Chlorine in PDB 7tgi: Single-Domain Vhh Intrabodies Neutralize Ricin Toxin

All present enzymatic activity of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin:
3.2.2.22;

The structure of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin, PDB code: 7tgi was solved by M.J.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.20 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	44.129, 84.407, 109.945, 90, 97.06, 90
R / Rfree (%)	17.6 / 22.2

The binding sites of Chlorine atom in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin (pdb code 7tgi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin, PDB code: 7tgi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:29.8 occ:0.50 N A:ALA118 3.2 34.7 1.0 CA A:PHE117 3.8 32.4 1.0 CE2 A:PHE119 3.9 30.8 1.0 CB A:ALA118 3.9 32.2 1.0 CD1 A:PHE117 4.0 32.9 1.0 C A:PHE117 4.0 33.1 1.0 CD2 A:PHE119 4.1 32.6 1.0 CA A:ALA118 4.2 36.1 1.0 CB A:PHE117 4.2 32.8 1.0 CG A:PHE117 4.6 32.2 1.0 O A:THR116 4.9 34.1 1.0 N A:PHE119 4.9 31.2 1.0 CZ A:PHE119 5.0 29.1 1.0

Chlorine binding site 2 out of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:41.8 occ:1.00 OG1 A:THR13 3.0 29.9 1.0 OE2 A:GLU145 3.0 76.4 1.0 N A:HIS65 3.2 44.4 1.0 O A:HOH474 3.3 53.9 1.0 CG A:GLU145 3.4 56.2 1.0 CB A:HIS65 3.6 54.7 1.0 N A:ALA14 3.6 35.1 1.0 CD A:GLU145 3.7 71.1 1.0 CB A:GLU145 3.7 44.4 1.0 C A:THR13 3.7 35.3 1.0 CB A:THR13 3.8 31.5 1.0 CB A:ASN64 3.8 44.5 1.0 CA A:ALA14 3.8 37.8 1.0 CA A:HIS65 3.9 52.4 1.0 O A:THR13 4.0 38.3 1.0 CA A:ASN64 4.0 38.4 1.0 C A:ASN64 4.0 41.9 1.0 O A:HOH470 4.3 44.4 1.0 CA A:THR13 4.3 29.2 1.0 CB A:ALA14 4.4 37.9 1.0 O A:HOH435 4.5 52.5 1.0 CA A:GLU145 4.9 34.8 1.0 CG A:ASN64 4.9 47.0 1.0 CG A:HIS65 4.9 55.6 1.0 OE1 A:GLU145 4.9 79.1 1.0 ND2 A:ASN141 4.9 42.4 1.0

Chlorine binding site 3 out of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:68.4 occ:1.00 O A:GLU127 3.7 32.8 1.0 C A:GLU127 4.1 34.1 1.0 CD2 A:LEU133 4.1 47.4 1.0 N A:GLN128 4.3 34.6 1.0 CA A:GLN128 4.4 36.2 1.0 CG A:LEU133 4.5 48.2 1.0 C A:ASN132 4.5 43.1 1.0 CB A:GLU127 4.5 34.1 1.0 O A:ASN132 4.5 38.6 1.0 N A:ASN132 4.5 40.0 1.0 C A:GLY131 4.7 41.4 1.0 N A:LEU133 4.8 43.6 1.0 CA A:ASN132 4.8 41.6 1.0 CA A:GLU127 4.9 35.2 1.0

Chlorine binding site 4 out of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:66.0 occ:1.00 N A:PHE108 3.0 35.5 1.0 CD2 A:TYR6 3.8 45.7 1.0 CA A:PHE108 3.8 39.2 1.0 CD1 A:PHE108 3.9 37.7 1.0 CD1 A:LEU59 3.9 31.1 1.0 CA A:LEU107 3.9 34.3 1.0 C A:LEU107 3.9 35.7 1.0 CD2 A:LEU107 4.1 36.2 1.0 CE2 A:TYR6 4.2 47.2 1.0 O A:HIS106 4.3 42.8 1.0 CE1 A:PHE108 4.4 37.3 1.0 CG A:PHE108 4.5 37.8 1.0 CD2 A:LEU59 4.6 34.4 1.0 CB A:LEU107 4.6 38.4 1.0 CG A:LEU59 4.7 33.9 1.0 CB A:PHE108 4.8 34.0 1.0 N A:THR109 4.8 44.0 1.0 C A:PHE108 4.9 42.3 1.0 CG A:TYR6 4.9 44.5 1.0 N A:LEU107 5.0 35.6 1.0

Chlorine binding site 5 out of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:64.8 occ:1.00 N A:GLU135 3.2 37.8 1.0 CG A:GLU135 3.4 66.9 1.0 CD1 A:ILE205 3.5 44.1 1.0 N A:ARG134 3.5 37.8 1.0 CB A:LEU133 3.7 47.4 1.0 CB A:GLU135 3.7 55.7 1.0 CB A:ARG134 3.8 33.5 1.0 CA A:ARG134 4.0 35.8 1.0 CD A:GLU135 4.0 77.4 1.0 CA A:GLU135 4.0 46.3 1.0 C A:ARG134 4.0 37.4 1.0 OE2 A:GLU127 4.0 38.0 1.0 CG2 A:ILE205 4.1 38.4 1.0 C A:LEU133 4.2 40.3 1.0 OE2 A:GLU135 4.3 82.7 1.0 CA A:LEU133 4.4 42.9 1.0 CG A:LEU133 4.6 48.2 1.0 CD2 A:LEU133 4.6 47.4 1.0 CG1 A:ILE205 4.6 41.1 1.0 OE1 A:GLU135 4.7 79.5 1.0 NE A:ARG134 4.7 34.4 1.0 CD1 A:LEU133 4.7 50.5 1.0 CB A:ILE205 4.9 39.2 1.0 CG A:ARG134 5.0 32.1 1.0 CD A:GLU127 5.0 38.8 1.0

T.F.Czajka, D.J.Vance, S.Davis, M.J.Rudolph, N.J.Mantis. Single-Domain Antibodies Neutralize Ricin Toxin Intracellularly By Blocking Access to Ribosomal P-Stalk Proteins. J.Biol.Chem. V. 298 01742 2022.
ISSN: ESSN 1083-351X
PubMed: 35182523
DOI: 10.1016/J.JBC.2022.101742