Chlorine in PDB 6mhi: Photoactive Yellow Protein with Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore

The structure of Photoactive Yellow Protein with Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore, PDB code: 6mhi 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)	40.46 / 1.35
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	65.970, 65.970, 40.420, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 18.6

The binding sites of Chlorine atom in the Photoactive Yellow Protein with Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore (pdb code 6mhi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Photoactive Yellow Protein with Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore, PDB code: 6mhi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Photoactive Yellow Protein with Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore


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 Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:12.8 occ:1.00 CL13 A:YYZ201 0.0 12.8 1.0 C3' A:YYZ201 1.8 11.9 1.0 C4' A:YYZ201 2.7 13.6 1.0 C2' A:YYZ201 2.7 12.4 1.0 O4' A:YYZ201 2.9 12.4 1.0 OE2 A:GLU46 3.1 11.6 1.0 CE2 A:PHE96 3.3 10.8 1.0 CZ A:PHE96 3.3 12.0 1.0 CZ A:PHE62 3.5 11.0 1.0 CE1 A:PHE62 3.6 12.5 1.0 CD1 A:ILE31 3.6 12.9 1.0 C5' A:YYZ201 4.0 13.0 1.0 C1' A:YYZ201 4.1 13.2 1.0 CG2 A:VAL122 4.2 9.9 1.0 CD A:GLU46 4.2 9.9 1.0 CD2 A:PHE96 4.2 10.0 1.0 CE1 A:PHE96 4.3 10.6 1.0 C6' A:YYZ201 4.6 15.3 1.0 CE2 A:PHE62 4.8 11.9 1.0 CG1 A:VAL120 4.8 11.9 1.0 CG2 A:THR50 4.9 12.3 1.0 CD1 A:PHE62 4.9 11.7 1.0 OE1 A:GLU46 5.0 12.2 1.0 CG1 A:ILE31 5.0 12.1 1.0

Chlorine binding site 2 out of 2 in the Photoactive Yellow Protein with Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore


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 Covalently Bound 3,5-Dichloro-4- Hydroxycinnamic Acid Chromophore within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:16.6 occ:1.00 CL14 A:YYZ201 0.0 16.6 1.0 C5' A:YYZ201 1.7 13.0 1.0 C6' A:YYZ201 2.7 15.3 1.0 C4' A:YYZ201 2.7 13.6 1.0 OH A:TYR42 3.0 11.4 1.0 O4' A:YYZ201 3.0 12.4 1.0 CD A:ARG52 3.3 13.9 1.0 CG A:ARG52 3.4 14.1 1.0 CG1 A:VAL66 3.5 12.8 1.0 NE A:ARG52 3.5 16.1 1.0 OG1 A:THR50 3.6 11.4 1.0 CB A:THR50 3.7 13.0 1.0 CB A:ARG52 3.8 14.3 1.0 C1' A:YYZ201 3.9 13.2 1.0 CZ A:TYR42 4.0 11.3 1.0 CZ A:ARG52 4.0 16.4 1.0 C3' A:YYZ201 4.0 11.9 1.0 CG2 A:THR50 4.0 12.3 1.0 CE2 A:TYR42 4.2 10.6 1.0 NH1 A:ARG52 4.3 16.1 1.0 C2' A:YYZ201 4.5 12.4 1.0 NH2 A:ARG52 4.7 19.0 1.0 O A:VAL66 4.9 11.8 1.0 CB A:VAL66 5.0 12.7 1.0 CG1 A:VAL57 5.0 17.5 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