Bromine in PDB 6vd4: Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol, PDB code: 6vd4 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)	30.42 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.867, 68.078, 67.631, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.2

The structure of Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol 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 Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol (pdb code 6vd4). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol, PDB code: 6vd4:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-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 B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br203 b:48.7 occ:0.70 BR1 A:MWJ203 0.0 48.7 0.7 C1 A:MWJ203 0.6 29.1 0.2 C2 A:MWJ203 1.5 29.4 0.2 C6 A:MWJ203 1.9 44.0 0.7 C7 A:MWJ203 2.4 29.1 0.2 C3 A:MWJ203 2.5 29.7 0.2 C5 A:MWJ203 2.8 41.3 0.7 O1 A:MWJ203 2.9 31.1 0.2 C7 A:MWJ203 2.9 40.9 0.7 C1C A:MH0201 3.4 33.9 1.0 C2C A:MH0201 3.5 35.5 1.0 C6 A:MWJ203 3.7 29.1 0.2 C4 A:MWJ203 3.7 29.2 0.2 CD2 A:LEU100 3.7 26.3 1.0 NC A:MH0201 3.8 33.3 1.0 CHC A:MH0201 3.8 32.9 1.0 C3C A:MH0201 3.8 35.6 1.0 CMC A:MH0201 3.9 35.0 1.0 C4C A:MH0201 4.0 35.8 1.0 CE1 A:PHE21 4.0 26.1 1.0 C4 A:MWJ203 4.1 39.2 0.7 C5 A:MWJ203 4.2 29.2 0.2 C2 A:MWJ203 4.2 38.3 0.7 CD1 A:PHE21 4.2 25.9 1.0 CG1 A:VAL59 4.3 21.5 1.0 CBC A:MH0201 4.3 37.9 1.0 CD1 A:LEU100 4.3 25.7 1.0 C4B A:MH0201 4.4 33.8 1.0 CG A:LEU100 4.6 24.7 1.0 CAC A:MH0201 4.7 36.2 1.0 C3 A:MWJ203 4.7 38.5 0.7 CE2 A:PHE24 4.7 22.2 1.0 CZ A:PHE35 4.8 31.6 1.0 CHD A:MH0201 4.9 35.0 1.0 FE A:MH0201 4.9 32.5 1.0 NB A:MH0201 4.9 33.3 1.0 CZ A:PHE21 5.0 27.4 1.0

Bromine binding site 2 out of 3 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-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 B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br203 b:28.9 occ:0.20 BR1 A:MWJ203 0.0 28.9 0.2 CE1 A:PHE60 0.7 22.6 0.7 CZ A:PHE60 1.4 22.7 0.7 C6 A:MWJ203 1.9 29.1 0.2 CD1 A:PHE60 2.1 22.7 0.7 CE2 A:PHE60 2.6 24.0 0.7 C5 A:MWJ203 2.8 29.2 0.2 C7 A:MWJ203 2.9 29.1 0.2 CD1 A:PHE60 2.9 21.3 0.3 CG A:PHE60 3.1 22.4 0.7 CE1 A:PHE60 3.2 22.0 0.3 CD2 A:PHE60 3.3 23.4 0.7 O A:ALA17 3.7 19.9 1.0 CB A:PHE21 4.1 22.1 1.0 C4 A:MWJ203 4.1 29.2 0.2 C2 A:MWJ203 4.2 29.4 0.2 N A:PHE21 4.2 19.2 1.0 CG A:PHE60 4.2 21.1 0.3 C5 A:MWJ203 4.2 41.3 0.7 CG2 A:ILE20 4.3 19.2 1.0 CE A:MET63 4.3 29.2 1.0 CG1 A:VAL59 4.4 21.5 1.0 CG2 A:THR56 4.4 21.3 0.4 CA A:PHE21 4.4 20.2 1.0 CA A:ALA17 4.5 19.4 1.0 CZ A:PHE60 4.5 22.6 0.3 CB A:PHE60 4.5 21.4 0.7 C A:ALA17 4.5 19.8 1.0 CB A:ILE20 4.6 18.5 1.0 CD1 A:LEU100 4.6 25.7 1.0 C3 A:MWJ203 4.7 29.7 0.2 CB A:PHE60 4.8 20.4 0.3 C4 A:MWJ203 4.8 39.2 0.7 O A:THR56 4.9 20.7 1.0 CG A:PHE21 4.9 23.9 1.0 C A:ILE20 4.9 19.1 1.0 CB A:ALA17 4.9 19.8 1.0 CD1 A:PHE21 5.0 25.9 1.0

Bromine binding site 3 out of 3 in the Crystal Structure of Dehaloperoxidase B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-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 B in Complex with Cofactor Iron(III) Mesoporphyrin IX and Substrate 4-Bromo-Ortho-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:33.7 occ:0.68 BR1 B:MWJ202 0.0 33.7 0.7 CE1 B:PHE60 0.6 18.4 0.3 CZ B:PHE60 1.3 19.2 0.3 C6 B:MWJ202 1.9 31.9 0.7 CD1 B:PHE60 2.0 17.7 0.3 CE2 B:PHE60 2.6 19.2 0.3 C5 B:MWJ202 2.8 30.9 0.7 C7 B:MWJ202 2.9 30.4 0.7 CG B:PHE60 3.0 18.0 0.3 CD2 B:PHE60 3.2 18.6 0.3 CD1 B:PHE60 3.7 20.7 0.7 O B:ALA17 3.9 18.6 1.0 C4 B:MWJ202 4.1 31.1 0.7 C2 B:MWJ202 4.2 29.7 0.7 CB B:PHE21 4.2 20.4 1.0 CE1 B:PHE60 4.2 21.9 0.7 N B:PHE21 4.3 18.7 1.0 CG2 B:ILE20 4.3 18.2 1.0 CG B:PHE60 4.3 20.4 0.7 CG1 B:VAL59 4.3 24.9 1.0 CB B:PHE60 4.3 18.2 0.3 CD1 B:LEU100 4.5 25.1 1.0 CB B:PHE60 4.5 19.8 0.7 CA B:PHE21 4.5 19.0 1.0 CB B:ILE20 4.5 18.1 1.0 CA B:ALA17 4.6 18.0 1.0 C3 B:MWJ202 4.7 29.4 0.7 CE B:MET63 4.7 26.5 1.0 CG2 B:THR56 4.7 23.5 0.4 C B:ALA17 4.7 18.6 1.0 C B:ILE20 4.9 18.1 1.0 CA B:PHE60 4.9 18.8 0.7 CA B:PHE60 4.9 18.1 0.3 CD2 B:LEU100 4.9 25.6 1.0 N B:PHE60 5.0 18.6 0.3 N B:PHE60 5.0 19.1 0.7 O B:THR56 5.0 22.0 1.0 CD1 B:PHE21 5.0 22.8 1.0 CG B:PHE21 5.0 22.1 1.0

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