Magnesium in PDB 6l6r: Crystal Structure of LRP6 E1E2-Sost Complex

The structure of Crystal Structure of LRP6 E1E2-Sost Complex, PDB code: 6l6r was solved by H.-J.Choi, J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.86 / 3.80
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	252.792, 252.792, 86.286, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 25.6

The binding sites of Magnesium atom in the Crystal Structure of LRP6 E1E2-Sost Complex (pdb code 6l6r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of LRP6 E1E2-Sost Complex, PDB code: 6l6r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of LRP6 E1E2-Sost Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of LRP6 E1E2-Sost Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:76.0 occ:1.00 OD1 A:ASN117 2.4 67.9 1.0 O A:ASP138 2.4 98.6 1.0 NE2 A:GLN139 2.4 0.5 1.0 O A:SER114 2.8 69.2 1.0 ND2 A:ASN117 3.0 95.8 1.0 CG A:ASN117 3.1 78.6 1.0 C A:ASP138 3.6 91.3 1.0 O A:GLU115 3.6 99.8 1.0 CD A:GLN139 3.7 0.8 1.0 OD1 A:ASP138 3.8 97.9 1.0 C A:SER114 3.9 75.4 1.0 CA A:GLU115 4.2 84.5 1.0 CA A:ASP138 4.3 85.1 1.0 C A:GLU115 4.3 91.6 1.0 CG A:GLN139 4.5 91.6 1.0 O A:LEU137 4.5 68.6 1.0 N A:GLU115 4.5 79.1 1.0 CB A:ASN117 4.6 68.1 1.0 N A:GLN139 4.6 85.9 1.0 OE1 A:GLN139 4.6 0.3 1.0 CA A:GLN139 4.8 77.6 1.0 CG A:ASP138 4.9 96.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of LRP6 E1E2-Sost Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of LRP6 E1E2-Sost Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1008 b:76.0 occ:1.00 O A:ILE143 2.8 89.3 1.0 O A:LEU100 2.9 90.9 1.0 CE1 A:HIS272 3.2 94.0 1.0 NE2 A:HIS272 3.2 93.7 1.0 CB A:ALA101 3.8 91.6 1.0 C A:LEU100 4.0 82.0 1.0 C A:ILE143 4.0 77.5 1.0 CA A:ALA101 4.1 80.3 1.0 OD2 A:ASP270 4.2 74.5 1.0 OD2 A:ASP57 4.4 0.4 1.0 N A:ALA101 4.5 75.9 1.0 ND1 A:HIS272 4.5 86.4 1.0 CD2 A:HIS272 4.6 90.4 1.0 CG A:ASP57 4.7 0.4 1.0 O A:VAL56 4.7 0.2 1.0 N A:ILE143 4.7 62.8 1.0 CA A:ALA144 4.8 64.7 1.0 CG2 A:ILE143 4.9 74.9 1.0 N A:ALA144 4.9 64.2 1.0 CB A:ASP57 4.9 98.8 1.0 CA A:ILE143 5.0 63.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of LRP6 E1E2-Sost Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of LRP6 E1E2-Sost Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1007 b:76.0 occ:1.00 O B:ASP138 2.6 70.9 1.0 O B:SER114 2.6 68.0 1.0 OD1 B:ASN117 2.9 68.6 1.0 ND2 B:ASN117 3.5 81.8 1.0 NE2 B:GLN139 3.5 95.6 1.0 CG B:ASN117 3.6 69.1 1.0 CG B:GLN139 3.7 74.1 1.0 C B:ASP138 3.7 73.7 1.0 C B:SER114 3.8 84.3 1.0 O B:GLU115 3.9 81.7 1.0 OD1 B:ASP138 4.1 90.2 1.0 CD B:GLN139 4.1 84.8 1.0 CA B:GLU115 4.3 81.3 1.0 C B:GLU115 4.5 77.5 1.0 N B:GLU115 4.5 79.8 1.0 N B:GLN139 4.6 74.5 1.0 CA B:GLN139 4.6 73.0 1.0 CA B:ASP138 4.7 78.6 1.0 CB B:GLN139 4.7 68.7 1.0 CA B:SER114 4.9 82.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of LRP6 E1E2-Sost Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of LRP6 E1E2-Sost Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1008 b:76.0 occ:1.00 O B:ILE143 2.5 70.7 1.0 NE2 B:HIS272 3.1 80.8 1.0 CE1 B:HIS272 3.3 80.2 1.0 O B:LEU100 3.5 65.3 1.0 C B:ILE143 3.7 65.8 1.0 CB B:ALA101 4.0 82.9 1.0 CA B:ALA144 4.3 66.9 1.0 N B:ALA144 4.4 66.4 1.0 CD2 B:HIS272 4.4 75.6 1.0 OD2 B:ASP57 4.5 93.9 1.0 CB B:ALA144 4.5 67.0 1.0 CA B:ALA101 4.5 75.2 1.0 C B:LEU100 4.6 65.3 1.0 N B:ILE143 4.6 65.1 1.0 ND1 B:HIS272 4.6 77.5 1.0 OD2 B:ASP270 4.8 86.4 1.0 CA B:ILE143 4.8 65.5 1.0 O B:LEU187 4.8 0.2 1.0 CG B:ASP57 4.8 94.9 1.0 N B:ALA101 5.0 65.7 1.0

J.Kim, W.Han, T.Park, E.J.Kim, I.Bang, H.S.Lee, Y.Jeong, K.Roh, J.Kim, J.S.Kim, C.Kang, C.Seok, J.-K.Han, H.-J.Choi. Sclerostin Inhibits Wnt Signaling Through Tandem Interaction with Two LRP6 Ectodomains. Nat Commun V. 11 5357 2020.
ISSN: ESSN 2041-1723
PubMed: 33097721
DOI: 10.1038/S41467-020-19155-4