Chlorine in PDB 6i7f: Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol

The structure of Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol, PDB code: 6i7f was solved by T.Moreno-Chicano, A.E.Ebrahim, J.A.R.Worrall, R.W.Strange, D.Axford, D.A.Sherrell, H.Sugimoto, K.Tono, S.Owada, H.Duyvesteyn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.36 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.940, 67.150, 68.720, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.9

The structure of Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol (pdb code 6i7f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol, PDB code: 6i7f:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Dehaloperoxidase B From Amphitrite Ornata - 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 Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:51.1 occ:0.59 CL1 A:5JC202 0.0 51.1 0.6 CAI A:5JC202 1.7 48.1 0.6 CAG A:5JC202 2.6 48.9 0.6 OAA A:5JC202 2.7 51.0 0.6 CAF A:5JC202 2.7 46.8 0.6 C2C A:HEM201 3.4 49.2 1.0 C1C A:HEM201 3.6 47.6 1.0 CE1 A:PHE21 3.6 47.4 1.0 C3C A:HEM201 3.6 51.0 1.0 CMC A:HEM201 3.8 48.0 1.0 CD2 A:LEU100 3.8 44.7 1.0 NC A:HEM201 3.9 46.0 1.0 C4C A:HEM201 3.9 48.6 1.0 CAD A:5JC202 3.9 48.5 0.6 CD1 A:PHE21 3.9 45.6 1.0 CD1 A:LEU100 4.0 41.0 1.0 CAH A:5JC202 4.0 47.1 0.6 CE2 A:PHE24 4.0 37.4 1.0 CHC A:HEM201 4.1 48.0 1.0 CAC A:HEM201 4.3 52.8 1.0 CD2 A:PHE24 4.3 35.3 1.0 CBC A:HEM201 4.4 53.7 1.0 CG A:LEU100 4.4 38.6 1.0 CAE A:5JC202 4.5 46.7 0.6 CZ A:PHE21 4.6 51.9 1.0 CZ A:PHE35 4.7 50.0 1.0 CHD A:HEM201 4.7 48.4 1.0 CZ A:PHE24 4.8 39.3 1.0 CG1 A:VAL59 4.8 41.3 1.0 C4B A:HEM201 4.8 45.7 1.0 CB A:LEU100 4.9 37.7 1.0

Chlorine binding site 2 out of 4 in the Dehaloperoxidase B From Amphitrite Ornata - 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 Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:42.6 occ:0.59 CL2 A:5JC202 0.0 42.6 0.6 CAH A:5JC202 1.7 47.1 0.6 CAE A:5JC202 2.7 46.7 0.6 CAF A:5JC202 2.7 46.8 0.6 CD1 A:PHE60 3.4 48.0 1.0 O A:ALA17 3.8 33.2 1.0 CE1 A:PHE60 3.9 57.8 1.0 CAD A:5JC202 4.0 48.5 0.6 CAI A:5JC202 4.0 48.1 0.6 CB A:PHE21 4.2 37.8 1.0 CG1 A:VAL59 4.2 41.3 1.0 N A:PHE21 4.2 30.8 1.0 CE A:MET63 4.2 56.4 1.0 CG2 A:ILE20 4.3 34.5 1.0 CA A:PHE21 4.4 34.1 1.0 CG A:PHE60 4.4 46.1 1.0 CAG A:5JC202 4.5 48.9 0.6 CA A:ALA17 4.5 35.4 1.0 CB A:ILE20 4.6 33.7 1.0 C A:ALA17 4.6 34.0 1.0 CD1 A:LEU100 4.7 41.0 1.0 CB A:PHE60 4.7 37.8 1.0 CD1 A:PHE21 4.8 45.6 1.0 CG A:PHE21 4.8 43.3 1.0 C A:ILE20 4.8 31.5 1.0 CB A:ALA17 4.9 36.1 1.0 O A:THR56 4.9 35.0 1.0 CB A:VAL59 5.0 41.5 1.0

