Chlorine in PDB 5ixl: Structure of P. Vulgaris Higb Toxin Y91A Variant

The structure of Structure of P. Vulgaris Higb Toxin Y91A Variant, PDB code: 5ixl was solved by M.A.Schureck, A.A.Repack, S.J.Miles, J.Marquez, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.340, 64.030, 94.080, 90.00, 98.14, 90.00
R / Rfree (%)	16.8 / 21.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Structure of P. Vulgaris Higb Toxin Y91A Variant (pdb code 5ixl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Structure of P. Vulgaris Higb Toxin Y91A Variant, PDB code: 5ixl:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:25.6 occ:1.00 NZ A:LYS11 3.2 25.2 1.0 N A:PHE5 3.3 16.1 1.0 CA A:SER4 3.7 17.0 1.0 CE A:LYS11 3.8 22.5 1.0 O A:PHE5 3.9 20.4 1.0 C A:SER4 4.0 16.5 1.0 CB A:SER4 4.0 18.4 1.0 CD A:LYS11 4.1 19.4 1.0 CA A:PHE5 4.2 16.4 1.0 CB A:PHE5 4.3 17.1 1.0 C A:PHE5 4.5 18.4 1.0 CD2 A:PHE5 4.5 18.1 1.0 O A:LYS3 4.7 19.8 1.0 NZ A:LYS8 4.7 32.5 1.0 CG A:PHE5 4.9 17.2 1.0 N A:SER4 4.9 18.0 1.0

Chlorine binding site 2 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:25.2 occ:1.00 N B:PHE5 3.2 14.9 1.0 CE B:LYS11 3.7 22.4 1.0 NZ B:LYS11 3.7 26.1 1.0 CA B:SER4 3.8 16.2 1.0 O B:HOH388 3.8 43.6 1.0 O B:PHE5 3.9 17.0 1.0 C B:SER4 4.0 14.9 1.0 CD B:LYS11 4.0 18.2 1.0 CA B:PHE5 4.1 14.8 1.0 CB B:PHE5 4.1 13.8 1.0 CB B:SER4 4.2 18.1 1.0 O B:HOH303 4.2 47.1 1.0 CD1 B:PHE5 4.4 14.0 1.0 C B:PHE5 4.5 16.0 1.0 O B:LYS3 4.7 18.2 1.0 CG B:PHE5 4.8 14.0 1.0 CG B:LYS11 5.0 16.1 1.0 OE2 B:GLU15 5.0 23.2 1.0 N B:SER4 5.0 16.8 1.0

Chlorine binding site 3 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:29.2 occ:1.00 N B:ILE43 3.3 15.7 1.0 CG2 B:ILE43 3.7 17.6 1.0 CA B:GLU42 3.9 21.3 1.0 CB B:ILE43 3.9 17.2 1.0 CE2 B:PHE78 3.9 18.6 1.0 CD2 B:PHE78 4.0 17.8 1.0 C B:GLU42 4.1 17.8 1.0 CA B:ILE43 4.2 15.4 1.0 CB B:GLU42 4.4 25.7 1.0 O B:THR41 4.7 22.5 1.0

Chlorine binding site 4 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:37.7 occ:1.00 CG B:PRO55 4.0 18.3 1.0 CE B:LYS57 4.4 29.8 1.0 NZ B:LYS57 4.5 31.0 1.0 CD B:PRO55 5.0 17.6 1.0

Chlorine binding site 5 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:28.7 occ:1.00 NZ C:LYS11 3.1 27.1 1.0 N C:PHE5 3.2 14.1 1.0 CA C:SER4 3.7 14.7 1.0 O C:PHE5 3.8 19.2 1.0 C C:SER4 4.0 14.1 1.0 CB C:SER4 4.0 14.8 1.0 CA C:PHE5 4.1 15.2 1.0 CB C:PHE5 4.2 14.9 1.0 CD C:LYS11 4.2 20.4 1.0 CE C:LYS11 4.2 24.8 1.0 CD2 C:PHE5 4.3 15.9 1.0 C C:PHE5 4.5 16.8 1.0 O C:LYS3 4.8 16.9 1.0 CG C:PHE5 4.8 15.3 1.0 N C:SER4 4.9 15.3 1.0 OE2 C:GLU15 4.9 28.1 1.0 CG C:LYS11 4.9 17.8 1.0

