Chlorine in PDB 7kdm: Ricin Bound to Vhh Antibody V5G6

All present enzymatic activity of Ricin Bound to Vhh Antibody V5G6:
3.2.2.22;

The structure of Ricin Bound to Vhh Antibody V5G6, PDB code: 7kdm 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)	19.65 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.345, 77.438, 101.577, 89.97, 90.18, 89.98
R / Rfree (%)	18.7 / 23.8

The structure of Ricin Bound to Vhh Antibody V5G6 also contains other interesting chemical elements:

Zinc

(Zn)

9 atoms

The binding sites of Chlorine atom in the Ricin Bound to Vhh Antibody V5G6 (pdb code 7kdm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ricin Bound to Vhh Antibody V5G6, PDB code: 7kdm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:50.9 occ:1.00 N B:ILE98 2.6 27.0 1.0 O B:GLN129 2.9 21.9 1.0 CG1 B:VAL106 3.1 30.9 1.0 O B:LEU107 3.1 22.6 1.0 CD1 B:TRP131 3.1 15.0 1.0 O B:ILE98 3.2 25.6 1.0 NE1 B:TRP131 3.3 21.1 1.0 CA B:THR97 3.4 29.9 1.0 C B:THR97 3.5 28.9 1.0 CA B:ILE98 3.5 23.9 1.0 C B:ILE98 3.7 24.9 1.0 CG2 B:THR97 3.7 23.7 1.0 N B:LEU107 3.7 19.6 1.0 C B:GLN129 3.8 23.6 1.0 CB B:ILE98 3.9 24.7 1.0 C B:LEU107 4.0 20.4 1.0 CB B:GLN129 4.1 27.2 1.0 CB B:THR97 4.1 28.4 1.0 O B:GLY96 4.1 30.1 1.0 CA B:GLN129 4.2 26.7 1.0 CB B:LEU107 4.2 21.0 1.0 CA B:LEU107 4.2 17.9 1.0 CB B:VAL106 4.2 28.4 1.0 C B:VAL106 4.4 21.2 1.0 O B:HOH431 4.4 20.6 1.0 CG B:TRP131 4.5 15.0 1.0 CG1 B:ILE98 4.5 24.8 1.0 OG1 B:THR97 4.6 31.9 1.0 CA B:VAL106 4.6 22.6 1.0 N B:THR97 4.6 31.5 1.0 CE2 B:TRP131 4.6 16.1 1.0 CG2 B:VAL106 4.7 27.7 1.0 O B:THR97 4.7 29.5 1.0 N B:ILE99 4.8 24.2 1.0 C B:GLY96 4.8 25.8 1.0 N B:GLY130 4.9 26.6 1.0

Chlorine binding site 2 out of 3 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl305 b:64.7 occ:1.00 NE2 D:HIS40 2.5 38.4 1.0 O D:HOH508 2.8 33.1 1.0 CE1 D:HIS40 3.0 38.6 1.0 O D:HOH413 3.4 21.5 1.0 O D:SER221 3.6 31.2 1.0 CD2 D:HIS40 3.8 36.0 1.0 O D:GLN219 3.9 30.6 1.0 OG D:SER221 4.0 32.2 1.0 O E:HOH465 4.2 47.1 1.0 ND1 D:HIS40 4.3 41.5 1.0 O D:ILE218 4.3 26.3 1.0 C D:SER221 4.5 30.3 1.0 C D:GLN219 4.6 31.5 1.0 CG D:HIS40 4.7 38.7 1.0 N D:SER221 4.7 33.6 1.0 N D:GLN223 4.9 41.9 1.0

Chlorine binding site 3 out of 3 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl302 b:37.5 occ:1.00 O E:HOH501 2.3 33.9 1.0 O E:HOH438 2.3 41.5 1.0 ND1 D:HIS40 2.3 41.5 1.0 OD2 E:ASP94 2.6 36.6 1.0 OD1 E:ASP94 2.9 41.7 1.0 CE1 D:HIS40 3.0 38.6 1.0 O E:HOH541 3.0 43.0 1.0 CG E:ASP94 3.0 37.9 1.0 O E:HOH493 3.3 42.6 1.0 CG D:HIS40 3.5 38.7 1.0 CB D:HIS40 4.1 35.5 1.0 NE2 D:HIS40 4.2 38.4 1.0 CA D:HIS40 4.2 33.2 1.0 C D:GLN223 4.4 31.9 1.0 CB E:ASP94 4.4 34.9 1.0 CA D:GLN223 4.4 40.9 1.0 N E:ASP94 4.4 21.2 1.0 CD2 D:HIS40 4.5 36.0 1.0 O E:ILE92 4.6 27.7 1.0 N D:GLY224 4.6 27.7 1.0 O D:GLN223 4.7 30.4 1.0 N D:HIS40 4.7 33.9 1.0 CA E:ASP94 4.8 28.3 1.0

M.J.Rudolph, A.Y.Poon, S.Kavaliauskiene, A.G.Myrann, C.Reynolds-Peterson, S.A.Davis, K.Sandvig, D.J.Vance, N.J.Mantis. Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies That Bridge Ricin'S A-B Subunit Interface. J.Mol.Biol. V. 433 67086 2021.
ISSN: ESSN 1089-8638
PubMed: 34089718
DOI: 10.1016/J.JMB.2021.167086