Chlorine in PDB 5boz: Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1)

All present enzymatic activity of Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1):
3.2.2.22;

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1), PDB code: 5boz 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)	49.68 / 3.10
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	239.610, 242.884, 355.693, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 27.7

The binding sites of Chlorine atom in the Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1) (pdb code 5boz). 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 A Chain Bound to Camelid Nanobody (VHH9)(E1), PDB code: 5boz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl302 b:46.4 occ:1.00 NH1 D:ARG125 2.9 0.8 1.0 N D:GLY120 3.7 95.1 1.0 CZ D:ARG125 4.2 0.9 1.0 CA D:PHE119 4.3 0.9 1.0 C D:PHE119 4.5 0.6 1.0 CA D:GLY120 4.6 0.0 1.0 CD D:ARG125 4.7 77.6 1.0 CB D:PHE119 4.7 81.4 1.0 O D:ALA118 4.8 0.2 1.0 NE D:ARG125 4.9 0.6 1.0

Chlorine binding site 2 out of 3 in the Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1) within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl304 b:30.0 occ:1.00 NH1 E:ARG125 2.7 61.5 1.0 N E:GLY120 3.3 64.5 1.0 CA E:GLY120 3.9 97.2 1.0 CZ E:ARG125 4.0 94.0 1.0 OD1 E:ASN122 4.1 53.7 1.0 CD E:ARG125 4.3 79.4 1.0 ND2 E:ASN122 4.3 33.0 1.0 C E:PHE119 4.3 99.6 1.0 CA E:PHE119 4.4 71.1 1.0 CB E:ARG125 4.5 0.6 1.0 NE E:ARG125 4.6 27.8 1.0 CG E:ARG125 4.7 29.9 1.0 CG E:ASN122 4.7 0.5 1.0 CB E:PHE119 4.7 66.4 1.0 C E:GLY120 4.9 36.2 1.0 NH2 E:ARG125 5.0 30.6 1.0

Chlorine binding site 3 out of 3 in the Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ricin A Chain Bound to Camelid Nanobody (VHH9)(E1) within 5.0Å range: probe atom residue distance (Å) B Occ K:Cl201 b:42.5 occ:1.00 OH K:TYR60 3.0 96.8 1.0 OG1 K:THR58 3.5 43.9 1.0 CZ K:TYR60 3.7 25.5 1.0 CE1 K:TYR60 3.9 63.6 1.0 CG2 K:THR69 4.0 79.4 1.0 CB K:THR58 4.6 87.9 1.0 CE2 K:TYR60 4.8 24.9 1.0

M.J.Rudolph, D.J.Vance, M.S.Cassidy, Y.Rong, N.J.Mantis. Structural Analysis of Single Domain Antibodies Bound to A Second Neutralizing Hot Spot on Ricin Toxin'S Enzymatic Subunit. J. Biol. Chem. V. 292 872 2017.
ISSN: ESSN 1083-351X
PubMed: 27903650
DOI: 10.1074/JBC.M116.758102