Bromine in PDB 7m1j: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol, PDB code: 7m1j 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)	30.40 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.756, 66.594, 68.283, 90, 90, 90
R / Rfree (%)	14.6 / 20.6

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

Iron

(Fe)

2 atoms

The binding sites of Bromine atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol (pdb code 7m1j). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol, PDB code: 7m1j:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol


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 B in Complex with 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:97.8 occ:0.70 BR1 B:94N202 0.0 97.8 0.7 NE2 B:HIS55 0.9 14.8 0.3 CE1 B:HIS55 1.6 15.4 0.3 CD2 B:HIS55 1.8 14.2 0.3 C2 B:94N202 1.9 56.7 0.7 ND1 B:HIS55 2.4 15.2 0.3 CG B:HIS55 2.5 13.9 0.3 C3 B:94N202 2.8 53.6 0.7 C1 B:94N202 2.8 44.7 0.7 CBD B:HEM201 2.9 33.1 1.0 O B:94N202 3.0 53.4 0.7 CB B:HIS55 3.6 27.2 0.7 C3D B:HEM201 3.7 25.2 1.0 C4D B:HEM201 3.7 21.4 1.0 CHA B:HEM201 3.7 21.4 1.0 O B:HOH301 3.8 38.8 0.7 CAD B:HEM201 3.9 29.9 1.0 CB B:HIS55 3.9 16.2 0.3 CE1 B:PHE35 3.9 27.1 1.0 O1A B:HEM201 4.0 29.8 0.3 CGD B:HEM201 4.0 41.2 1.0 C B:94N202 4.1 25.3 0.7 C4 B:94N202 4.1 51.8 0.7 O2D B:HEM201 4.2 50.4 1.0 C2D B:HEM201 4.2 24.3 1.0 ND B:HEM201 4.3 21.9 1.0 CG B:HIS55 4.3 33.5 0.7 CG2 B:VAL59 4.3 18.7 1.0 CD1 B:PHE35 4.5 28.1 1.0 C1A B:HEM201 4.5 21.2 1.0 ND1 B:HIS55 4.5 35.1 0.7 C1D B:HEM201 4.5 20.8 1.0 CA B:HIS55 4.6 19.7 0.7 C5 B:94N202 4.6 41.1 0.7 O B:HIS55 4.7 17.8 0.7 C B:HIS55 4.7 17.9 0.7 OH B:TYR38 4.8 28.5 1.0 CA B:HIS55 4.8 16.3 0.3 CGA B:HEM201 4.9 27.7 0.3 CBA B:HEM201 4.9 22.9 0.3 CBA B:HEM201 4.9 23.6 0.7 C B:HIS55 5.0 17.2 0.3 CZ B:PHE35 5.0 28.7 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol


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 B in Complex with 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:107.7 occ:0.70 BR B:94N202 0.0 107.7 0.7 C4 B:94N202 1.9 51.8 0.7 CD1 B:PHE21 2.7 26.0 1.0 C5 B:94N202 2.8 41.1 0.7 C3 B:94N202 2.9 53.6 0.7 CE1 B:PHE21 2.9 27.4 1.0 CG B:PHE21 3.0 15.7 1.0 O B:HOH388 3.2 33.8 1.0 O B:94N202 3.2 53.4 0.7 CZ B:PHE21 3.6 27.5 1.0 CD2 B:PHE21 3.7 20.8 1.0 CB B:PHE21 3.7 14.2 1.0 CG1 B:VAL59 3.9 18.2 1.0 CE2 B:PHE21 3.9 22.6 1.0 CG2 B:THR56 4.0 16.9 0.4 C B:94N202 4.1 25.3 0.7 CE1 B:PHE60 4.1 18.3 1.0 C2 B:94N202 4.1 56.7 0.7 CB B:VAL59 4.3 17.9 1.0 CE1 B:HIS55 4.3 15.4 0.3 CG2 B:VAL59 4.3 18.7 1.0 CG2 B:THR56 4.5 17.3 0.6 C1 B:94N202 4.6 44.7 0.7 CD1 B:PHE60 4.7 19.3 1.0 ND1 B:HIS55 4.7 15.2 0.3 O B:HOH301 4.7 38.8 0.7 CA B:PHE21 4.7 13.4 1.0 OG1 B:THR56 4.7 20.2 0.4 CB B:THR56 4.8 17.7 0.4 CA B:THR56 4.9 16.7 0.4 CA B:THR56 4.9 16.3 0.6 CB B:THR56 5.0 16.8 0.6

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