Chlorine in PDB 8ejn: Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol

The structure of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol, PDB code: 8ejn was solved by M.S.Aktar, V.S.De Serrano, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.09 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.881, 67.323, 69.199, 90, 90, 90
R / Rfree (%)	16 / 21.1

The structure of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol (pdb code 8ejn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol, PDB code: 8ejn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:13.5 occ:0.30 CL1 A:5JC202 0.0 13.5 0.3 NE2 A:HIS55 0.9 8.0 0.4 OAA A:5JC202 1.0 19.5 0.3 CAG A:5JC202 1.1 17.6 0.3 CAI A:5JC202 1.7 10.5 0.3 CD2 A:HIS55 1.9 8.8 0.4 CE1 A:HIS55 1.9 7.7 0.4 CAD A:5JC202 2.0 17.2 0.3 CAI A:5JC202 2.1 19.8 0.3 CAF A:5JC202 2.7 10.4 0.3 CAG A:5JC202 2.7 11.1 0.3 ND1 A:HIS55 2.8 8.4 0.4 CG A:HIS55 2.9 9.2 0.4 OAA A:5JC202 2.9 11.8 0.3 CL1 A:5JC202 3.0 22.7 0.3 C4D A:HEM201 3.2 12.9 1.0 CAE A:5JC202 3.2 17.0 0.3 CAF A:5JC202 3.2 18.0 0.3 CBD A:HEM201 3.3 24.3 1.0 C3D A:HEM201 3.3 14.2 1.0 O A:HOH379 3.4 127.7 0.4 CHA A:HEM201 3.5 12.3 1.0 CE1 A:PHE35 3.5 11.2 1.0 ND A:HEM201 3.6 11.7 1.0 CAH A:5JC202 3.6 18.5 0.3 C2D A:HEM201 3.7 12.5 1.0 CAD A:HEM201 3.8 17.1 1.0 C1D A:HEM201 3.8 12.1 1.0 O2D A:HEM201 3.9 62.9 0.8 CAH A:5JC202 4.0 9.8 0.3 CAD A:5JC202 4.0 10.2 0.3 CD1 A:PHE35 4.0 9.7 1.0 CGD A:HEM201 4.0 44.9 0.8 CG2 A:VAL59 4.0 12.0 1.0 C1A A:HEM201 4.1 12.6 1.0 CB A:HIS55 4.3 10.0 0.4 CB A:HIS55 4.5 15.1 0.6 CAE A:5JC202 4.5 10.8 0.3 NA A:HEM201 4.6 11.7 1.0 CMD A:HEM201 4.6 15.9 1.0 FE A:HEM201 4.7 11.4 1.0 CZ A:PHE35 4.7 10.8 1.0 CHD A:HEM201 4.7 13.5 1.0 O A:HIS55 4.8 11.5 0.6 C2A A:HEM201 5.0 12.1 1.0

Chlorine binding site 2 out of 6 in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:22.7 occ:0.30 CL1 A:5JC202 0.0 22.7 0.3 ND1 A:HIS55 0.9 8.4 0.4 OAA A:5JC202 1.1 11.8 0.3 CE1 A:HIS55 1.4 7.7 0.4 CAG A:5JC202 1.7 11.1 0.3 CAI A:5JC202 1.7 19.8 0.3 CG A:HIS55 2.2 9.2 0.4 NE2 A:HIS55 2.5 8.0 0.4 CAI A:5JC202 2.5 10.5 0.3 CAD A:5JC202 2.6 10.2 0.3 CAF A:5JC202 2.7 18.0 0.3 CAG A:5JC202 2.7 17.6 0.3 CD2 A:HIS55 2.8 8.8 0.4 OAA A:5JC202 2.9 19.5 0.3 CL1 A:5JC202 3.0 13.5 0.3 CB A:HIS55 3.2 10.0 0.4 CG2 A:THR56 3.5 20.8 1.0 OH A:TYR38 3.5 23.9 1.0 CAF A:5JC202 3.7 10.4 0.3 CE2 A:TYR38 3.7 15.1 1.0 CAE A:5JC202 3.8 10.8 0.3 CZ A:PHE21 3.8 10.0 1.0 N A:THR56 3.9 11.3 1.0 CE2 A:PHE21 3.9 12.2 1.0 C A:HIS55 4.0 13.2 0.6 CAD A:5JC202 4.0 17.2 0.3 CAH A:5JC202 4.0 18.5 0.3 CZ A:TYR38 4.1 17.2 1.0 CA A:THR56 4.1 13.0 1.0 CB A:HIS55 4.2 15.1 0.6 C A:HIS55 4.2 12.2 0.4 CAH A:5JC202 4.2 9.8 0.3 CE1 A:PHE21 4.3 11.7 1.0 O A:HIS55 4.3 11.5 0.6 CA A:HIS55 4.3 12.9 0.4 CE1 A:PHE35 4.4 11.2 1.0 CD2 A:PHE21 4.4 10.3 1.0 CB A:THR56 4.4 18.0 1.0 CD1 A:PHE35 4.5 9.7 1.0 CAE A:5JC202 4.5 17.0 0.3 CA A:HIS55 4.6 16.6 0.6 O A:PHE52 4.7 10.6 1.0 CD1 A:PHE21 4.7 12.0 1.0 CG2 A:VAL59 4.7 12.0 1.0 CG A:PHE21 4.8 10.0 1.0 O A:HIS55 4.9 11.0 0.4 O A:HOH302 4.9 56.4 1.0 CD2 A:TYR38 4.9 13.4 1.0 O2D A:HEM201 5.0 62.9 0.8

