / 22.1

The binding sites of Calcium atom in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6 (pdb code 8dvm). 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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6, PDB code: 8dvm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6


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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:74.2 occ:1.00 O A:HOH1405 2.3 44.7 1.0 O A:HOH1411 2.3 54.4 1.0 O A:HOH1481 2.4 34.5 1.0 O A:HOH1498 2.6 41.2 1.0 O A:HOH1544 2.7 37.8 1.0 CA A:CA1304 3.2 75.0 1.0 O A:HOH1527 3.5 45.8 1.0 O A:HOH1525 3.9 41.4 1.0 O A:HOH1521 3.9 44.1 1.0 O A:LEU1107 4.2 30.9 1.0 OD1 A:ASP1018 4.3 30.0 1.0 O A:HOH1452 4.4 37.5 1.0 O A:LEU1019 4.4 29.7 1.0 OD2 A:ASP1190 4.4 32.8 1.0 OD2 A:ASP1018 4.5 28.9 1.0 O A:ILE1062 4.5 26.3 1.0 O A:ILE970 4.6 27.3 1.0 ND1 A:HIS1192 4.6 35.6 1.0 OD1 A:ASP1190 4.8 27.4 1.0 CG A:ASP1018 4.9 29.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6


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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:66.4 occ:1.00 O A:HOH1431 2.4 44.0 1.0 O A:HOH1510 2.5 39.9 1.0 O A:THR724 2.6 40.7 1.0 O B:HOH101 2.6 45.0 1.0 OG A:SER749 2.7 48.7 1.0 OD1 A:ASN727 2.7 43.4 1.0 CG A:ASN727 3.5 44.8 1.0 ND2 A:ASN727 3.6 45.6 1.0 C A:THR724 3.7 40.9 1.0 CB A:SER749 3.7 44.0 1.0 N A:SER749 3.8 49.4 1.0 CA A:SER749 3.9 38.1 1.0 OD1 A:ASP748 4.2 47.2 1.0 O A:HOH1500 4.2 56.8 1.0 O A:GLY725 4.4 40.2 1.0 NZ B:LYS7 4.4 45.8 1.0 CA A:THR724 4.5 39.5 1.0 N A:GLY725 4.7 35.4 1.0 CA A:GLY725 4.7 37.9 1.0 C A:ASP748 4.8 50.0 1.0 C A:GLY725 4.8 46.2 1.0 CB A:THR724 4.9 45.3 1.0 CB A:ASN727 4.9 33.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6


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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1304 b:75.0 occ:1.00 O A:HOH1498 2.4 41.2 1.0 O A:ILE1191 2.4 28.5 1.0 O A:HOH1521 2.6 44.1 1.0 O A:HOH1411 2.6 54.4 1.0 O A:LEU1150 2.7 27.9 1.0 O A:HOH1525 2.8 41.4 1.0 CA A:CA1302 3.2 74.2 1.0 OD1 A:ASP1190 3.6 27.4 1.0 C A:ILE1191 3.7 30.6 1.0 C A:LEU1150 3.8 34.7 1.0 CB A:THR1151 3.9 31.0 1.0 ND1 A:HIS1192 4.2 35.6 1.0 CA A:HIS1192 4.2 27.0 1.0 O A:HOH1481 4.2 34.5 1.0 OG1 A:THR1151 4.2 29.7 1.0 OD2 A:ASP1190 4.3 32.8 1.0 CG A:ASP1190 4.3 34.6 1.0 CB A:HIS1192 4.4 29.0 1.0 CA A:THR1151 4.4 28.8 1.0 N A:LEU1150 4.4 32.0 1.0 N A:HIS1192 4.4 30.3 1.0 N A:THR1151 4.5 29.8 1.0 N A:ILE1191 4.6 27.4 1.0 O A:LEU1107 4.7 30.9 1.0 CG A:HIS1192 4.7 29.6 1.0 CG2 A:ILE1191 4.7 26.2 1.0 CA A:ILE1191 4.7 31.9 1.0 CA A:LEU1150 4.7 35.6 1.0 O A:HOH1608 4.9 32.0 1.0

A.K.Thakur, S.E.Miller, N.P.D.Liau, S.Hwang, S.Hansen, F.De Sousa E Melo, J.Sudhamsu, R.N.Hannoush. Synthetic Multivalent Disulfide-Constrained Peptide Agonists Potentiate WNT1/ Beta-Catenin Signaling Via LRP6 Coreceptor Clustering. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 36893429
DOI: 10.1021/ACSCHEMBIO.2C00753