Fluorine in PDB 7m1k: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol, PDB code: 7m1k was solved by R.A.Ghiladi, V.S.De Serrano, T.Malewschik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.12 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.145, 66.697, 68.028, 90, 90, 90
R / Rfree (%)	17.1 / 22.3

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol (pdb code 7m1k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol, PDB code: 7m1k:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:27.4 occ:0.40 F1 A:FFP203 0.0 27.4 0.4 C6 A:FFP203 1.3 25.2 0.4 C1 A:FFP203 2.3 23.7 0.4 C5 A:FFP203 2.4 25.4 0.4 O A:FFP203 2.7 22.0 0.4 OD1 A:ASP79 2.7 20.3 1.0 CD1 A:LEU62 3.4 19.6 0.6 CG2 A:VAL66 3.5 14.6 1.0 CG A:ASP79 3.5 19.2 1.0 C2 A:FFP203 3.6 23.8 0.4 C4 A:FFP203 3.6 24.6 0.4 CA A:ASP79 3.7 18.1 1.0 CB A:ASP79 3.7 19.0 1.0 O A:ASP79 3.7 17.2 1.0 NH2 A:ARG69 4.0 15.2 1.0 CG2 A:THR82 4.0 23.4 1.0 CB A:THR82 4.0 21.9 1.0 CG A:LEU62 4.0 17.9 0.6 C3 A:FFP203 4.1 24.3 0.4 CD2 A:LEU62 4.1 18.5 0.6 C A:ASP79 4.2 18.0 1.0 OD2 A:ASP79 4.6 17.9 1.0 CG A:LEU83 4.6 23.8 1.0 OG1 A:THR82 4.7 20.1 1.0 F2 A:FFP203 4.7 22.3 0.4 CD1 A:LEU83 4.9 24.9 1.0 N A:LEU83 5.0 24.7 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:22.3 occ:0.40 F2 A:FFP203 0.0 22.3 0.4 C2 A:FFP203 1.3 23.8 0.4 C1 A:FFP203 2.4 23.7 0.4 C3 A:FFP203 2.4 24.3 0.4 O A:FFP203 2.8 22.0 0.4 C6 A:FFP203 3.6 25.2 0.4 C4 A:FFP203 3.6 24.6 0.4 CD1 A:LEU62 4.0 19.6 0.6 CG2 A:THR82 4.1 23.4 1.0 C5 A:FFP203 4.1 25.4 0.4 CD1 A:LEU62 4.2 16.4 0.4 O A:HOH349 4.4 28.8 1.0 CD2 A:LEU62 4.5 18.5 0.6 CG A:LEU62 4.5 16.0 0.4 F1 A:FFP203 4.7 27.4 0.4 CG A:LEU62 4.8 17.9 0.6

Fluorine binding site 3 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:F204 b:40.1 occ:0.80 F1 B:FFP204 0.0 40.1 0.8 C6 B:FFP204 1.3 27.8 0.8 C1 B:FFP204 2.3 29.5 0.8 CE1 B:HIS55 2.3 23.6 1.0 C5 B:FFP204 2.4 27.1 0.8 ND1 B:HIS55 2.5 25.7 1.0 O B:FFP204 2.7 28.0 0.8 OG1 B:THR56 3.0 16.7 0.4 CA B:THR56 3.1 16.2 0.4 CA B:THR56 3.2 15.3 0.6 NE2 B:HIS55 3.3 25.3 1.0 CG2 B:VAL59 3.4 16.5 1.0 CB B:THR56 3.5 16.3 0.4 CG2 B:THR56 3.5 14.7 0.6 CG B:HIS55 3.5 23.2 1.0 C2 B:FFP204 3.6 29.8 0.8 N B:THR56 3.6 16.1 1.0 C4 B:FFP204 3.6 25.6 0.8 CG2 B:THR56 3.7 16.4 0.4 O B:HIS55 3.7 16.8 1.0 C B:HIS55 3.8 16.9 1.0 CB B:VAL59 3.8 16.2 1.0 CE2 B:PHE21 3.9 19.7 1.0 CB B:THR56 3.9 14.4 0.6 CD2 B:PHE21 3.9 17.9 1.0 CD2 B:HIS55 3.9 23.5 1.0 CZ B:PHE21 4.1 19.8 1.0 C3 B:FFP204 4.1 26.9 0.8 CG B:PHE21 4.2 16.3 1.0 CG1 B:VAL59 4.2 16.2 1.0 O B:HOH301 4.2 6.5 0.2 CE1 B:PHE21 4.2 19.0 1.0 C B:THR56 4.3 16.2 1.0 CD1 B:PHE21 4.3 17.7 1.0 O B:THR56 4.4 15.4 1.0 CB B:HIS55 4.5 20.9 1.0 F2 B:FFP204 4.7 32.6 0.8 CA B:HIS55 4.8 18.5 1.0 CB B:PHE21 4.8 13.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:F204 b:32.6 occ:0.80 F2 B:FFP204 0.0 32.6 0.8 C2 B:FFP204 1.4 29.8 0.8 C1 B:FFP204 2.3 29.5 0.8 C3 B:FFP204 2.4 26.9 0.8 O B:FFP204 2.7 28.0 0.8 O B:HOH301 3.0 6.5 0.2 C1C B:HEM202 3.4 21.3 1.0 C2C B:HEM202 3.4 22.0 1.0 C6 B:FFP204 3.6 27.8 0.8 C4 B:FFP204 3.6 25.6 0.8 NC B:HEM202 3.7 21.0 1.0 CE1 B:PHE21 3.7 19.0 1.0 C3C B:HEM202 3.8 22.8 1.0 CHC B:HEM202 3.8 21.1 1.0 C4C B:HEM202 3.9 23.0 1.0 CMC B:HEM202 4.0 21.8 1.0 CD2 B:LEU100 4.0 14.7 1.0 CZ B:PHE35 4.1 22.2 1.0 C5 B:FFP204 4.1 27.1 0.8 CD1 B:PHE21 4.1 17.7 1.0 C4B B:HEM202 4.4 19.6 1.0 CG1 B:VAL59 4.5 16.2 1.0 CD1 B:LEU100 4.5 14.8 1.0 CAC B:HEM202 4.5 24.6 1.0 CE2 B:PHE24 4.6 16.7 1.0 CZ B:PHE21 4.6 19.8 1.0 F1 B:FFP204 4.7 40.1 0.8 CHD B:HEM202 4.7 23.2 1.0 CBC B:HEM202 4.8 25.2 1.0 CG B:LEU100 4.8 14.1 1.0 CD2 B:PHE24 4.8 15.9 1.0 FE B:HEM202 4.8 20.7 1.0 CE2 B:PHE35 4.8 21.7 1.0 NB B:HEM202 4.8 19.6 1.0 CE1 B:PHE35 4.9 22.5 1.0

T.Malewschik, L.M.Carey, V.De Serrano, R.A.Ghiladi. Bridging the Functional Gap Between Reactivity and Inhibition in Dehaloperoxidase B From Amphitrite Ornata: Mechanistic and Structural Studies with 2,4- and 2,6-Dihalophenols. J.Inorg.Biochem. V. 236 11944 2022.
ISSN: ISSN 0162-0134
PubMed: 35969974
DOI: 10.1016/J.JINORGBIO.2022.111944