Chlorine in PDB 9o8v: Apo Form of Photoactive Yellow Protein

The structure of Apo Form of Photoactive Yellow Protein, PDB code: 9o8v was solved by S.D.E.Fried, S.M.Mukherjee, I.I.Mathews, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.30 / 1.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.631, 50.723, 71.252, 90, 132.93, 90
R / Rfree (%)	15.8 / 18.5

The binding sites of Chlorine atom in the Apo Form of Photoactive Yellow Protein (pdb code 9o8v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Apo Form of Photoactive Yellow Protein, PDB code: 9o8v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Apo Form of Photoactive Yellow Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Apo Form of Photoactive Yellow Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:15.7 occ:1.00 OH A:TYR42 3.0 16.1 1.0 OE2 A:GLU46 3.1 16.9 1.0 NH1 A:ARG52 3.2 16.6 1.0 CE2 A:TYR42 3.6 16.1 1.0 CZ A:TYR42 3.7 14.8 1.0 CD A:ARG52 3.8 15.8 1.0 CG A:GLU46 3.8 15.3 1.0 CE1 A:PHE62 3.8 15.8 1.0 CG2 A:THR50 3.8 18.9 1.0 CD A:GLU46 3.9 16.2 1.0 CD1 A:ILE31 4.1 17.6 1.0 CZ A:ARG52 4.2 15.9 1.0 OG1 A:THR50 4.3 16.9 1.0 NE A:ARG52 4.5 16.3 1.0 CE2 A:PHE96 4.5 23.2 1.0 CB A:THR50 4.5 17.4 1.0 CG1 A:VAL66 4.5 17.8 1.0 CZ A:PHE96 4.6 25.7 1.0 CD1 A:PHE62 4.6 15.7 1.0 CZ A:PHE62 4.8 16.7 1.0 CB A:ALA67 4.8 19.6 1.0 CD2 A:TYR42 4.9 15.3 1.0 CD2 A:PHE96 5.0 21.8 1.0

Chlorine binding site 2 out of 6 in the Apo Form of Photoactive Yellow Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Apo Form of Photoactive Yellow Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:18.9 occ:1.00 NH2 A:ARG52 3.2 17.6 1.0 N A:TYR98 3.4 18.7 1.0 CB A:CYS69 3.4 23.0 1.0 N A:ASP97 3.4 20.3 1.0 SG A:CYS69 3.4 29.1 1.0 CA A:ALA67 3.6 17.7 1.0 N A:CYS69 3.6 20.3 1.0 CB A:TYR98 3.6 19.2 1.0 C A:ALA67 3.7 18.8 1.0 CB A:ALA67 3.8 19.6 1.0 CA A:PHE96 3.9 19.4 1.0 CD1 A:PHE96 3.9 28.2 1.0 O A:ALA67 4.1 17.8 1.0 NH1 A:ARG52 4.1 16.6 1.0 CA A:CYS69 4.1 20.9 1.0 CZ A:ARG52 4.1 15.9 1.0 N A:PRO68 4.1 20.1 1.0 CB A:PHE96 4.1 18.8 1.0 CA A:TYR98 4.1 18.1 1.0 C A:PHE96 4.1 18.9 1.0 C A:ASP97 4.3 20.0 1.0 CA A:ASP97 4.4 21.2 1.0 CG A:PHE96 4.4 19.3 1.0 CD A:PRO68 4.5 21.8 1.0 N A:THR70 4.7 16.5 1.0 C A:PRO68 4.7 20.3 1.0 C A:CYS69 4.8 19.0 1.0 CE1 A:PHE96 4.9 31.6 1.0 CG2 A:THR70 4.9 17.8 1.0 O A:TYR98 4.9 21.1 1.0 CG A:TYR98 4.9 19.4 1.0 N A:ALA67 5.0 17.3 1.0 O A:VAL66 5.0 18.8 1.0

Chlorine binding site 3 out of 6 in the Apo Form of Photoactive Yellow Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Apo Form of Photoactive Yellow Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:73.7 occ:1.00 NZ A:LYS64 3.2 36.7 1.0 CE A:LYS64 3.5 35.4 1.0 OH A:TYR76 3.6 30.9 1.0 O A:HOH316 3.6 33.4 1.0 CE2 A:TYR76 3.6 26.4 1.0 CZ A:TYR76 4.1 24.9 1.0 NZ A:LYS80 4.3 39.4 1.0 CD2 A:TYR76 4.7 23.4 1.0 CD A:LYS64 4.9 33.6 1.0

