Fluorine in PDB 6ong: Dehaloperoxidate B in Complex with Substrate 4-F-Cresol

The structure of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol, PDB code: 6ong was solved by R.A.Ghiladi, V.S.De Serrano, T.Malewschik, A.Mcguire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.55 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.084, 67.237, 67.825, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.4

The structure of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Fluorine atom in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol (pdb code 6ong). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol, PDB code: 6ong:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:11.2 occ:0.80 F1 A:MWM202 0.0 11.2 0.8 C6 A:MWM202 1.4 9.1 0.8 C5 A:MWM202 2.3 8.8 0.8 C7 A:MWM202 2.4 9.5 0.8 C1C A:HEM201 3.2 10.1 1.0 C2C A:HEM201 3.2 9.6 1.0 NC A:HEM201 3.5 9.6 1.0 CHC A:HEM201 3.6 8.4 1.0 C4 A:MWM202 3.6 7.9 0.8 C3C A:HEM201 3.6 10.8 1.0 C2 A:MWM202 3.6 8.4 0.8 CD2 A:LEU100 3.6 7.5 1.0 CMC A:HEM201 3.7 10.9 1.0 C4C A:HEM201 3.8 10.7 1.0 CE1 A:PHE21 4.0 10.9 0.7 CG1 A:VAL59 4.1 7.6 1.0 C3 A:MWM202 4.1 8.2 0.8 C4B A:HEM201 4.3 9.4 1.0 CD1 A:PHE21 4.3 9.9 0.7 CD1 A:LEU100 4.4 7.6 1.0 CAC A:HEM201 4.4 11.2 1.0 CG A:LEU100 4.6 7.0 1.0 CBC A:HEM201 4.6 12.8 1.0 CE1 A:PHE21 4.6 3.1 0.3 NB A:HEM201 4.7 8.6 1.0 CD1 A:PHE21 4.7 3.2 0.3 CHD A:HEM201 4.8 10.9 1.0 CZ A:PHE21 4.8 12.4 0.7 FE A:HEM201 4.8 10.1 1.0 CZ A:PHE35 4.9 13.5 1.0 CG2 A:VAL59 4.9 7.4 1.0 C1 A:MWM202 4.9 9.2 0.8

Fluorine binding site 2 out of 3 in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:9.4 occ:0.55 F1 B:MWM404 0.0 9.4 0.6 C1 B:MWM404 0.7 5.3 0.2 C2 B:MWM404 1.3 5.4 0.2 C6 B:MWM404 1.4 8.2 0.6 C3 B:MWM404 2.2 5.3 0.2 C5 B:MWM404 2.3 8.6 0.6 C7 B:MWM404 2.4 7.7 0.6 C7 B:MWM404 2.4 5.4 0.2 O1 B:MWM404 2.6 4.8 0.2 C1C B:HEM402 3.3 7.3 1.0 C2C B:HEM402 3.4 7.8 1.0 C4 B:MWM404 3.5 5.2 0.2 NC B:HEM402 3.6 7.7 1.0 C6 B:MWM404 3.6 5.5 0.2 C4 B:MWM404 3.6 7.4 0.6 C2 B:MWM404 3.6 8.3 0.6 CHC B:HEM402 3.7 7.1 1.0 C3C B:HEM402 3.8 8.4 1.0 CD2 B:LEU100 3.9 9.3 1.0 C4C B:HEM402 3.9 8.2 1.0 C5 B:MWM404 4.0 5.2 0.2 CG1 B:VAL59 4.0 5.6 1.0 CMC B:HEM402 4.0 7.8 1.0 C3 B:MWM404 4.1 8.0 0.6 C4B B:HEM402 4.2 7.0 1.0 CE1 B:PHE21 4.2 9.8 1.0 CD1 B:PHE21 4.4 8.0 1.0 CD1 B:LEU100 4.5 8.1 1.0 CZ B:PHE35 4.5 11.8 1.0 NB B:HEM402 4.6 7.3 1.0 CAC B:HEM402 4.7 8.9 1.0 FE B:HEM402 4.7 8.2 1.0 F1 B:MWM404 4.7 5.1 0.2 CHD B:HEM402 4.7 8.5 1.0 CG B:LEU100 4.8 7.8 1.0 CBC B:HEM402 4.8 8.5 0.7 CG2 B:VAL59 4.8 6.5 1.0 C1 B:MWM404 4.9 8.0 0.6 CB B:VAL59 5.0 5.6 1.0

Fluorine binding site 3 out of 3 in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:5.1 occ:0.20 F1 B:MWM404 0.0 5.1 0.2 CE1 B:PHE60 1.0 5.8 0.8 C6 B:MWM404 1.4 5.5 0.2 CZ B:PHE60 1.8 7.4 0.8 CD1 B:PHE60 2.3 6.4 0.8 C5 B:MWM404 2.4 5.2 0.2 C7 B:MWM404 2.4 5.4 0.2 CE2 B:PHE60 3.1 7.5 0.8 CD2 B:PHE60 3.3 7.0 0.2 CG B:PHE60 3.4 5.9 0.8 C5 B:MWM404 3.6 8.6 0.6 C4 B:MWM404 3.6 5.2 0.2 C2 B:MWM404 3.6 5.4 0.2 CE2 B:PHE60 3.7 7.2 0.2 CD2 B:PHE60 3.7 7.3 0.8 O B:ALA17 4.0 6.2 1.0 CB B:PHE21 4.0 6.3 1.0 C3 B:MWM404 4.1 5.3 0.2 C4 B:MWM404 4.2 7.4 0.6 CD1 B:LEU100 4.2 8.1 1.0 OG1 B:THR56 4.2 6.1 0.3 N B:PHE21 4.2 4.6 1.0 CA B:PHE21 4.3 5.0 1.0 CG1 B:VAL59 4.3 5.6 1.0 CG B:PHE60 4.4 6.6 0.2 CE B:MET63 4.5 9.1 1.0 CG2 B:ILE20 4.6 7.0 1.0 C6 B:MWM404 4.6 8.2 0.6 CG B:PHE21 4.7 8.2 1.0 CG2 B:THR56 4.7 6.8 0.7 CD2 B:LEU100 4.7 9.3 1.0 F1 B:MWM404 4.7 9.4 0.6 CB B:PHE60 4.7 5.5 0.8 CD1 B:PHE21 4.8 8.0 1.0 CA B:ALA17 4.8 5.9 1.0 C B:ALA17 4.8 5.4 1.0 CB B:PHE60 4.8 6.0 0.2 CB B:ILE20 4.9 6.5 1.0 C1 B:MWM404 4.9 5.3 0.2 O B:THR56 4.9 6.0 1.0 C B:ILE20 4.9 5.5 1.0 CZ B:PHE60 5.0 7.4 0.2

T.Malewschik, V.De Serrano, A.H.Mcguire, R.A.Ghiladi. The Multifunctional Globin Dehaloperoxidase Strikes Again: Simultaneous Peroxidase and Peroxygenase Mechanisms in the Oxidation of Epa Pollutants. Arch.Biochem.Biophys. V. 673 08079 2019.
ISSN: ESSN 1096-0384
PubMed: 31445024
DOI: 10.1016/J.ABB.2019.108079