Chlorine in PDB 6mmd: Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42

The structure of Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42, PDB code: 6mmd was solved by B.D.Thomson, J.Both, Y.Wu, R.M.Parrish, T.Martinez, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.03 / 1.23
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	65.909, 65.909, 40.503, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 18.1

The binding sites of Chlorine atom in the Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42 (pdb code 6mmd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42, PDB code: 6mmd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl42 b:17.4 occ:1.00 CL1 A:2LT42 0.0 17.4 1.0 CE1 A:2LT42 1.7 13.2 1.0 CZ A:2LT42 2.6 13.5 1.0 CD1 A:2LT42 2.7 14.4 1.0 HA2 A:GLY47 2.8 17.2 1.0 OH A:2LT42 2.8 14.7 1.0 HB2 A:ARG52 3.1 19.2 1.0 HG3 A:PRO54 3.1 29.0 1.0 HA3 A:GLY47 3.2 17.2 1.0 O A:ARG52 3.2 15.7 1.0 HA A:PRO54 3.3 25.9 1.0 CA A:GLY47 3.3 14.4 1.0 H A:GLY47 3.3 16.5 1.0 N A:GLY47 3.3 13.8 1.0 HD3 A:PRO54 3.4 24.3 1.0 HB3 A:ARG52 3.5 19.2 1.0 C A:ARG52 3.5 15.8 1.0 CB A:ARG52 3.6 16.0 1.0 HG3 A:GLU46 3.7 15.0 1.0 HB3 A:GLU46 3.7 14.4 1.0 N A:PRO54 3.7 17.2 1.0 CG A:PRO54 3.8 24.2 1.0 CD A:PRO54 3.8 20.2 1.0 CA A:PRO54 3.9 21.6 1.0 CE2 A:2LT42 3.9 12.5 1.0 CG A:2LT42 3.9 12.4 1.0 C A:GLU46 4.0 12.5 1.0 HG21 A:VAL57 4.0 22.0 1.0 C A:ASP53 4.1 16.5 1.0 CA A:ARG52 4.1 15.3 1.0 H A:ARG52 4.2 16.1 1.0 O A:ASN43 4.2 13.7 1.0 N A:ASP53 4.2 16.0 1.0 CB A:PRO54 4.3 22.4 1.0 HB3 A:PRO54 4.3 26.9 1.0 CG A:GLU46 4.3 12.5 1.0 HG2 A:GLU46 4.3 15.0 1.0 CB A:GLU46 4.3 12.0 1.0 CD2 A:2LT42 4.4 13.8 1.0 N A:ARG52 4.4 13.4 1.0 HG1 A:THR50 4.4 17.5 1.0 O A:GLU46 4.5 14.2 1.0 HG22 A:VAL57 4.5 22.0 1.0 O A:ASP53 4.5 17.7 1.0 HA A:ASP53 4.5 19.9 1.0 CA A:ASP53 4.6 16.6 1.0 OG1 A:THR50 4.6 14.6 1.0 HG2 A:PRO54 4.6 29.0 1.0 HG11 A:VAL57 4.7 24.0 1.0 CG2 A:VAL57 4.7 18.3 1.0 C A:GLY47 4.7 14.9 1.0 CA A:GLU46 4.8 12.5 1.0 HD2 A:PRO54 4.8 24.3 1.0 H A:ASP53 4.8 19.2 1.0 O4' A:HC4201 5.0 15.2 1.0 HA A:ARG52 5.0 18.3 1.0