Chlorine binding site 4 out of 6 in the Apo Form of Photoactive Yellow Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Apo Form of Photoactive Yellow Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:15.7 occ:1.00 OH B:TYR42 3.0 16.1 1.0 OE2 B:GLU46 3.1 16.8 1.0 NH1 B:ARG52 3.2 16.7 1.0 CE2 B:TYR42 3.6 16.0 1.0 CG B:GLU46 3.7 15.8 1.0 CZ B:TYR42 3.7 15.4 1.0 CD B:ARG52 3.8 16.6 1.0 CG2 B:THR50 3.8 18.4 1.0 CE1 B:PHE62 3.8 16.5 1.0 CD B:GLU46 3.9 15.7 1.0 CD1 B:ILE31 4.1 17.5 1.0 CZ B:ARG52 4.3 16.2 1.0 OG1 B:THR50 4.3 17.1 1.0 CZ B:PHE96 4.4 26.8 1.0 NE B:ARG52 4.5 16.5 1.0 CG1 B:VAL66 4.5 18.0 1.0 CB B:THR50 4.5 17.5 1.0 CE2 B:PHE96 4.5 24.5 1.0 CD1 B:PHE62 4.6 15.2 1.0 CZ B:PHE62 4.8 17.0 1.0 CE1 B:PHE96 4.8 30.3 1.0 CB B:ALA67 4.8 18.8 1.0 CD2 B:TYR42 4.8 14.8 1.0

Chlorine binding site 5 out of 6 in the Apo Form of Photoactive Yellow Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Apo Form of Photoactive Yellow Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:19.1 occ:1.00 NH2 B:ARG52 3.2 17.4 1.0 N B:TYR98 3.3 18.4 1.0 N B:ASP97 3.4 20.2 1.0 CB B:CYS69 3.4 23.1 1.0 SG B:CYS69 3.4 31.5 1.0 CA B:ALA67 3.6 17.9 1.0 N B:CYS69 3.6 20.1 1.0 CB B:TYR98 3.7 18.8 1.0 C B:ALA67 3.7 18.3 1.0 CB B:ALA67 3.8 18.8 1.0 CD1 B:PHE96 3.8 29.0 1.0 CA B:PHE96 3.9 19.3 1.0 O B:ALA67 4.1 18.2 1.0 NH1 B:ARG52 4.1 16.7 1.0 CA B:CYS69 4.1 20.8 1.0 CZ B:ARG52 4.1 16.2 1.0 N B:PRO68 4.1 20.1 1.0 C B:PHE96 4.1 19.3 1.0 CA B:TYR98 4.1 18.6 1.0 CB B:PHE96 4.2 20.1 1.0 C B:ASP97 4.3 20.5 1.0 CA B:ASP97 4.3 23.3 1.0 CG B:PHE96 4.4 21.2 1.0 CD B:PRO68 4.5 22.7 1.0 N B:THR70 4.7 17.4 1.0 C B:PRO68 4.7 19.9 1.0 CE1 B:PHE96 4.8 30.3 1.0 C B:CYS69 4.8 18.5 1.0 CG2 B:THR70 4.9 18.8 1.0 O B:TYR98 4.9 20.4 1.0 N B:ALA67 5.0 18.0 1.0 O B:VAL66 5.0 19.6 1.0 CG B:TYR98 5.0 19.5 1.0

Chlorine binding site 6 out of 6 in the Apo Form of Photoactive Yellow Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Apo Form of Photoactive Yellow Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:72.1 occ:1.00 OH B:TYR76 3.5 29.7 1.0 NZ B:LYS64 3.5 37.2 1.0 CE B:LYS64 3.6 36.2 1.0 CE2 B:TYR76 3.6 26.3 1.0 O B:HOH321 3.7 32.6 1.0 NZ B:LYS80 4.0 40.5 1.0 CZ B:TYR76 4.0 25.6 1.0 CD2 B:TYR76 4.8 23.6 1.0 CD B:LYS80 5.0 30.5 1.0

S.M.Mukherjee, S.D.E.Fried, N.Y.Hong, N.Bagheri, J.Kozuch, I.I.Mathews, S.G.Boxer. Detection of Drug Binding in Live Cells Using Quantum Cascade Laser Spectroscopy with Nitrile-Incorporated Proteins To Be Published.