Chlorine binding site 6 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:22.3 occ:1.00 N D:PHE5 3.2 12.5 1.0 NZ D:LYS11 3.4 26.6 1.0 CA D:SER4 3.7 12.8 1.0 O D:PHE5 3.8 17.9 1.0 C D:SER4 3.9 12.4 1.0 CB D:SER4 4.0 12.4 1.0 CD D:LYS11 4.0 19.3 1.0 CA D:PHE5 4.1 13.2 1.0 CB D:PHE5 4.1 13.5 1.0 CE D:LYS11 4.1 23.5 1.0 CD2 D:PHE5 4.3 14.0 1.0 C D:PHE5 4.4 15.1 1.0 CG D:PHE5 4.7 13.5 1.0 O D:LYS3 4.8 16.7 1.0 CG D:LYS11 4.9 15.7 1.0 N D:SER4 5.0 13.9 1.0

Chlorine binding site 7 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl202 b:26.3 occ:1.00 N D:ASN80 3.4 15.9 1.0 CA D:ILE79 4.0 15.0 1.0 O D:HOH351 4.0 29.0 1.0 C D:ILE79 4.2 15.4 1.0 CA D:ASN80 4.2 18.4 1.0 O D:PHE78 4.4 15.8 1.0 CG2 D:ILE79 4.4 20.4 1.0 CB D:ILE79 4.7 18.6 1.0 CB D:ASN80 4.8 21.1 1.0 O D:HOH326 5.0 28.4 1.0

Chlorine binding site 8 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl201 b:26.7 occ:1.00 N E:PHE5 3.3 16.9 1.0 NZ E:LYS11 3.4 26.7 1.0 CA E:SER4 3.8 17.3 1.0 O E:PHE5 4.0 18.9 1.0 C E:SER4 4.0 16.8 1.0 CB E:SER4 4.1 17.4 1.0 CB E:PHE5 4.1 15.4 1.0 CA E:PHE5 4.2 16.1 1.0 CD E:LYS11 4.2 20.6 1.0 CE E:LYS11 4.2 24.3 1.0 CD2 E:PHE5 4.3 14.5 1.0 C E:PHE5 4.5 17.7 1.0 O E:LYS3 4.7 20.5 1.0 CG E:PHE5 4.7 14.3 1.0 CG E:LYS11 4.9 17.0 1.0 N E:SER4 5.0 18.4 1.0

Chlorine binding site 9 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl201 b:35.5 occ:1.00 N F:PHE5 3.3 24.7 1.0 NZ F:LYS11 3.5 30.3 1.0 CA F:SER4 3.8 24.5 1.0 O F:PHE5 3.9 28.1 1.0 CE F:LYS11 4.0 29.1 1.0 C F:SER4 4.1 23.9 1.0 CB F:SER4 4.1 25.2 1.0 CD F:LYS11 4.2 26.7 1.0 CA F:PHE5 4.2 24.6 1.0 CB F:PHE5 4.2 22.8 1.0 CD2 F:PHE5 4.4 20.2 1.0 C F:PHE5 4.5 27.2 1.0 O F:LYS3 4.7 27.0 1.0 CG F:PHE5 4.8 21.2 1.0 N F:SER4 4.9 24.7 1.0

Chlorine binding site 10 out of 12 in the Structure of P. Vulgaris Higb Toxin Y91A Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of P. Vulgaris Higb Toxin Y91A Variant within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:24.6 occ:1.00 N G:PHE5 3.3 13.7 1.0 NZ G:LYS11 3.5 27.4 1.0 CA G:SER4 3.7 14.2 1.0 O G:PHE5 3.9 17.9 1.0 C G:SER4 4.0 12.4 1.0 CB G:SER4 4.1 15.7 1.0 CA G:PHE5 4.1 14.1 1.0 CB G:PHE5 4.2 14.4 1.0 CE G:LYS11 4.2 25.4 1.0 CD G:LYS11 4.3 22.2 1.0 CD2 G:PHE5 4.4 14.1 1.0 C G:PHE5 4.5 16.2 1.0 O G:LYS3 4.8 15.0 1.0 CG G:PHE5 4.8 14.4 1.0 N G:SER4 4.9 14.3 1.0

M.A.Schureck, A.Repack, S.J.Miles, J.Marquez, C.M.Dunham. Mechanism of Endonuclease Cleavage By the Higb Toxin. Nucleic Acids Res. V. 44 7944 2016.
ISSN: ESSN 1362-4962
PubMed: 27378776
DOI: 10.1093/NAR/GKW598