Chlorine in PDB 7th2: 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: 7th2 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)	47.45 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.644, 63.812, 99.298, 90, 107.12, 90
R / Rfree (%)	14.9 / 18.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Chlorine atom in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin (pdb code 7th2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 21 binding sites of Chlorine where determined in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin, PDB code: 7th2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 21 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:53.4 occ:1.00 HE2 B:HIS65 1.8 32.3 1.0 H A:ASN10 2.2 15.7 1.0 NE2 B:HIS65 2.6 26.9 1.0 OD1 A:ASN10 2.7 18.7 1.0 HA A:ILE9 2.9 20.5 1.0 O A:HOH417 2.9 33.4 1.0 N A:ASN10 3.0 13.1 1.0 HB2 A:ASN10 3.1 23.2 1.0 HE1 B:HIS65 3.4 52.4 1.0 CE1 B:HIS65 3.4 43.7 1.0 CG A:ASN10 3.5 17.1 1.0 CB A:ASN10 3.6 19.4 1.0 HG23 A:ILE9 3.7 20.8 1.0 CD2 B:HIS65 3.7 38.9 1.0 CA A:ILE9 3.7 17.1 1.0 O B:HOH482 3.8 39.0 1.0 C A:ILE9 3.8 17.9 1.0 CA A:ASN10 3.9 13.1 1.0 HD2 B:HIS65 4.0 46.6 1.0 O A:ILE8 4.0 18.3 1.0 HD13 A:ILE9 4.1 54.6 1.0 HG22 A:ILE9 4.3 20.8 1.0 CG2 A:ILE9 4.3 17.3 1.0 HB3 A:ASN10 4.5 23.2 1.0 O A:ASN10 4.5 14.5 1.0 HD12 A:ILE9 4.6 54.6 1.0 HG22 A:ILE8 4.6 24.7 1.0 HA A:ASN10 4.6 15.7 1.0 ND1 B:HIS65 4.6 31.7 1.0 CB A:ILE9 4.7 16.8 1.0 ND2 A:ASN10 4.7 15.6 1.0 N A:ILE9 4.7 15.8 1.0 O A:HOH451 4.7 43.6 1.0 C A:ILE8 4.7 16.5 1.0 C A:ASN10 4.7 16.3 1.0 CG B:HIS65 4.8 34.1 1.0 CD1 A:ILE9 4.8 45.5 1.0 HD21 A:ASN10 5.0 18.7 1.0

Chlorine binding site 2 out of 21 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:53.7 occ:1.00 HH11 A:ARG114 2.2 30.6 1.0 HD2 A:ARG114 2.6 40.2 1.0 HG22 A:VAL111 2.7 45.8 1.0 O A:VAL111 2.9 38.0 1.0 HA A:THR109 2.9 36.8 1.0 NH1 A:ARG114 3.0 25.5 1.0 HG23 A:VAL111 3.1 45.8 1.0 O A:PHE108 3.2 27.6 1.0 H A:VAL111 3.2 33.5 1.0 HH12 A:ARG114 3.3 30.6 1.0 CG2 A:VAL111 3.3 38.2 1.0 CD A:ARG114 3.5 33.5 1.0 HG2 A:ARG114 3.7 30.3 1.0 HG3 A:ARG114 3.7 30.3 1.0 N A:VAL111 3.7 27.9 1.0 CA A:THR109 3.7 30.7 1.0 C A:THR109 3.8 35.2 1.0 CG A:ARG114 3.8 25.2 1.0 C A:VAL111 3.9 23.9 1.0 HG21 A:VAL111 4.0 45.8 1.0 CZ A:ARG114 4.1 28.7 1.0 HD3 A:ARG114 4.1 40.2 1.0 N A:ASP110 4.2 33.2 1.0 CA A:VAL111 4.2 30.4 1.0 C A:PHE108 4.2 25.6 1.0 O A:THR109 4.2 42.8 1.0 NE A:ARG114 4.3 27.9 1.0 CB A:VAL111 4.4 33.3 1.0 H A:ASP110 4.4 39.9 1.0 O A:HOH564 4.4 39.0 1.0 N A:THR109 4.4 25.5 1.0 C A:ASP110 4.5 24.1 1.0 CA A:ASP110 4.8 34.6 1.0 HB A:THR109 4.8 38.4 1.0 HG22 A:THR109 4.8 50.1 1.0 CB A:THR109 4.9 32.0 1.0 HA A:ASP110 4.9 41.5 1.0 HG13 A:VAL111 4.9 49.1 1.0 O A:HOH421 5.0 37.9 1.0