Chlorine binding site 2 out of 4 in the Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl42 b:15.4 occ:1.00 CL2 A:2LT42 0.0 15.4 1.0 CE2 A:2LT42 1.7 12.5 1.0 CZ A:2LT42 2.7 13.5 1.0 CD2 A:2LT42 2.7 13.8 1.0 HE1 A:PHE62 2.9 16.7 1.0 OH A:2LT42 3.0 14.7 1.0 HD1 A:PHE62 3.2 16.2 1.0 HD13 A:ILE31 3.2 18.5 1.0 HG11 A:VAL66 3.3 18.8 1.0 O4' A:HC4201 3.3 15.2 1.0 HD13 A:ILE39 3.4 17.9 1.0 HG12 A:ILE31 3.5 17.1 1.0 HD11 A:ILE31 3.6 18.5 1.0 CE1 A:PHE62 3.6 13.9 1.0 HD11 A:ILE39 3.7 17.9 1.0 C4' A:HC4201 3.7 14.5 1.0 CD1 A:PHE62 3.8 13.5 1.0 CD1 A:ILE31 3.8 15.4 1.0 HG21 A:VAL57 3.8 22.0 1.0 HG2 A:GLU46 3.9 15.0 1.0 CE1 A:2LT42 3.9 13.2 1.0 CD1 A:ILE39 4.0 14.9 1.0 CG A:2LT42 4.0 12.4 1.0 H3' A:HC4201 4.0 16.5 1.0 HG21 A:ILE31 4.0 17.4 1.0 C3' A:HC4201 4.1 13.8 1.0 CG1 A:ILE31 4.1 14.3 1.0 CG1 A:VAL66 4.1 15.7 1.0 HG12 A:VAL66 4.2 18.8 1.0 HG23 A:ILE31 4.2 17.4 1.0 HG11 A:VAL57 4.3 24.0 1.0 HB A:VAL57 4.4 23.1 1.0 HG12 A:ILE39 4.4 18.2 1.0 CD1 A:2LT42 4.5 14.4 1.0 C5' A:HC4201 4.5 13.8 1.0 CG2 A:ILE31 4.5 14.5 1.0 HG3 A:GLU46 4.5 15.0 1.0 HG21 A:ILE39 4.6 17.2 1.0 CG A:GLU46 4.6 12.5 1.0 CG2 A:VAL57 4.7 18.3 1.0 HD12 A:ILE31 4.7 18.5 1.0 H5' A:HC4201 4.7 16.5 1.0 HG13 A:VAL66 4.7 18.8 1.0 HD12 A:ILE39 4.7 17.9 1.0 CG1 A:ILE39 4.8 15.2 1.0 HG13 A:ILE31 4.8 17.1 1.0 HG21 A:VAL66 4.9 19.9 1.0 HB A:VAL66 4.9 16.5 1.0 HG23 A:VAL57 4.9 22.0 1.0 CB A:VAL57 4.9 19.3 1.0 CZ A:PHE62 4.9 12.7 1.0 OE2 A:GLU46 4.9 14.2 1.0 CB A:ILE31 5.0 13.8 1.0

Chlorine binding site 3 out of 4 in the Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl42 b:17.3 occ:1.00 CL1 B:2LT42 0.0 17.3 1.0 CE1 B:2LT42 1.7 12.6 1.0 CD1 B:2LT42 2.6 15.3 1.0 CZ B:2LT42 2.7 13.6 1.0 HA2 B:GLY47 2.8 17.3 1.0 OH B:2LT42 2.9 14.7 1.0 HB2 B:ARG52 3.1 19.7 1.0 HG3 B:PRO54 3.1 28.1 1.0 O B:ARG52 3.2 15.7 1.0 HA3 B:GLY47 3.2 17.3 1.0 HA B:PRO54 3.3 25.4 1.0 CA B:GLY47 3.3 14.4 1.0 H B:GLY47 3.3 16.0 1.0 N B:GLY47 3.3 13.3 1.0 HD3 B:PRO54 3.4 24.4 1.0 HB3 B:ARG52 3.5 19.7 1.0 C B:ARG52 3.5 15.4 1.0 CB B:ARG52 3.6 16.4 1.0 HB3 B:GLU46 3.6 15.2 1.0 HG3 B:GLU46 3.7 15.1 1.0 N B:PRO54 3.7 17.9 1.0 CG B:PRO54 3.8 23.4 1.0 CD B:PRO54 3.8 20.4 1.0 CA B:PRO54 3.9 21.1 1.0 CE2 B:2LT42 3.9 12.3 1.0 CG B:2LT42 3.9 12.6 1.0 C B:GLU46 4.0 12.9 1.0 HG21 B:VAL57 4.1 22.1 1.0 C B:ASP53 4.1 17.7 1.0 CA B:ARG52 4.1 15.1 1.0 H B:ARG52 4.2 16.6 1.0 O B:ASN43 4.2 13.5 1.0 N B:ASP53 4.2 16.9 1.0 CG B:GLU46 4.3 12.6 1.0 HB3 B:PRO54 4.3 25.9 1.0 CB B:PRO54 4.3 21.6 1.0 HG2 B:GLU46 4.3 15.1 1.0 CB B:GLU46 4.3 12.7 1.0 N B:ARG52 4.4 13.8 1.0 CD2 B:2LT42 4.4 13.3 1.0 HG1 B:THR50 4.4 18.0 1.0 O B:GLU46 4.5 13.9 1.0 HG22 B:VAL57 4.5 22.1 1.0 HA B:ASP53 4.5 20.2 1.0 O B:ASP53 4.5 18.1 1.0 CA B:ASP53 4.6 16.8 1.0 OG1 B:THR50 4.6 15.0 1.0 HG2 B:PRO54 4.6 28.1 1.0 HG11 B:VAL57 4.7 24.9 1.0 C B:GLY47 4.7 14.1 1.0 CG2 B:VAL57 4.7 18.4 1.0 H B:ASP53 4.8 20.3 1.0 CA B:GLU46 4.8 12.8 1.0 HD2 B:PRO54 4.8 24.4 1.0 O4' B:HC4201 5.0 15.6 1.0 HA B:ARG52 5.0 18.1 1.0