Chlorine binding site 3 out of 4 in the Dehaloperoxidase B From Amphitrite Ornata - 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 Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:38.0 occ:0.95 CL1 B:5JC202 0.0 38.0 0.9 CAI B:5JC202 1.7 35.6 0.9 CAG B:5JC202 2.7 36.3 0.9 CAF B:5JC202 2.7 37.2 0.9 OAA B:5JC202 2.8 36.9 0.9 C2C B:HEM201 3.4 38.5 1.0 C1C B:HEM201 3.6 37.7 1.0 C3C B:HEM201 3.6 39.4 1.0 CE1 B:PHE21 3.8 37.4 1.0 NC B:HEM201 3.9 38.1 1.0 C4C B:HEM201 3.9 40.6 1.0 CMC B:HEM201 3.9 39.2 1.0 CAH B:5JC202 4.0 35.9 0.9 CAD B:5JC202 4.0 35.4 0.9 CHC B:HEM201 4.1 38.2 1.0 CZ B:PHE35 4.1 43.0 1.0 CD1 B:PHE21 4.2 35.8 1.0 CE2 B:PHE24 4.2 37.5 1.0 CD2 B:LEU100 4.3 35.6 1.0 CAC B:HEM201 4.3 44.4 1.0 CBC B:HEM201 4.5 46.9 1.0 CD2 B:PHE24 4.5 34.5 1.0 CAE B:5JC202 4.5 34.5 0.9 CD1 B:LEU100 4.5 33.2 1.0 CHD B:HEM201 4.7 40.2 1.0 C4B B:HEM201 4.7 35.9 1.0 CE2 B:PHE35 4.8 40.4 1.0 CG1 B:VAL59 4.8 34.4 1.0 CZ B:PHE21 4.9 36.5 1.0 CG B:LEU100 4.9 32.6 1.0 CE1 B:PHE35 5.0 40.9 1.0

Chlorine binding site 4 out of 4 in the Dehaloperoxidase B From Amphitrite Ornata - 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 Dehaloperoxidase B From Amphitrite Ornata - Complex with 2,4- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:36.9 occ:0.95 CL2 B:5JC202 0.0 36.9 0.9 CAH B:5JC202 1.7 35.9 0.9 CAF B:5JC202 2.7 37.2 0.9 CAE B:5JC202 2.7 34.5 0.9 CD1 B:PHE60 3.8 37.5 1.0 O B:ALA17 3.9 30.7 1.0 CAI B:5JC202 4.0 35.6 0.9 CAD B:5JC202 4.0 35.4 0.9 N B:PHE21 4.1 29.9 1.0 CG2 B:ILE20 4.1 33.3 1.0 CE B:MET63 4.1 38.5 1.0 CB B:PHE21 4.2 31.1 1.0 CA B:PHE21 4.3 30.0 1.0 CB B:ILE20 4.4 30.9 1.0 CE1 B:PHE60 4.4 40.2 1.0 CAG B:5JC202 4.5 36.3 0.9 CD1 B:LEU100 4.6 33.2 1.0 CG B:PHE60 4.6 35.6 1.0 C B:ILE20 4.6 30.4 1.0 CG1 B:VAL59 4.7 34.4 1.0 CA B:ALA17 4.7 31.6 1.0 C B:ALA17 4.7 32.9 1.0 CB B:PHE60 4.8 32.8 1.0 CD1 B:PHE21 4.8 35.8 1.0 CG B:PHE21 4.8 34.1 1.0

T.Moreno-Chicano, A.Ebrahim, D.Axford, M.V.Appleby, J.H.Beale, A.K.Chaplin, H.M.E.Duyvesteyn, R.A.Ghiladi, S.Owada, D.A.Sherrell, R.W.Strange, H.Sugimoto, K.Tono, J.A.R.Worrall, R.L.Owen, M.A.Hough. High-Throughput Structures of Protein-Ligand Complexes at Room Temperature Using Serial Femtosecond Crystallography. Iucrj V. 6 1074 2019.
ISSN: ESSN 2052-2525
PubMed: 31709063
DOI: 10.1107/S2052252519011655