Chlorine binding site 3 out of 21 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:48.5 occ:1.00 H A:GLY212 2.4 19.1 1.0 HB3 A:TRP211 3.0 20.3 1.0 N A:GLY212 3.2 15.9 1.0 H A:TRP211 3.4 16.9 1.0 O A:HOH510 3.5 21.5 1.0 HE3 A:TRP211 3.6 18.5 1.0 HA3 A:GLY212 3.7 21.8 1.0 O A:GLU208 3.8 17.9 1.0 N A:TRP211 3.8 14.1 1.0 CB A:TRP211 3.9 16.9 1.0 CA A:GLY212 4.0 18.1 1.0 O A:ASN209 4.0 20.3 1.0 C A:TRP211 4.1 18.5 1.0 CA A:TRP211 4.1 19.9 1.0 O A:HOH486 4.2 42.7 1.0 HB2 A:TRP211 4.3 20.3 1.0 O A:HOH410 4.3 24.2 1.0 C A:ASN209 4.3 22.1 1.0 O A:HOH579 4.3 33.3 1.0 HH12 A:ARG180 4.4 22.0 1.0 O A:HOH570 4.4 47.3 1.0 HA A:ASN209 4.4 21.3 1.0 HA2 A:GLY212 4.5 21.8 1.0 CE3 A:TRP211 4.5 15.4 1.0 C A:SER210 4.6 18.3 1.0 N A:SER210 4.7 13.7 1.0 H A:ARG213 4.8 22.8 1.0 CG A:TRP211 4.9 13.9 1.0 CA A:ASN209 4.9 17.7 1.0 NH1 A:ARG180 4.9 18.3 1.0 C A:GLU208 4.9 14.7 1.0

Chlorine binding site 4 out of 21 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:60.1 occ:1.00 HE1 A:HIS94 3.2 41.4 1.0 HA A:ASN97 3.3 38.7 1.0 O A:PRO95 3.5 29.3 1.0 O A:HOH551 3.6 66.4 1.0 HB2 A:PRO95 3.7 38.9 1.0 C A:ASN97 3.7 29.3 1.0 CA A:ASN97 3.8 32.3 1.0 O A:ASN97 3.8 28.1 1.0 N A:ASN97 3.8 26.2 1.0 CE1 A:HIS94 3.8 34.5 1.0 H A:ASN97 4.0 31.4 1.0 HB2 A:ALA101 4.0 33.7 1.0 C A:ASP96 4.2 26.3 1.0 HA A:GLN98 4.2 50.9 1.0 N A:GLN98 4.2 34.5 1.0 C A:PRO95 4.2 33.0 1.0 HD2 A:PRO95 4.3 32.0 1.0 O A:ASP96 4.3 30.4 1.0 HD1 A:HIS94 4.4 42.4 1.0 ND1 A:HIS94 4.5 35.4 1.0 CB A:PRO95 4.5 32.4 1.0 H A:GLN98 4.6 41.4 1.0 HG2 A:PRO95 4.7 42.3 1.0 NE2 A:HIS94 4.7 36.8 1.0 CA A:GLN98 4.7 42.5 1.0 N A:ASP96 4.8 26.2 1.0 HA A:ASP96 4.9 33.2 1.0 CA A:ASP96 4.9 27.7 1.0 CA A:PRO95 4.9 27.2 1.0 CB A:ALA101 4.9 28.1 1.0 HB3 A:ALA101 5.0 33.7 1.0 CD A:PRO95 5.0 26.7 1.0