Chlorine binding site 3 out of 6 in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:13.0 occ:0.30 CL2 A:5JC202 0.0 13.0 0.3 CL2 A:5JC202 0.9 25.6 0.3 CAH A:5JC202 1.7 9.8 0.3 CAH A:5JC202 2.0 18.5 0.3 CAE A:5JC202 2.5 17.0 0.3 CAE A:5JC202 2.7 10.8 0.3 CAF A:5JC202 2.7 10.4 0.3 O A:HOH379 3.1 127.7 0.4 CAF A:5JC202 3.2 18.0 0.3 C1C A:HEM201 3.2 9.4 1.0 NC A:HEM201 3.4 11.8 1.0 C2C A:HEM201 3.4 10.5 1.0 CHC A:HEM201 3.6 9.3 1.0 C3C A:HEM201 3.7 11.5 1.0 C4C A:HEM201 3.7 12.0 1.0 CAD A:5JC202 3.9 17.2 0.3 CAD A:5JC202 4.0 10.2 0.3 CAI A:5JC202 4.0 10.5 0.3 CD2 A:LEU100 4.0 10.5 1.0 CE1 A:PHE21 4.0 11.7 1.0 CMC A:HEM201 4.1 11.9 1.0 C4B A:HEM201 4.1 8.2 1.0 CD1 A:PHE21 4.2 12.0 1.0 CZ A:PHE35 4.2 10.8 1.0 CAI A:5JC202 4.4 19.8 0.3 FE A:HEM201 4.4 11.4 1.0 CG1 A:VAL59 4.4 11.8 1.0 NB A:HEM201 4.4 9.9 1.0 CAG A:5JC202 4.5 11.1 0.3 CE2 A:PHE24 4.6 12.8 1.0 CHD A:HEM201 4.6 13.5 1.0 CAC A:HEM201 4.6 13.2 1.0 CD1 A:LEU100 4.6 12.6 1.0 CAG A:5JC202 4.7 17.6 0.3 CE1 A:PHE35 4.7 11.2 1.0 CG A:LEU100 4.8 10.4 1.0 CD2 A:PHE24 4.9 10.6 1.0 CE1 A:HIS55 5.0 7.7 0.4

Chlorine binding site 4 out of 6 in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:25.6 occ:0.30 CL2 A:5JC202 0.0 25.6 0.3 CL2 A:5JC202 0.9 13.0 0.3 CAH A:5JC202 1.4 9.8 0.3 CAH A:5JC202 1.7 18.5 0.3 CAE A:5JC202 1.9 10.8 0.3 CAF A:5JC202 2.7 10.4 0.3 CAE A:5JC202 2.7 17.0 0.3 CAF A:5JC202 2.7 18.0 0.3 CAD A:5JC202 3.3 10.2 0.3 O A:HOH379 3.3 127.7 0.4 CD1 A:PHE21 3.4 12.0 1.0 CE1 A:PHE21 3.5 11.7 1.0 CAI A:5JC202 3.8 10.5 0.3 CAD A:5JC202 4.0 17.2 0.3 CAI A:5JC202 4.0 19.8 0.3 CAG A:5JC202 4.0 11.1 0.3 C1C A:HEM201 4.1 9.4 1.0 CG1 A:VAL59 4.1 11.8 1.0 CD2 A:LEU100 4.1 10.5 1.0 NC A:HEM201 4.2 11.8 1.0 C2C A:HEM201 4.3 10.5 1.0 CHC A:HEM201 4.3 9.3 1.0 CD1 A:LEU100 4.4 12.6 1.0 CZ A:PHE35 4.5 10.8 1.0 CAG A:5JC202 4.5 17.6 0.3 C4C A:HEM201 4.5 12.0 1.0 C3C A:HEM201 4.6 11.5 1.0 CG A:PHE21 4.6 10.0 1.0 CE1 A:HIS55 4.6 7.7 0.4 C4B A:HEM201 4.7 8.2 1.0 CE2 A:PHE24 4.7 12.8 1.0 CZ A:PHE21 4.7 10.0 1.0 CD2 A:PHE24 4.7 10.6 1.0 CG A:LEU100 4.9 10.4 1.0 CG2 A:VAL59 4.9 12.0 1.0 CE1 A:PHE35 4.9 11.2 1.0 NB A:HEM201 4.9 9.9 1.0 CMC A:HEM201 4.9 11.9 1.0 FE A:HEM201 5.0 11.4 1.0 CB A:VAL59 5.0 10.0 1.0

