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

Protein crystallography data

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

Other elements in 6vd4:

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

Bromine Binding Sites:

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 6vd4

Go back to Bromine Binding Sites List in 6vd4
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 6vd4

Go back to Bromine Binding Sites List in 6vd4
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 6vd4

Go back to Bromine Binding Sites List in 6vd4
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

Reference:

A.H.Mcguire, A.R.Petit, J.Kang, T.Malewschik, V.De Serrano, L.M.Carey, R.A.Ghiladi. Nonnative Heme Incorporation Into Multifunctional Globin Increases Peroxygenase Activity An Order and Magnitude Compared to Native Enzyme To Be Published.
Page generated: Mon Jul 7 10:37:52 2025

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