Sodium in PDB 6vg1: Xenopus Protocadherin 8.1 EC1-6

The structure of Xenopus Protocadherin 8.1 EC1-6, PDB code: 6vg1 was solved by O.J.Harrison, B.Brasch, L.S.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.27 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	146.645, 42.393, 167.471, 90.00, 110.60, 90.00
R / Rfree (%)	25.3 / 29.7

The structure of Xenopus Protocadherin 8.1 EC1-6 also contains other interesting chemical elements:

Calcium	(Ca)	30 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Xenopus Protocadherin 8.1 EC1-6 (pdb code 6vg1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Xenopus Protocadherin 8.1 EC1-6, PDB code: 6vg1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na724 b:14.7 occ:1.00 O A:HOH849 2.2 39.0 1.0 OD1 A:ASP235 2.2 52.9 1.0 O A:HOH811 2.2 64.4 1.0 O A:SER269 2.3 46.0 1.0 O A:LEU234 2.3 15.0 1.0 OD1 A:ASP233 2.4 89.6 1.0 HA A:ASP235 3.3 29.6 1.0 C A:LEU234 3.3 23.4 1.0 CG A:ASP235 3.4 26.5 1.0 CG A:ASP233 3.5 56.0 1.0 C A:SER269 3.5 20.7 1.0 HA3 A:GLY270 3.7 11.5 1.0 OD2 A:ASP233 3.9 88.1 1.0 CA A:ASP235 3.9 24.1 1.0 N A:ASP235 4.0 16.1 1.0 HH A:TYR249 4.0 37.4 1.0 HA A:SER269 4.1 29.2 1.0 HB2 A:SER269 4.2 28.8 1.0 CB A:ASP235 4.3 39.0 1.0 N A:LEU234 4.3 27.7 1.0 C A:ASP233 4.3 21.7 1.0 OD2 A:ASP235 4.3 72.5 1.0 CA A:SER269 4.3 23.7 1.0 O A:ASP233 4.4 46.2 1.0 N A:GLY270 4.4 35.8 1.0 CA A:GLY270 4.4 9.8 1.0 CA A:LEU234 4.4 21.1 1.0 OH A:TYR249 4.5 30.6 1.0 HE2 A:TYR249 4.5 59.0 1.0 O A:HOH866 4.5 35.3 1.0 H A:LEU234 4.6 34.0 1.0 CZ A:TYR249 4.6 10.4 1.0 HB3 A:ASP235 4.6 47.5 1.0 CE2 A:TYR249 4.6 48.5 1.0 CB A:ASP233 4.7 16.2 1.0 CB A:SER269 4.8 23.4 1.0 C A:GLY270 4.8 31.7 1.0 HA A:ASP233 4.8 7.9 1.0 H A:ASP235 4.9 20.1 1.0 CA A:ASP233 4.9 9.0 1.0 H A:ARG271 5.0 14.4 1.0 HB3 A:ASP233 5.0 20.2 1.0 HB2 A:LEU234 5.0 7.3 1.0

Sodium binding site 2 out of 2 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na723 b:46.7 occ:1.00 OD1 B:ASP235 2.1 83.4 1.0 O B:LEU234 2.2 41.9 1.0 OD1 B:ASP233 2.3 77.5 1.0 O B:SER269 2.5 39.6 1.0 HA B:ASP235 3.3 41.0 1.0 CG B:ASP235 3.3 94.0 1.0 C B:LEU234 3.3 46.3 1.0 CG B:ASP233 3.3 84.1 1.0 C B:SER269 3.7 35.5 1.0 OD2 B:ASP233 3.7 97.6 1.0 CA B:ASP235 3.9 33.6 1.0 N B:ASP235 4.0 46.4 1.0 HA3 B:GLY270 4.0 49.2 1.0 OD2 B:ASP235 4.1 0.6 1.0 CB B:ASP235 4.2 46.2 1.0 HA B:SER269 4.2 34.6 1.0 C B:ASP233 4.3 32.8 1.0 N B:LEU234 4.3 28.0 1.0 HB2 B:SER269 4.3 40.0 1.0 HH B:TYR249 4.4 51.0 1.0 O B:ASP233 4.4 54.1 1.0 CA B:LEU234 4.4 22.0 1.0 CA B:SER269 4.5 28.2 1.0 H B:LEU234 4.5 34.3 1.0 OH B:TYR249 4.6 42.0 1.0 CB B:ASP233 4.6 60.8 1.0 N B:GLY270 4.6 39.3 1.0 CA B:GLY270 4.7 40.4 1.0 HE2 B:TYR249 4.7 41.5 1.0 HB3 B:ASP235 4.7 56.2 1.0 HA B:ASP233 4.7 39.7 1.0 CZ B:TYR249 4.7 26.7 1.0 CA B:ASP233 4.8 32.5 1.0 CE2 B:TYR249 4.8 34.0 1.0 HB2 B:LEU234 4.8 22.6 1.0 H B:ASP235 4.9 56.4 1.0 C B:GLY270 4.9 31.1 1.0 HB3 B:ASP233 4.9 73.6 1.0 HB2 B:ASP235 4.9 56.2 1.0 CB B:SER269 4.9 32.8 1.0

O.J.Harrison, J.Brasch, P.S.Katsamba, G.Ahlsen, A.J.Noble, H.Dan, R.V.Sampogna, C.S.Potter, B.Carragher, B.Honig, L.Shapiro. Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003