Chlorine in PDB 6cwk: Anti-Rta Vhh Antibody

The structure of Anti-Rta Vhh Antibody, PDB code: 6cwk was solved by M.J.Rudolph, N.Mantis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.77 / 1.26
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.294, 60.294, 81.389, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 17.6

The binding sites of Chlorine atom in the Anti-Rta Vhh Antibody (pdb code 6cwk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Anti-Rta Vhh Antibody, PDB code: 6cwk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Anti-Rta Vhh Antibody


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Anti-Rta Vhh Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:80.5 occ:1.00 H A:GLY68 2.0 37.0 1.0 O A:HOH431 2.6 48.2 1.0 O A:HOH403 2.6 25.9 1.0 N A:GLY68 2.8 30.9 1.0 HA2 A:GLY68 2.8 38.4 1.0 HB3 A:TYR62 3.0 18.6 1.0 CA A:GLY68 3.3 31.9 1.0 HB2 A:MET66 3.4 71.2 1.0 O A:ALA63 3.4 24.3 1.0 HB2 A:TYR62 3.5 18.6 1.0 H A:GLN67 3.5 47.4 1.0 N A:GLN67 3.6 39.4 1.0 CB A:TYR62 3.6 15.5 1.0 O A:HOH423 3.7 52.0 1.0 C A:MET66 3.8 62.9 1.0 H A:MET66 3.9 74.3 1.0 C A:GLN67 3.9 32.8 1.0 HA3 A:GLY68 4.0 38.4 1.0 H A:ARG69 4.1 32.8 1.0 CB A:MET66 4.2 59.3 1.0 O A:HOH408 4.2 59.3 1.0 CG A:TYR62 4.2 14.1 1.0 O A:MET66 4.2 34.7 1.0 CA A:GLN67 4.3 34.6 1.0 C A:GLY68 4.3 37.4 1.0 HA A:ASP64 4.3 39.9 1.0 CA A:MET66 4.3 69.0 1.0 H A:PHE70 4.5 23.0 0.4 HA A:GLN67 4.5 41.6 1.0 N A:MET66 4.5 61.9 1.0 H A:PHE70 4.5 24.3 0.6 N A:ARG69 4.5 27.3 1.0 C A:ALA63 4.6 22.3 1.0 HD1 A:TYR62 4.6 16.9 1.0 HB3 A:MET66 4.6 71.2 1.0 O A:ASP64 4.6 39.8 1.0 CD1 A:TYR62 4.7 14.1 1.0 O A:HOH410 4.7 57.4 1.0 C A:ASP64 4.9 40.2 1.0 O A:HOH421 4.9 74.7 1.0 HB2 A:PHE70 4.9 23.1 0.4 CA A:ASP64 5.0 33.2 1.0 CD2 A:TYR62 5.0 14.2 1.0 CA A:TYR62 5.0 13.8 1.0 HD2 A:PHE70 5.0 22.8 0.4

Chlorine binding site 2 out of 2 in the Anti-Rta Vhh Antibody


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Anti-Rta Vhh Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:55.1 occ:1.00 H A:ASP113 2.2 22.6 0.4 H A:ASP113 2.2 22.6 0.6 O A:HOH386 2.9 43.9 1.0 O A:HOH419 3.0 42.1 1.0 HA A:SER112 3.0 17.1 0.6 N A:ASP113 3.0 18.8 1.0 HA A:SER112 3.0 19.9 0.4 O A:HOH406 3.1 50.8 1.0 HB3 A:ASP113 3.3 21.1 1.0 O A:SER111 3.3 16.5 1.0 O A:HOH316 3.3 51.6 1.0 OD1 A:ASP113 3.4 25.2 1.0 HE2 A:PHE37 3.4 15.6 1.0 CG A:ASP113 3.4 21.4 1.0 CB A:ASP113 3.7 17.6 1.0 OD2 A:ASP113 3.8 25.7 1.0 CA A:SER112 3.8 14.2 0.6 CA A:SER112 3.8 16.6 0.4 C A:SER112 3.9 17.2 0.6 C A:SER112 3.9 14.0 0.4 CA A:ASP113 3.9 16.4 1.0 CE2 A:PHE37 4.3 13.0 1.0 C A:SER111 4.3 14.2 1.0 HG A:SER112 4.4 24.2 0.6 HA A:ASP113 4.5 19.7 1.0 N A:SER112 4.5 13.6 0.6 O A:ARG45 4.6 18.0 1.0 N A:SER112 4.6 15.0 0.4 HB2 A:ASP113 4.6 21.1 1.0 H A:ARG114 4.7 24.2 1.0 HD2 A:PHE37 4.7 14.4 1.0 OG A:SER112 4.9 20.1 0.6 HG A:SER112 4.9 27.1 0.4 CB A:SER112 5.0 16.4 0.6 O A:HOH394 5.0 24.1 1.0 HB3 A:SER112 5.0 27.1 0.4 HB2 A:PHE47 5.0 15.3 1.0 HB2 A:ARG45 5.0 17.3 1.0 CD2 A:PHE37 5.0 12.0 1.0 HZ A:PHE37 5.0 15.1 1.0 CB A:SER112 5.0 22.6 0.4 H A:PHE47 5.0 15.8 1.0

M.J.Rudolph, D.J.Vance, S.Kelow, S.K.Angalakurthi, S.Nguyen, S.A.Davis, Y.Rong, C.R.Middaugh, D.D.Weis, R.Dunbrack Jr., J.Karanicolas, N.J.Mantis. Contribution of An Unusual CDR2 Element of A Single Domain Antibody in Ricin Toxin Binding Affinity and Neutralizing Activity. Protein Eng. Des. Sel. V. 31 277 2018.
ISSN: ESSN 1741-0134
PubMed: 30265352
DOI: 10.1093/PROTEIN/GZY022