Chlorine binding site 5 out of 21 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:64.4 occ:1.00 HG A:LEU133 3.3 33.2 1.0 HA A:ASN132 3.6 27.4 1.0 HD21 A:LEU133 3.9 39.9 1.0 HD23 A:LEU133 3.9 39.9 1.0 H A:LEU133 4.0 24.7 1.0 C A:GLY131 4.0 28.4 1.0 N A:ASN132 4.0 22.7 1.0 O A:GLY131 4.0 26.0 1.0 CA A:ASN132 4.1 22.9 1.0 CG A:LEU133 4.1 27.6 1.0 N A:LEU133 4.2 20.6 1.0 C A:ASN132 4.2 23.1 1.0 CD2 A:LEU133 4.2 33.3 1.0 HA2 A:GLY131 4.2 33.4 1.0 H A:ASN132 4.4 27.2 1.0 O A:HOH425 4.4 28.1 1.0 O A:GLU127 4.6 21.3 1.0 CA A:GLY131 4.7 27.9 1.0 O A:HOH413 4.7 37.1 1.0 HB3 A:GLU127 4.7 21.4 1.0 HD11 A:LEU133 4.7 45.2 1.0 HA A:GLN128 4.8 29.0 1.0 O A:ASN132 4.8 22.3 1.0

Chlorine binding site 6 out of 21 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 6 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:72.1 occ:1.00 OG1 A:THR77 3.3 19.5 1.0 HB A:THR77 3.3 25.6 1.0 O A:HOH541 3.3 20.7 1.0 HB2 A:ARG48 3.5 29.9 1.0 HD2 A:ARG48 3.6 68.3 1.0 HB3 A:ASN78 3.7 24.4 1.0 HD22 A:ASN78 3.8 30.1 1.0 CB A:THR77 3.8 21.3 1.0 HG1 A:THR77 4.0 23.4 1.0 HG23 A:VAL256 4.1 28.7 1.0 O A:THR77 4.2 16.7 1.0 HD3 A:ARG48 4.2 68.3 1.0 HG21 A:VAL256 4.2 28.7 1.0 HB3 A:ARG48 4.3 29.9 1.0 CB A:ARG48 4.3 24.9 1.0 CD A:ARG48 4.3 56.9 1.0 ND2 A:ASN78 4.3 25.1 1.0 C A:THR77 4.4 15.3 1.0 O A:HOH493 4.5 28.1 1.0 CB A:ASN78 4.6 20.3 1.0 CG2 A:VAL256 4.6 23.9 1.0 HG21 A:THR77 4.7 25.3 1.0 O A:HOH445 4.7 14.8 1.0 H A:ARG48 4.7 21.9 1.0 HD21 A:ASN78 4.7 30.1 1.0 CG A:ASN78 4.8 19.8 1.0 CA A:THR77 4.8 16.7 1.0 HG22 A:VAL256 4.8 28.7 1.0 CG A:ARG48 4.9 40.5 1.0 CG2 A:THR77 4.9 21.1 1.0 N A:ASN78 5.0 16.9 1.0