Chlorine binding site 4 out of 4 in the Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Photoactive Yellow Protein with 3,5-Dichlorotyrosine Substituted at Position 42 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl42 b:15.5 occ:1.00 CL2 B:2LT42 0.0 15.5 1.0 CE2 B:2LT42 1.7 12.3 1.0 CZ B:2LT42 2.6 13.6 1.0 CD2 B:2LT42 2.7 13.3 1.0 HE1 B:PHE62 2.9 17.2 1.0 OH B:2LT42 3.0 14.7 1.0 HD1 B:PHE62 3.2 16.8 1.0 HD13 B:ILE31 3.2 18.1 1.0 HG11 B:VAL66 3.3 18.3 1.0 O4' B:HC4201 3.3 15.6 1.0 HD13 B:ILE39 3.4 17.1 1.0 HG12 B:ILE31 3.5 17.0 1.0 CE1 B:PHE62 3.6 14.4 1.0 HD11 B:ILE31 3.6 18.1 1.0 C4' B:HC4201 3.7 13.6 1.0 CD1 B:PHE62 3.7 14.0 1.0 HD11 B:ILE39 3.8 17.1 1.0 CD1 B:ILE31 3.8 15.1 1.0 HG21 B:VAL57 3.8 22.1 1.0 HG2 B:GLU46 3.9 15.1 1.0 CE1 B:2LT42 3.9 12.6 1.0 CG B:2LT42 4.0 12.6 1.0 H3' B:HC4201 4.0 17.0 1.0 CD1 B:ILE39 4.0 14.2 1.0 HG21 B:ILE31 4.0 17.1 1.0 C3' B:HC4201 4.1 14.2 1.0 CG1 B:VAL66 4.1 15.3 1.0 CG1 B:ILE31 4.1 14.1 1.0 HG12 B:VAL66 4.2 18.3 1.0 HG23 B:ILE31 4.2 17.1 1.0 HG11 B:VAL57 4.3 24.9 1.0 HB B:VAL57 4.3 22.6 1.0 CD1 B:2LT42 4.5 15.3 1.0 C5' B:HC4201 4.5 13.4 1.0 HG12 B:ILE39 4.5 18.0 1.0 CG2 B:ILE31 4.5 14.3 1.0 HG3 B:GLU46 4.6 15.1 1.0 HG21 B:ILE39 4.6 17.9 1.0 CG2 B:VAL57 4.6 18.4 1.0 CG B:GLU46 4.6 12.6 1.0 HG13 B:VAL66 4.7 18.3 1.0 H5' B:HC4201 4.7 16.1 1.0 HD12 B:ILE31 4.7 18.1 1.0 HD12 B:ILE39 4.7 17.1 1.0 HG21 B:VAL66 4.8 20.1 1.0 HG13 B:ILE31 4.9 17.0 1.0 HB B:VAL66 4.9 16.1 1.0 CB B:VAL57 4.9 18.9 1.0 HG23 B:VAL57 4.9 22.1 1.0 CG1 B:ILE39 4.9 15.0 1.0 CZ B:PHE62 4.9 13.0 1.0 OE2 B:GLU46 4.9 14.3 1.0

B.Thomson, J.Both, Y.Wu, R.M.Parrish, T.J.Martinez, S.G.Boxer. Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein Via Noncanonical Amino Acid Incorporation. J.Phys.Chem.B V. 123 4844 2019.
ISSN: ISSN 1089-5647
PubMed: 31117606
DOI: 10.1021/ACS.JPCB.9B01571