Chlorine in PDB 5j57: V5E1-Rta Complex

All present enzymatic activity of V5E1-Rta Complex:
3.2.2.22;

The structure of V5E1-Rta Complex, PDB code: 5j57 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)	33.63 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.692, 68.216, 71.570, 90.00, 92.47, 90.00
R / Rfree (%)	16.3 / 19

The binding sites of Chlorine atom in the V5E1-Rta Complex (pdb code 5j57). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the V5E1-Rta Complex, PDB code: 5j57:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the V5E1-Rta Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of V5E1-Rta Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:33.9 occ:1.00 N A:LYS239 3.3 22.3 1.0 CA A:SER238 3.9 21.6 1.0 CB A:LYS239 4.0 24.8 1.0 CG A:LYS239 4.0 25.8 1.0 C A:SER238 4.1 20.9 1.0 CA A:LYS239 4.3 22.0 1.0 CB A:SER238 4.4 27.7 1.0 CD A:LYS239 4.5 33.5 1.0 O A:HOH494 4.6 35.7 1.0 O A:GLY237 4.7 20.1 1.0 O A:LYS239 4.9 26.0 1.0 N A:SER238 5.0 20.7 1.0

Chlorine binding site 2 out of 5 in the V5E1-Rta Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of V5E1-Rta Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:35.9 occ:1.00 O A:HOH471 2.8 22.9 1.0 OE1 A:GLU135 2.8 33.0 1.0 N A:GLU135 2.9 16.1 1.0 CG A:GLU135 3.2 23.2 1.0 CB A:GLU135 3.4 20.2 1.0 CD1 A:ILE205 3.4 21.5 1.0 CD A:GLU135 3.4 30.3 1.0 N A:ARG134 3.5 14.7 1.0 CB A:LEU133 3.6 15.8 1.0 CA A:GLU135 3.7 16.4 1.0 CB A:ARG134 3.8 14.3 1.0 C A:ARG134 3.8 15.2 1.0 CA A:ARG134 3.9 15.3 1.0 OE2 A:GLU127 4.0 18.2 1.0 C A:LEU133 4.1 16.1 1.0 O A:HOH411 4.2 45.8 1.0 CG2 A:ILE205 4.3 18.6 1.0 CG1 A:ILE205 4.3 18.6 1.0 CA A:LEU133 4.4 13.9 1.0 CD1 A:LEU133 4.4 23.5 1.0 CG A:LEU133 4.5 20.5 1.0 O A:HOH640 4.6 39.0 1.0 O A:HOH526 4.6 21.9 1.0 O A:HOH602 4.6 37.5 1.0 OE2 A:GLU135 4.7 32.1 1.0 NE A:ARG134 4.9 14.3 1.0 CB A:ILE205 4.9 16.8 1.0 CD2 A:LEU133 4.9 22.9 1.0 O A:LEU133 4.9 15.2 1.0 O A:ARG134 4.9 15.3 1.0 C A:GLU135 5.0 18.2 1.0 CD A:GLU127 5.0 18.6 1.0 CG A:ARG134 5.0 14.2 1.0

Chlorine binding site 3 out of 5 in the V5E1-Rta Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of V5E1-Rta Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:45.0 occ:1.00 N A:ASP124 3.1 14.5 1.0 O A:HOH533 3.2 32.3 1.0 CG A:ASP124 3.3 32.9 1.0 OD1 A:ASP124 3.3 33.2 1.0 N A:TYR123 3.5 15.4 1.0 CB A:ASP124 3.6 23.9 1.0 OD2 A:ASP124 3.7 37.1 1.0 O A:HOH485 3.8 48.2 1.0 CB A:ASN122 3.8 20.3 1.0 CA A:ASP124 3.9 18.7 1.0 OD1 A:ASN122 3.9 28.8 1.0 CB A:TYR123 3.9 13.6 1.0 CA A:TYR123 3.9 14.9 1.0 C A:TYR123 3.9 13.3 1.0 O A:HOH557 4.1 20.0 1.0 C A:ASN122 4.2 16.1 1.0 CG A:ASN122 4.3 25.5 1.0 O A:HOH597 4.4 44.0 1.0 O A:HOH643 4.4 22.2 1.0 CA A:ASN122 4.5 15.2 1.0 O A:HOH421 4.6 23.4 1.0 O A:HOH588 4.8 45.0 1.0 CD2 A:TYR123 4.9 16.6 1.0 CG A:TYR123 4.9 14.8 1.0 O A:ASN122 4.9 15.2 1.0

Chlorine binding site 4 out of 5 in the V5E1-Rta Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of V5E1-Rta Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:37.5 occ:1.00 O A:HOH645 2.2 41.3 1.0 O A:ASN10 2.7 20.1 1.0 O A:HOH474 2.9 18.3 1.0 CA A:PHE24 3.3 10.6 1.0 CB A:PHE24 3.5 10.2 1.0 N A:PHE24 3.8 12.6 1.0 CD1 A:PHE24 3.8 14.6 1.0 C A:ASN10 3.9 18.6 1.0 CG2 A:ILE9 4.0 17.2 1.0 O A:HOH606 4.1 46.3 1.0 CG A:PHE24 4.1 11.3 1.0 O A:HOH541 4.3 24.6 1.0 C A:ASN23 4.4 13.0 1.0 O A:ASN23 4.5 14.6 1.0 O A:HOH598 4.6 20.0 1.0 C A:PHE24 4.6 12.3 1.0 N A:ASN10 4.6 18.6 1.0 O A:SER20 4.6 11.7 1.0 O A:HOH619 4.7 36.0 1.0 CA A:PHE11 4.8 14.3 1.0 N A:PHE11 4.8 15.3 1.0 CB A:PHE11 4.8 14.1 1.0 O A:PHE24 4.8 13.3 1.0 CD1 A:PHE11 4.8 16.1 1.0 CA A:ASN10 4.9 18.5 1.0 O A:HOH661 5.0 51.5 1.0 CB A:ALA27 5.0 15.6 1.0

Chlorine binding site 5 out of 5 in the V5E1-Rta Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of V5E1-Rta Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:47.9 occ:1.00 OG B:SER17 2.8 33.1 1.0 O B:GLY15 2.8 30.0 1.0 N B:SER85 3.2 28.0 1.0 O B:GLY16 3.6 22.7 1.0 C B:GLY16 3.6 25.2 1.0 C B:GLY15 3.9 28.5 1.0 CA B:SER85 3.9 29.4 1.0 N B:SER17 4.0 26.2 1.0 CA B:GLY16 4.0 26.7 1.0 CB B:SER17 4.0 30.8 1.0 CA B:ASP84 4.1 28.5 1.0 C B:ASP84 4.1 28.7 1.0 CB B:ASP84 4.1 30.6 1.0 OG B:SER85 4.4 37.0 1.0 CA B:SER17 4.4 29.5 1.0 N B:GLY16 4.4 25.8 1.0 OD1 B:ASP84 4.5 33.6 1.0 O B:HOH371 4.5 51.5 1.0 O B:HOH374 4.7 41.5 1.0 CG B:ASP84 4.7 34.0 1.0 CB B:SER85 4.8 31.6 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