Sodium in PDB 6vfr: Crystal Structure of Human Protocadherin 18 EC1-EC4

The structure of Crystal Structure of Human Protocadherin 18 EC1-EC4, PDB code: 6vfr was solved by O.J.Harrison, J.Brasch, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.959, 176.942, 71.872, 90.00, 101.42, 90.00
R / Rfree (%)	23.6 / 27.2

The structure of Crystal Structure of Human Protocadherin 18 EC1-EC4 also contains other interesting chemical elements:

Calcium

(Ca)

18 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Protocadherin 18 EC1-EC4 (pdb code 6vfr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Protocadherin 18 EC1-EC4, PDB code: 6vfr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Protocadherin 18 EC1-EC4


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 Human Protocadherin 18 EC1-EC4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na524 b:77.6 occ:1.00 O A:ARG276 2.2 84.5 1.0 O A:HOH613 2.2 0.9 1.0 O A:LEU241 2.2 82.5 1.0 OD1 A:ASN242 2.4 96.1 1.0 OD1 A:ASP240 2.4 0.8 1.0 O A:HOH621 2.5 87.1 1.0 C A:LEU241 3.2 98.8 1.0 C A:ARG276 3.4 0.2 1.0 CG A:ASP240 3.5 0.7 1.0 CG A:ASN242 3.6 0.6 1.0 HA3 A:GLY277 3.7 0.3 1.0 OD2 A:ASP240 3.9 0.3 1.0 CA A:ASN242 3.9 96.7 1.0 N A:ASN242 3.9 95.8 1.0 HA A:ARG276 4.0 0.7 1.0 N A:LEU241 4.1 97.1 1.0 HD2 A:HIS278 4.1 0.6 1.0 HB3 A:ARG276 4.1 0.4 1.0 H A:LEU241 4.2 0.5 1.0 CA A:ARG276 4.2 0.5 1.0 CA A:LEU241 4.3 0.3 1.0 CB A:ASN242 4.3 97.1 1.0 N A:GLY277 4.3 0.8 1.0 C A:ASP240 4.3 0.2 1.0 CA A:GLY277 4.3 0.3 1.0 HH A:TYR256 4.4 0.1 1.0 O A:GLY277 4.5 85.6 1.0 HE2 A:TYR256 4.6 0.8 1.0 C A:GLY277 4.6 0.9 1.0 HE2 A:HIS278 4.6 0.9 1.0 ND2 A:ASN242 4.6 0.5 1.0 O A:ASP240 4.6 90.8 1.0 HA A:ASP240 4.6 0.0 1.0 OH A:TYR256 4.6 0.9 1.0 CD2 A:HIS278 4.7 0.5 1.0 CB A:ARG276 4.7 0.5 1.0 CB A:ASP240 4.7 0.6 1.0 C1 A:NAG501 4.8 0.4 1.0 CE2 A:TYR256 4.8 95.7 1.0 CA A:ASP240 4.8 0.8 1.0 HB2 A:LEU241 4.8 0.5 1.0 CZ A:TYR256 4.9 96.2 1.0 HA A:LEU241 4.9 0.2 1.0 NE2 A:HIS278 4.9 0.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Protocadherin 18 EC1-EC4


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 Human Protocadherin 18 EC1-EC4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na521 b:76.7 occ:1.00 O B:LEU241 2.2 78.9 1.0 O B:HOH606 2.2 0.5 1.0 O B:HOH605 2.2 88.3 1.0 O B:ARG276 2.3 81.2 1.0 OD1 B:ASN242 2.5 0.4 1.0 OD1 B:ASP240 2.5 0.8 1.0 C B:LEU241 3.2 84.6 1.0 CG B:ASP240 3.3 0.3 1.0 C B:ARG276 3.5 95.8 1.0 OD2 B:ASP240 3.6 0.3 1.0 CG B:ASN242 3.7 0.2 1.0 HA3 B:GLY277 3.9 0.1 1.0 N B:ASN242 3.9 94.8 1.0 HD2 B:HIS278 4.0 0.8 1.0 CA B:ASN242 4.0 97.6 1.0 HB2 B:ARG276 4.0 0.5 1.0 N B:LEU241 4.0 0.9 1.0 H B:LEU241 4.2 0.3 1.0 C B:ASP240 4.2 0.0 1.0 CA B:LEU241 4.2 97.5 1.0 HA B:ARG276 4.3 0.7 1.0 CB B:ASN242 4.3 0.3 1.0 CA B:ARG276 4.4 0.3 1.0 O B:ASP240 4.5 85.8 1.0 N B:GLY277 4.5 99.4 1.0 CA B:GLY277 4.5 96.7 1.0 O B:GLY277 4.5 97.3 1.0 HA B:ASP240 4.6 0.6 1.0 C B:GLY277 4.6 0.1 1.0 CB B:ASP240 4.6 0.9 1.0 HH B:TYR256 4.6 0.1 1.0 CD2 B:HIS278 4.6 0.8 1.0 CB B:ARG276 4.7 0.8 1.0 ND2 B:ASN242 4.7 0.5 1.0 CA B:ASP240 4.7 98.8 1.0 OH B:TYR256 4.8 0.0 1.0 HA B:LEU241 4.9 1.0 1.0 HB2 B:LEU241 4.9 0.5 1.0 O B:HOH614 4.9 98.0 1.0 NE2 B:HIS278 4.9 0.3 1.0 C1 B:NAG502 5.0 0.4 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