Sodium in PDB 8ffe: Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide

The structure of Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide, PDB code: 8ffe was solved by K.M.Jude, N.Tsutsumi, D.Waghray, K.C.Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.37 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.212, 91.385, 104.055, 90, 103.67, 90
R / Rfree (%)	18.5 / 23.1

The binding sites of Sodium atom in the Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide (pdb code 8ffe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide, PDB code: 8ffe:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:32.8 occ:1.00 O A:SER114 2.3 30.9 1.0 OD1 A:ASN117 2.3 32.0 1.0 O A:ASP138 2.4 31.9 1.0 O A:HOH916 2.4 36.7 1.0 O A:HOH821 3.2 38.0 1.0 CG A:ASN117 3.3 33.9 1.0 C A:SER114 3.4 29.2 1.0 O A:HOH1076 3.6 41.7 1.0 C A:ASP138 3.6 34.7 1.0 ND2 A:ASN117 3.7 35.7 1.0 NE2 A:GLN139 3.8 41.1 1.0 OD1 A:ASP138 4.0 44.0 1.0 CD A:GLN139 4.1 35.2 1.0 OE1 A:GLN139 4.2 32.2 1.0 CA A:GLU115 4.2 31.2 1.0 N A:GLU115 4.2 28.0 1.0 CA A:ASP138 4.2 32.0 1.0 CA A:SER114 4.2 28.5 1.0 O A:GLU115 4.4 29.0 1.0 C A:GLU115 4.6 28.7 1.0 N A:GLN139 4.6 27.7 1.0 CB A:ASN117 4.7 27.3 1.0 CB A:SER114 4.7 32.6 1.0 CA A:GLN139 4.8 30.6 1.0 CG A:GLN139 4.9 30.5 1.0 CA A:ASN117 5.0 29.2 1.0 N A:ASN117 5.0 28.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:27.9 occ:1.00 O A:GLU446 2.3 27.1 1.0 OD1 A:ASP425 2.3 32.0 1.0 O A:HOH1089 2.4 40.3 1.0 O A:THR422 2.4 29.8 1.0 OG1 A:THR422 2.5 28.1 1.0 O A:HOH980 2.6 37.2 1.0 C A:THR422 3.4 26.4 1.0 CG A:ASP425 3.5 36.6 1.0 C A:GLU446 3.5 28.9 1.0 CB A:THR422 3.6 28.1 1.0 CA A:THR422 3.6 27.1 1.0 OD2 A:ASP425 3.9 39.1 1.0 OE1 A:GLU447 4.1 29.9 1.0 O A:HOH1128 4.2 37.3 1.0 CD A:GLU447 4.3 31.1 1.0 CD A:PRO448 4.3 25.1 1.0 OE2 A:GLU447 4.4 33.7 1.0 O A:HOH1102 4.4 34.6 1.0 N A:GLU447 4.4 27.7 1.0 CA A:GLU446 4.4 32.6 1.0 CA A:GLU447 4.4 26.9 1.0 CG2 A:THR422 4.6 24.9 1.0 N A:GLY423 4.6 27.4 1.0 CB A:ASP425 4.8 29.1 1.0 O A:LEU445 4.9 37.0 1.0 CA A:ASP425 4.9 28.2 1.0 CG A:GLU447 5.0 26.4 1.0 N A:ASP425 5.0 27.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of LRP6 E1E2 Domains Bound to YW210.09 Fab and Engineered XWNT8 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:19.6 occ:1.00 O A:HOH1023 2.2 29.6 1.0 O A:PRO533 2.2 29.5 1.0 O A:HOH894 2.3 31.1 1.0 OD1 A:ASP512 2.4 31.4 1.0 O A:HOH1063 2.5 32.2 1.0 O A:ALA509 2.5 31.7 1.0 CG A:ASP512 3.1 29.1 1.0 OD2 A:ASP512 3.1 33.2 1.0 C A:PRO533 3.4 28.7 1.0 C A:ALA509 3.6 25.9 1.0 CA A:PRO533 4.0 26.6 1.0 O A:HOH1113 4.2 43.2 1.0 CA A:LYS510 4.2 27.1 1.0 O A:LYS510 4.2 26.4 1.0 N A:LYS510 4.3 26.0 1.0 N A:HIS534 4.5 24.9 1.0 CA A:ALA509 4.5 25.8 1.0 C A:LYS510 4.5 29.5 1.0 CB A:ASP512 4.6 25.6 1.0 CA A:HIS534 4.7 26.8 1.0 ND1 A:HIS534 4.7 31.1 1.0 CB A:PRO533 4.7 28.5 1.0 CB A:HIS534 4.9 23.8 1.0

N.Tsutsumi, S.Hwang, S.Hansen, D.Waghray, N.Wang, Y.Miao, C.R.Glassman, N.A.Caveney, K.M.Jude, C.Y.Janda, R.N.Hannoush, K.C.Garcia. Structure of the Wnt-Frizzled-LRP6 Initiation Complex Reveals the Basis For Co-Receptor Discrimination To Be Published.