Chlorine in PDB 3hdj: The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I

The structure of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I, PDB code: 3hdj was solved by K.Tan, A.Sather, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.41 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.405, 50.923, 106.999, 90.00, 100.98, 90.00
R / Rfree (%)	17.8 / 21.2

The binding sites of Chlorine atom in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I (pdb code 3hdj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I, PDB code: 3hdj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl311 b:29.1 occ:0.90 O A:HOH406 3.1 21.1 1.0 N A:ALA271 3.2 8.1 1.0 O A:HOH516 3.5 25.4 1.0 N A:ALA270 3.6 9.8 1.0 O A:HOH417 3.6 17.2 1.0 CB A:ALA271 3.8 7.9 1.0 CG1 A:VAL264 3.9 8.8 1.0 CB A:ALA269 3.9 9.6 1.0 CD2 A:LEU113 3.9 18.2 1.0 CA A:ALA270 4.0 8.0 1.0 CA A:VAL264 4.0 8.8 1.0 CG2 A:VAL264 4.0 10.3 1.0 CA A:ALA271 4.1 8.7 1.0 C A:ALA270 4.1 7.0 1.0 CB A:VAL264 4.2 9.8 1.0 C A:ALA269 4.3 9.9 1.0 O A:HOH439 4.3 36.5 1.0 O A:VAL264 4.3 8.4 1.0 CA A:ALA269 4.5 10.6 1.0 C A:VAL264 4.6 8.8 1.0 N A:ALA269 4.7 9.5 1.0 N A:ARG272 4.8 11.3 1.0 O A:ALA112 5.0 13.7 1.0 C A:ALA271 5.0 9.8 1.0

Chlorine binding site 2 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl312 b:35.0 occ:0.90 O A:HOH524 2.6 32.9 1.0 O B:HOH388 2.9 17.8 1.0 NH2 A:ARG38 3.0 13.1 0.5 N A:ARG38 3.0 11.2 0.5 N A:ARG38 3.0 11.6 0.5 CG A:ARG38 3.1 14.4 0.5 CG A:ARG38 3.7 16.6 0.5 CA A:GLN37 3.7 11.2 1.0 CB A:ARG38 3.7 12.2 0.5 CD A:ARG38 3.8 15.7 0.5 CB A:ARG38 3.8 13.4 0.5 O B:HOH429 3.8 30.7 1.0 C A:GLN37 3.8 11.4 1.0 CA A:ARG38 4.0 12.1 0.5 CG A:GLN37 4.0 9.4 1.0 CA A:ARG38 4.0 12.7 0.5 O A:MSE36 4.0 10.9 1.0 CZ A:ARG38 4.1 15.5 0.5 CG1 B:VAL40 4.1 10.1 1.0 CH2 A:TRP234 4.2 17.4 1.0 O A:HOH413 4.3 22.6 1.0 NE A:ARG38 4.4 16.3 0.5 CB A:GLN37 4.5 9.9 1.0 N A:GLN37 4.7 11.0 1.0 CD A:ARG38 4.8 20.2 0.5 C A:MSE36 4.8 11.0 1.0 O A:ARG38 4.8 12.6 0.5 OG1 B:THR42 4.8 12.3 1.0 O A:ARG38 4.9 12.2 0.5 CZ3 A:TRP234 4.9 16.0 1.0 OE2 A:GLU236 4.9 43.2 1.0 C A:ARG38 4.9 12.7 0.5 C A:ARG38 4.9 12.3 0.5 NE A:ARG38 5.0 24.5 0.5

Chlorine binding site 3 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl313 b:38.8 occ:0.90 NH1 A:ARG117 3.2 30.8 1.0 N A:ARG117 3.3 14.4 1.0 CD A:PRO116 3.5 14.4 1.0 N A:PRO116 3.6 13.9 1.0 CB A:PRO116 3.7 14.1 1.0 CB A:ARG117 3.8 14.6 1.0 O A:HOH519 3.8 34.0 1.0 CG A:ARG117 4.0 17.7 1.0 CG A:PRO116 4.0 15.2 1.0 CD A:ARG117 4.0 23.1 1.0 CA A:PRO116 4.1 14.2 1.0 NH2 A:ARG115 4.1 27.9 1.0 C A:PRO116 4.1 14.1 1.0 CA A:ARG117 4.1 14.2 1.0 O A:HOH420 4.2 32.2 1.0 C A:ARG115 4.3 13.8 1.0 CZ A:ARG117 4.3 29.2 1.0 CB A:ARG115 4.5 14.4 1.0 NE A:ARG117 4.6 26.8 1.0 CA A:ARG115 4.7 13.8 1.0 OD1 A:ASP275 4.9 27.5 1.0