Chlorine binding site 5 out of 6 in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:25.2 occ:0.40 CL1 B:5JC202 0.0 25.2 0.4 CE1 B:HIS55 1.1 9.6 0.6 NE2 B:HIS55 1.2 10.0 0.6 CAI B:5JC202 1.7 14.1 0.4 ND1 B:HIS55 2.2 10.9 0.6 CD2 B:HIS55 2.4 9.9 0.6 CAF B:5JC202 2.7 11.6 0.4 CAG B:5JC202 2.7 13.8 0.4 CG B:HIS55 2.8 9.7 0.6 OAA B:5JC202 2.9 13.8 0.4 O B:HOH346 3.0 58.0 1.0 CE1 B:PHE35 3.2 11.6 1.0 O1D B:HEM201 3.2 49.2 1.0 O B:HOH313 3.2 13.2 0.6 C4D B:HEM201 3.6 10.6 1.0 CD1 B:PHE35 3.7 12.6 1.0 C3D B:HEM201 3.8 11.2 1.0 CBD B:HEM201 3.8 14.1 1.0 ND B:HEM201 3.8 10.0 1.0 CAH B:5JC202 4.0 13.6 0.4 CGD B:HEM201 4.0 105.1 1.0 CAD B:5JC202 4.0 14.9 0.4 C2D B:HEM201 4.0 12.9 1.0 C1D B:HEM201 4.0 10.0 1.0 CG2 B:VAL59 4.0 9.5 1.0 CHA B:HEM201 4.1 9.8 1.0 CZ B:PHE35 4.3 11.9 1.0 CB B:HIS55 4.3 9.5 0.6 CAD B:HEM201 4.4 12.2 1.0 CAE B:5JC202 4.5 13.1 0.4 CB B:HIS55 4.6 12.1 0.4 C1A B:HEM201 4.6 9.6 1.0 O B:HIS55 4.7 12.1 0.4 CHD B:HEM201 4.7 9.7 1.0 CMD B:HEM201 4.8 14.9 1.0 CZ B:PHE21 4.8 11.8 1.0 FE B:HEM201 4.8 9.8 1.0 NA B:HEM201 4.9 10.0 1.0 OH B:TYR38 4.9 21.7 1.0 C B:HIS55 5.0 10.2 0.4

Chlorine binding site 6 out of 6 in the Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Dehaloperoxidase A in Complex with 2,4-Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:19.4 occ:0.40 CL2 B:5JC202 0.0 19.4 0.4 CAH B:5JC202 1.7 13.6 0.4 CAF B:5JC202 2.7 11.6 0.4 CAE B:5JC202 2.7 13.1 0.4 C1C B:HEM201 3.3 9.3 1.0 O B:HOH313 3.4 13.2 0.6 C2C B:HEM201 3.4 9.5 1.0 CHC B:HEM201 3.6 8.8 1.0 NC B:HEM201 3.7 9.8 1.0 CD2 B:LEU100 3.7 12.0 1.0 C3C B:HEM201 3.9 9.6 1.0 CE1 B:PHE21 3.9 15.2 1.0 C4C B:HEM201 3.9 9.7 1.0 CAI B:5JC202 4.0 14.1 0.4 CAD B:5JC202 4.0 14.9 0.4 CMC B:HEM201 4.0 10.3 1.0 C4B B:HEM201 4.2 9.0 1.0 CD1 B:LEU100 4.2 13.1 1.0 CG1 B:VAL59 4.2 9.1 1.0 CD1 B:PHE21 4.3 12.8 1.0 CG B:LEU100 4.5 10.8 1.0 CAG B:5JC202 4.5 13.8 0.4 CZ B:PHE35 4.5 11.9 1.0 NB B:HEM201 4.6 9.0 1.0 CE2 B:PHE24 4.7 10.7 1.0 FE B:HEM201 4.7 9.8 1.0 CAC B:HEM201 4.7 9.6 1.0 CZ B:PHE21 4.9 11.8 1.0 CHD B:HEM201 4.9 9.7 1.0 CG2 B:VAL59 4.9 9.5 1.0 CBC B:HEM201 5.0 11.9 1.0 CD2 B:PHE24 5.0 10.3 1.0

M.S.Aktar, V.De Serrano, R.Ghiladi, S.Franzen. Comparative Study of the Binding and Activation of 2,4-Dichlorophenol By Dehaloperoxidase A and B. J.Inorg.Biochem. V. 247 12332 2023.
ISSN: ISSN 0162-0134
PubMed: 37480762
DOI: 10.1016/J.JINORGBIO.2023.112332