Chlorine 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
Sodium	(Na)	2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl721 b:43.4 occ:1.00 HD21 A:ASN500 2.7 91.1 1.0 HD21 A:ASN537 3.0 0.6 1.0 ND2 A:ASN500 3.5 75.3 1.0 CA A:CA718 3.6 69.0 1.0 OD1 A:ASN537 3.8 0.1 1.0 ND2 A:ASN537 3.8 87.4 1.0 HD22 A:ASN500 4.0 91.1 1.0 OD1 A:ASN500 4.1 51.5 1.0 HB2 A:GLU502 4.1 69.0 1.0 HG2 A:GLU502 4.1 55.1 1.0 OD1 A:ASP536 4.2 0.7 1.0 OE2 A:GLU502 4.2 62.0 1.0 CG A:ASN500 4.2 49.6 1.0 CG A:ASN537 4.3 96.0 1.0 HD22 A:ASN537 4.5 0.6 1.0 CG A:GLU502 4.7 48.8 1.0 CB A:GLU502 4.8 56.9 1.0 CD A:GLU502 4.8 74.2 1.0 HB3 A:GLU502 5.0 69.0 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl720 b:69.1 occ:1.00 HD21 B:ASN500 2.5 0.2 1.0 HD21 B:ASN537 2.6 0.5 1.0 ND2 B:ASN500 3.3 0.6 1.0 ND2 B:ASN537 3.5 97.4 1.0 HD22 B:ASN500 3.7 0.2 1.0 OE1 B:GLU502 3.8 71.8 1.0 HG2 B:GLU502 3.9 0.1 1.0 HD22 B:ASN537 3.9 0.5 1.0 CA B:CA717 4.1 83.8 1.0 CG B:ASN500 4.1 70.6 1.0 OD1 B:ASN500 4.1 79.3 1.0 OD1 B:ASP536 4.2 0.1 1.0 HB2 B:GLU502 4.3 89.3 1.0 OD1 B:ASN537 4.3 1.0 1.0 CG B:ASN537 4.3 79.7 1.0 CD B:GLU502 4.4 86.2 1.0 CG B:GLU502 4.5 91.2 1.0 CB B:GLU502 4.9 73.9 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