Chlorine binding site 4 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl314 b:40.7 occ:0.90 CB A:ASP244 3.1 59.9 1.0 N A:GLU218 3.1 18.2 1.0 O A:HOH523 3.3 23.3 1.0 N A:LEU219 3.4 17.4 1.0 CG A:ASP244 3.7 60.7 1.0 OD1 A:ASP244 3.8 61.7 1.0 CA A:GLU218 3.9 17.3 1.0 CA A:ARG217 3.9 20.8 1.0 C A:ARG217 4.0 20.0 1.0 CG A:LEU219 4.1 20.4 1.0 CB A:GLU218 4.1 17.4 1.0 CB A:LEU219 4.1 18.6 1.0 C A:GLU218 4.1 17.1 1.0 CB A:ARG217 4.2 20.9 1.0 CA A:LEU219 4.3 18.7 1.0 CA A:ASP244 4.4 59.7 1.0 CD A:LYS282 4.5 20.8 1.0 OD2 A:ASP244 4.5 61.6 1.0 CD1 A:LEU219 4.6 18.0 1.0 CB A:ALA208 4.6 12.5 1.0 N A:ASP244 4.6 59.6 1.0 NZ A:LYS282 4.7 21.4 1.0 O A:LEU219 4.7 20.1 1.0 CE A:LYS282 4.7 22.1 1.0 CG A:GLU218 4.9 17.5 1.0

Chlorine binding site 5 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl311 b:26.8 occ:0.90 NZ B:LYS65 3.0 11.4 1.0 NH1 B:ARG101 3.2 17.6 1.0 NH2 B:ARG39 3.3 23.6 1.0 CE B:LYS65 3.6 11.6 1.0 NH2 B:ARG101 3.9 17.5 1.0 CZ B:ARG101 3.9 17.0 1.0 CE1 B:PHE76 4.1 15.5 1.0 O B:HOH522 4.2 48.1 1.0 OH B:TYR67 4.2 15.1 1.0 CE2 B:TYR67 4.3 14.0 1.0 CG2 B:THR98 4.4 11.3 1.0 CZ B:TYR67 4.5 12.2 1.0 CD1 B:LEU52 4.6 17.0 1.0 CZ B:ARG39 4.6 23.9 1.0 O B:HOH570 4.6 40.9 1.0 CZ B:PHE76 4.8 15.2 1.0 O B:VAL284 4.8 13.1 1.0 CA B:GLY285 4.8 13.0 1.0 OD2 B:ASP290 4.9 22.9 1.0 CD2 B:LEU52 5.0 14.3 1.0

Chlorine binding site 6 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl312 b:31.0 occ:0.90 O B:HOH324 3.1 22.9 1.0 N B:MSE36 3.3 10.9 1.0 O B:HOH505 3.5 31.9 1.0 CA B:ALA35 3.6 10.4 1.0 CE1 B:PHE29 3.7 16.5 1.0 O B:MSE36 3.8 11.4 1.0 CB B:ALA35 3.8 11.5 1.0 CZ2 B:TRP234 3.9 11.6 1.0 C B:ALA35 3.9 10.8 1.0 CA B:MSE36 4.3 9.7 1.0 CZ B:PHE29 4.4 19.8 1.0 CH2 B:TRP234 4.4 10.8 1.0 C B:MSE36 4.5 10.8 1.0 CE2 B:TRP234 4.5 13.6 1.0 CB B:MSE36 4.7 11.9 1.0 O A:HOH380 4.7 10.4 1.0 O B:ALA34 4.8 11.7 1.0 CD1 B:PHE29 4.8 15.7 1.0 NE1 B:TRP234 4.8 13.9 1.0 O B:HOH425 4.9 36.9 1.0 N B:ALA35 4.9 11.1 1.0

Chlorine binding site 7 out of 7 in the The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl313 b:35.2 occ:0.90 O B:HOH418 2.9 22.1 1.0 N B:ARG117 3.2 10.6 1.0 CG B:ARG115 3.5 15.7 1.0 CD B:PRO116 3.6 11.3 1.0 CB B:ARG117 3.6 10.2 1.0 N B:PRO116 3.8 11.0 1.0 CG B:ARG117 3.8 14.4 1.0 CD B:ARG117 3.8 16.2 1.0 NH1 B:ARG117 3.8 26.3 1.0 CB B:PRO116 3.8 10.9 1.0 CA B:ARG117 4.0 11.4 1.0 CG B:PRO116 4.1 11.8 1.0 C B:PRO116 4.1 10.7 1.0 CA B:PRO116 4.1 10.7 1.0 CD B:ARG115 4.3 19.8 1.0 NH2 B:ARG115 4.4 22.3 1.0 C B:ARG115 4.5 10.5 1.0 NE B:ARG117 4.7 21.7 1.0 CZ B:ARG117 4.8 25.1 1.0 CB B:ARG115 4.8 12.0 1.0 CA B:ARG115 4.9 11.4 1.0

K.Tan, A.Sather, S.Clancy, A.Joachimiak. The Crystal Structure of Probable Ornithine Cyclodeaminase From Bordetella Pertussis Tohama I To Be Published.