Bromine in PDB 8vzr: Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol

The structure of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol, PDB code: 8vzr was solved by M.S.Aktar, V.S.De Serrano, R.A.Ghiladi, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.14 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.404, 67.756, 68.169, 90, 90, 90
R / Rfree (%)	15.6 / 20.4

The structure of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Bromine atom in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol (pdb code 8vzr). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol, PDB code: 8vzr:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:30.2 occ:0.20 BR1 A:MWJ202 0.0 30.2 0.2 O1 A:OXY206 1.1 15.3 0.6 C1 A:MWJ202 1.3 29.9 0.2 O2 A:OXY206 1.7 15.9 0.6 C6 A:MWJ202 1.9 26.0 0.2 C2 A:MWJ202 1.9 31.7 0.2 O1 A:MWJ202 2.2 29.6 0.2 C3 A:MWJ202 2.3 31.8 0.2 C5 A:MWJ202 2.8 26.4 0.2 C7 A:MWJ202 2.8 26.0 0.2 NC A:HEM201 2.9 21.6 1.0 C7 A:MWJ202 3.1 34.7 0.2 C1C A:HEM201 3.1 20.9 1.0 C4C A:HEM201 3.3 22.1 1.0 CE1 A:PHE21 3.3 20.0 0.6 FE A:HEM201 3.6 22.1 1.0 C2C A:HEM201 3.6 20.0 1.0 C4 A:MWJ202 3.6 33.4 0.2 CHC A:HEM201 3.6 19.3 1.0 C3C A:HEM201 3.7 22.3 1.0 CZ A:PHE35 3.8 23.0 1.0 CHD A:HEM201 3.9 21.4 1.0 NB A:HEM201 4.0 20.2 1.0 C4B A:HEM201 4.0 18.7 1.0 CG1 A:VAL59 4.1 16.9 1.0 C4 A:MWJ202 4.1 25.6 0.2 ND A:HEM201 4.1 21.2 1.0 C2 A:MWJ202 4.2 26.1 0.2 CD1 A:PHE21 4.2 18.8 0.6 CZ A:PHE21 4.2 20.5 0.6 C6 A:MWJ202 4.2 37.0 0.2 C1D A:HEM201 4.2 24.1 1.0 CE1 A:PHE35 4.2 24.4 1.0 CE1 A:HIS55 4.2 22.8 0.8 CG2 A:VAL59 4.3 16.9 1.0 CE1 A:PHE21 4.3 12.5 0.4 C5 A:MWJ202 4.4 35.4 0.2 NE2 A:HIS55 4.6 24.6 0.8 CMC A:HEM201 4.6 19.0 1.0 CD1 A:PHE21 4.6 12.8 0.4 C3 A:MWJ202 4.7 25.7 0.2 CAC A:HEM201 4.7 25.9 1.0 CD2 A:LEU100 4.8 16.4 1.0 CB A:VAL59 4.8 16.0 1.0 CE2 A:PHE35 4.8 24.3 1.0 NA A:HEM201 4.9 23.5 1.0 C1B A:HEM201 5.0 19.6 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:46.0 occ:0.20 BR1 A:MWJ202 0.0 46.0 0.2 CE1 A:PHE60 0.9 11.1 0.8 CZ A:PHE60 1.2 11.5 0.8 CE1 A:PHE60 1.8 16.1 0.2 C6 A:MWJ202 1.9 37.0 0.2 CD1 A:PHE60 2.2 10.8 0.8 CD1 A:PHE60 2.2 16.2 0.2 CE2 A:PHE60 2.5 12.2 0.8 C7 A:MWJ202 2.8 34.7 0.2 C5 A:MWJ202 2.9 35.4 0.2 CZ A:PHE60 3.0 16.4 0.2 CG A:PHE60 3.1 10.8 0.8 CD2 A:PHE60 3.2 11.9 0.8 CG A:PHE60 3.5 15.5 0.2 CE2 A:PHE60 4.0 16.1 0.2 CD1 A:LEU100 4.1 16.8 1.0 O A:ALA17 4.1 14.1 1.0 C4 A:MWJ202 4.1 33.4 0.2 C2 A:MWJ202 4.2 31.7 0.2 CD2 A:PHE60 4.2 16.0 0.2 CD1 A:PHE21 4.2 18.8 0.6 CB A:PHE21 4.2 15.5 0.6 CB A:PHE21 4.2 12.7 0.4 N A:PHE21 4.3 12.9 0.4 N A:PHE21 4.3 13.8 0.6 CG1 A:VAL59 4.3 16.9 1.0 CE A:MET63 4.3 15.2 1.0 CG2 A:ILE20 4.4 12.7 1.0 CA A:PHE21 4.4 14.2 0.6 CA A:PHE21 4.4 12.8 0.4 CB A:PHE60 4.5 14.7 0.2 CB A:PHE60 4.6 12.3 0.8 CB A:ILE20 4.7 11.8 1.0 C3 A:MWJ202 4.7 31.8 0.2 CD2 A:LEU100 4.7 16.4 1.0 CG A:PHE21 4.7 17.4 0.6 CA A:ALA17 4.8 13.6 1.0 C A:ILE20 4.8 12.4 1.0 CG2 A:THR56 4.9 24.0 0.6 CG A:LEU100 4.9 16.1 1.0 C A:ALA17 4.9 13.8 1.0 CD1 A:PHE21 5.0 12.8 0.4