Chlorine binding site 7 out of 21 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 7 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:46.4 occ:1.00 H A:ASN236 2.6 27.3 1.0 HB2 A:ARG235 2.9 22.7 1.0 HB3 A:ARG234 3.0 25.8 1.0 HB3 A:ASN236 3.1 37.7 1.0 H A:ARG235 3.2 26.0 1.0 N A:ASN236 3.3 22.7 1.0 CG A:ASN236 3.5 36.7 1.0 HE A:ARG234 3.6 77.3 1.0 N A:ARG235 3.6 21.7 1.0 CB A:ASN236 3.7 31.4 1.0 O A:HOH521 3.7 26.9 1.0 ND2 A:ASN236 3.7 42.1 1.0 CB A:ARG235 3.8 18.9 1.0 OD1 A:ASN236 3.8 30.3 1.0 CB A:ARG234 3.8 21.5 1.0 NE A:ARG234 3.8 64.4 1.0 HB2 A:ARG234 3.8 25.8 1.0 HD22 A:ASN236 3.9 50.5 1.0 HH21 A:ARG234 3.9 87.2 1.0 CA A:ARG235 4.0 25.8 1.0 HD21 A:ASN236 4.0 50.5 1.0 C A:ARG235 4.0 23.6 1.0 CA A:ASN236 4.1 32.0 1.0 CZ A:ARG234 4.1 75.4 1.0 NH2 A:ARG234 4.2 72.7 1.0 HD3 A:ARG234 4.2 45.6 1.0 HB3 A:ARG235 4.4 22.7 1.0 C A:ARG234 4.4 22.0 1.0 HG3 A:ARG235 4.4 21.1 1.0 CD A:ARG234 4.5 38.0 1.0 HB2 A:ASN236 4.6 37.7 1.0 HA A:ASN236 4.6 38.4 1.0 HD2 A:ARG235 4.7 24.0 1.0 HH22 A:ARG234 4.7 87.2 1.0 CG A:ARG235 4.7 17.6 1.0 CA A:ARG234 4.7 18.0 1.0 CG A:ARG234 4.8 30.5 1.0 OE1 C:GLU110 4.9 63.1 1.0 HG A:SER238 4.9 50.5 1.0 NH1 A:ARG234 5.0 62.5 1.0 HA A:ARG235 5.0 30.9 1.0 HA A:ARG234 5.0 21.6 1.0

Chlorine binding site 8 out of 21 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 8 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:66.5 occ:1.00 H A:HIS40 2.3 47.2 1.0 HA A:ARG39 3.1 38.7 1.0 N A:HIS40 3.2 39.3 1.0 HH11 A:ARG39 3.6 103.3 1.0 HA A:HIS40 3.7 41.0 1.0 HD2 A:ARG39 3.7 84.7 1.0 NH1 A:ARG39 3.8 86.1 1.0 O A:HOH517 3.8 38.4 1.0 CA A:ARG39 4.0 32.2 1.0 HH12 A:ARG39 4.0 103.3 1.0 CA A:HIS40 4.0 34.1 1.0 C A:ARG39 4.0 39.1 1.0 ND1 A:HIS40 4.2 52.3 1.0 HD1 A:HIS40 4.3 62.7 1.0 O A:VAL38 4.3 37.6 1.0 CZ A:ARG39 4.3 92.2 1.0 CG A:HIS40 4.5 37.8 1.0 H A:GLU41 4.5 33.8 1.0 CE1 A:HIS40 4.5 50.7 1.0 CD A:ARG39 4.5 70.6 1.0 NE A:ARG39 4.6 80.8 1.0 HB3 A:ARG39 4.7 39.9 1.0 HE1 A:HIS40 4.8 60.9 1.0 CD2 A:HIS40 4.8 39.9 1.0 CB A:ARG39 4.8 33.2 1.0 CB A:HIS40 4.9 34.7 1.0 NE2 A:HIS40 4.9 51.7 1.0 N A:ARG39 4.9 30.0 1.0

Chlorine binding site 9 out of 21 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 9 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl309 b:55.2 occ:1.00 O A:HOH540 2.0 42.0 1.0 HG22 A:THR190 2.8 41.7 1.0 HA A:ARG191 3.1 16.8 1.0 HH11 A:ARG196 3.5 90.8 1.0 HB2 A:ARG196 3.5 63.2 1.0 HD3 A:ARG196 3.6 120.3 1.0 HG3 A:ARG191 3.6 24.2 1.0 HB2 A:TYR194 3.6 35.5 1.0 CG2 A:THR190 3.6 34.8 1.0 NH1 A:ARG196 3.7 75.7 1.0 HG2 A:ARG191 3.7 24.2 1.0 HG21 A:THR190 3.8 41.7 1.0 HD2 A:TYR194 3.8 37.0 1.0 HH12 A:ARG196 3.9 90.8 1.0 O A:THR190 3.9 19.3 1.0 CA A:ARG191 4.0 14.0 1.0 HG23 A:THR190 4.0 41.7 1.0 CG A:ARG191 4.1 20.2 1.0 N A:ARG191 4.1 16.0 1.0 C A:THR190 4.2 15.0 1.0 HG A:SER198 4.2 31.6 1.0 CZ A:ARG196 4.2 81.8 1.0 CD2 A:TYR194 4.3 30.9 1.0 CB A:ARG196 4.3 52.7 1.0 CD A:ARG196 4.4 100.2 1.0 HB3 A:ARG196 4.4 63.2 1.0 CB A:TYR194 4.5 29.6 1.0 NE A:ARG196 4.5 105.8 1.0 H A:ARG191 4.6 19.2 1.0 CB A:ARG191 4.6 21.6 1.0 OG A:SER198 4.7 26.3 1.0 HB3 A:TYR194 4.7 35.5 1.0 CG A:TYR194 4.7 26.6 1.0 CB A:THR190 4.8 25.4 1.0 HB A:THR190 4.8 30.5 1.0 NH2 A:ARG196 5.0 62.0 1.0 CG A:ARG196 5.0 76.7 1.0

Chlorine binding site 10 out of 21 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 10 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:44.9 occ:1.00 H B:ASN236 2.8 31.3 1.0 HB3 B:ARG234 2.9 31.1 1.0 HB3 B:ASN236 3.3 35.0 1.0 CG B:ASN236 3.4 35.1 1.0 H B:ARG235 3.4 28.1 1.0 HB2 B:ARG235 3.5 26.6 1.0 N B:ASN236 3.5 26.1 1.0 ND2 B:ASN236 3.5 33.3 1.0 HB2 B:ARG234 3.6 31.1 1.0 OD1 B:ASN236 3.6 28.9 1.0 HE B:ARG234 3.6 48.2 1.0 CB B:ARG234 3.7 25.9 1.0 NE B:ARG234 3.7 40.1 1.0 HD21 B:ASN236 3.7 39.9 1.0 CB B:ASN236 3.8 29.1 1.0 HD22 B:ASN236 3.8 39.9 1.0 N B:ARG235 3.8 23.4 1.0 HD3 B:ARG234 3.8 59.3 1.0 CZ B:ARG234 4.0 55.0 1.0 HH21 B:ARG234 4.1 64.5 1.0 O B:HOH507 4.1 25.2 1.0 NH2 B:ARG234 4.2 53.8 1.0 CD B:ARG234 4.2 49.4 1.0 CA B:ASN236 4.3 28.6 1.0 CB B:ARG235 4.3 22.1 1.0 C B:ARG235 4.3 28.7 1.0 CA B:ARG235 4.3 22.9 1.0 HG B:SER238 4.4 36.5 1.0 C B:ARG234 4.5 24.2 1.0 CG B:ARG234 4.6 32.5 1.0 NH1 B:ARG234 4.6 53.0 1.0 O B:HOH481 4.6 36.6 1.0 HH22 B:ARG234 4.7 64.5 1.0 HB2 B:ASN236 4.7 35.0 1.0 CA B:ARG234 4.7 24.8 1.0 HH11 B:ARG234 4.8 63.6 1.0 HB3 B:ARG235 4.9 26.6 1.0 HA B:ASN236 4.9 34.3 1.0 OG B:SER238 5.0 30.4 1.0 HG3 B:ARG235 5.0 24.8 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