Bromine binding site 3 out of 4 in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:30.3 occ:0.40 BR1 B:MWJ202 0.0 30.3 0.4 C1 B:MWJ202 0.4 55.2 0.2 C2 B:MWJ202 1.4 54.9 0.2 C6 B:MWJ202 1.9 23.5 0.4 O2 B:OXY208 2.1 7.6 0.4 C7 B:MWJ202 2.3 56.5 0.2 C3 B:MWJ202 2.5 53.4 0.2 O1 B:OXY208 2.8 8.3 0.4 C5 B:MWJ202 2.8 25.3 0.4 C7 B:MWJ202 2.8 21.8 0.4 CE1 B:PHE21 2.9 11.5 0.4 O1 B:MWJ202 3.0 50.1 0.2 C1C B:HEM201 3.4 15.2 1.0 C2C B:HEM201 3.5 15.7 1.0 C6 B:MWJ202 3.6 59.6 0.2 NC B:HEM201 3.7 16.1 1.0 CZ B:PHE21 3.8 11.8 0.4 CHC B:HEM201 3.8 14.1 1.0 C4 B:MWJ202 3.8 54.5 0.2 CD1 B:PHE21 3.8 11.6 0.4 CD2 B:LEU100 3.8 13.2 1.0 C3C B:HEM201 3.8 16.0 1.0 C4C B:HEM201 3.9 16.6 1.0 CMC B:HEM201 4.1 16.4 1.0 CE1 B:PHE21 4.1 15.8 0.6 C4 B:MWJ202 4.1 24.3 0.4 C2 B:MWJ202 4.1 22.5 0.4 C5 B:MWJ202 4.2 56.9 0.2 C4B B:HEM201 4.3 12.6 1.0 CZ B:PHE35 4.3 20.7 1.0 CG1 B:VAL59 4.3 13.5 1.0 CD1 B:PHE21 4.4 15.6 0.6 CD1 B:LEU100 4.4 13.2 1.0 NB B:HEM201 4.6 12.9 1.0 CE2 B:PHE24 4.6 14.3 1.0 C3 B:MWJ202 4.6 23.3 0.4 CG B:LEU100 4.6 12.8 1.0 FE B:HEM201 4.7 14.9 1.0 CAC B:HEM201 4.7 17.2 1.0 CHD B:HEM201 4.8 17.0 1.0 NE2 B:HIS55 4.8 16.1 0.6 CBC B:HEM201 4.8 19.2 1.0 CG2 B:VAL59 4.9 14.8 1.0 CD2 B:PHE24 4.9 14.2 1.0 CE1 B:PHE35 4.9 19.9 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:73.4 occ:0.20 BR1 B:MWJ202 0.0 73.4 0.2 CE1 B:PHE60 1.5 10.8 0.8 C6 B:MWJ202 1.9 59.6 0.2 CZ B:PHE60 2.0 11.8 0.8 CE1 B:PHE60 2.3 12.2 0.2 CD1 B:PHE60 2.8 10.6 0.8 C5 B:MWJ202 2.8 56.9 0.2 C7 B:MWJ202 2.8 56.5 0.2 CD1 B:PHE60 2.9 12.0 0.2 CD1 B:PHE21 3.1 11.6 0.4 CZ B:PHE60 3.2 12.1 0.2 CB B:PHE21 3.3 13.3 0.6 CB B:PHE21 3.3 11.4 0.4 CE2 B:PHE60 3.4 12.2 0.8 O B:ALA17 3.6 12.0 1.0 CG B:PHE21 3.6 11.4 0.4 CA B:PHE21 3.6 11.2 0.4 CA B:PHE21 3.6 12.2 0.6 N B:PHE21 3.7 11.2 0.4 N B:PHE21 3.7 11.6 0.6 CG B:PHE60 3.9 10.9 0.8 CG2 B:THR56 3.9 15.8 0.5 C5 B:MWJ202 4.0 25.3 0.4 CG B:PHE21 4.0 14.3 0.6 CD1 B:PHE21 4.1 15.6 0.6 CD2 B:PHE60 4.1 12.2 0.8 C4 B:MWJ202 4.1 54.5 0.2 CG B:PHE60 4.1 11.6 0.2 C2 B:MWJ202 4.2 54.9 0.2 CE1 B:PHE21 4.2 11.5 0.4 CD1 B:LEU100 4.3 13.2 1.0 CE2 B:PHE60 4.3 11.9 0.2 C B:ILE20 4.4 11.8 1.0 CG2 B:ILE20 4.5 13.0 1.0 CG1 B:VAL59 4.5 13.5 1.0 C B:ALA17 4.5 13.1 1.0 C4 B:MWJ202 4.5 24.3 0.4 C3 B:MWJ202 4.7 53.4 0.2 CB B:ILE20 4.7 12.2 1.0 CA B:ALA17 4.7 12.4 1.0 CD2 B:PHE60 4.7 11.8 0.2 CD2 B:PHE21 4.9 11.7 0.4 C6 B:MWJ202 4.9 23.5 0.4

M.S.Aktar, V.De Serrano, R.A.Ghiladi, S.Franzen. Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 38959050
DOI: 10.1021/ACS.BIOCHEM.4C00179